Next generation biobanking ontology(NGBO).
type: Ontology
version IRI: ngbo.owl
description: Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.
license: http://creativecommons.org/licenses/by/4.0/
version info: 2024-08-27

term source
type: AnnotationProperty

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred label: example
editor preferred label: example of usage
definition: 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
definition: 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred label: has curation status
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
definition source: OBI_0000281

definition
type: AnnotationProperty
editor preferred label: definition
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.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
definition editor: PERSON:Daniel Schober
alternative term: DEFINITION
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: editor note
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

definition editor
type: AnnotationProperty
editor preferred label: term editor
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
editor preferred label: alternative term
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred label: definition source
definition: 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
definition editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred label: has obsolescence reason
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred label: curator note
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg

ontology term requester
type: AnnotationProperty
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
definition: For external terms/classes, the ontology from which the term was imported
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred label: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
definition editor: Chris Mungall

expand assertion to
type: AnnotationProperty

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: 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 .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has associated axiom(nl)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

has axiom label
type: AnnotationProperty

term replaced by
type: AnnotationProperty
editor preferred label: term replaced by
has curation status: IAO_0000125
definition: Add as annotation triples in the granting ontology
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute Add as annotation triples in the granting ontology
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

Contributor
type: AnnotationProperty
description: 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.
comment: An entity responsible for making contributions to the content of the resource.

Creator
type: AnnotationProperty
description: 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.
has_obo_namespace: uberon
id: dc-creator
is metadata tag: true
shorthand: dc-creator
comment: An entity primarily responsible for making the content of the resource.
label: creator

Date
type: AnnotationProperty
description: 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.
comment: A date associated with an event in the life cycle of the resource.

Description
type: AnnotationProperty
description: 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.
comment: An account of the content of the resource.

Format
type: AnnotationProperty
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).
comment: The physical or digital manifestation of the resource.

Source
type: AnnotationProperty
description: 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.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: 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.
comment: The topic of the content of the resource.

Title
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

has_obo_namespace
type: AnnotationProperty

shorthand
type: AnnotationProperty

isDefinedBy
type: AnnotationProperty
OBO foundry unique label: is defined by

Axiom
annotated source: isDefinedBy
annotated property: OBO foundry unique label
annotated target: is defined by
comment: This is an experimental annotation

label
type: AnnotationProperty
editor preferred label: label

see also
type: AnnotationProperty
has_obo_namespace: uberon
id: seeAlso
is metadata tag: true
shorthand: seeAlso

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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
editor note: 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'.
alternative term: part_of
imported from: ido.owl
imported from: omrse.owl

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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
editor note: 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'.
alternative term: has_part
imported from: ido.owl
imported from: omrse.owl

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: ido.owl
imported from: omrse.owl
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: ido.owl
imported from: omrse.owl
comment: 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

preceded by
type: ObjectProperty
creator: OBO Foundry
comment: Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000063, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. For a full definition, refer to the inverse of this property, BFO_0000060. (Allyson Lister)

preceded by
type: ObjectProperty
sub property of: temporal relation
inverse of: followed by
type: TransitiveProperty
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
alternative term: is preceded by
alternative term: preceded_by
imported from: ro.owl

followed by
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: precedes
definition: The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'.
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
definition source: Modified by Allyson Lister from the preceded_by (which is the inverse of precedes / 'followed by') definition within RO: http://www.obofoundry.org/ro/ro.owl
imported from: ro.owl
creator: OBO Foundry
in subset: ro-eco
comment: Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000060, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. (Allyson Lister)
label: precedes

occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
editor preferred label: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

has temporal occupant
type: ObjectProperty
range: occurrent
imported from: bfo.owl

history of
type: ObjectProperty
sub property of: occurs in
type: FunctionalProperty
type: InverseFunctionalProperty
domain: process
range: material entity
definition: [copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001
imported from: bfo.owl

member of
type: ObjectProperty

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 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.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: omrse.owl

mentions
type: ObjectProperty
sub property of: is about
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
definition editor: PERSON: Jonathan Rees
definition editor: Person: Alan Ruttenberg

denotes
type: ObjectProperty
sub property of: is about
example of usage: 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.
definition: 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
editor note: 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
definition editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

is quality measurement of
type: ObjectProperty
sub property of: is about
domain: measurement datum
range: quality
definition: 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
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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.
definition editor: Alan Ruttenberg

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
definition: relates a process to a time-measurement-datum that represents the duration of the process
definition editor: Person:Alan Ruttenberg

has time stamp
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: time measurement datum
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
definition editor: Alan Ruttenberg

has measurement datum
type: ObjectProperty
sub property of: has part
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
definition: relates a time stamped measurement datum to the measurement datum that was measured
definition editor: Alan Ruttenberg

designates
type: ObjectProperty
inverse of: is designated by
type: AsymmetricProperty
type: IrreflexiveProperty
domain: information content entity
range: entity
definition: x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context..
definition editor: Mathias Brochhausen

is designated by
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
definition editor: Mathias Brochhausen

trace_from
type: ObjectProperty
inverse of: track_to
definition: A relation that is used to follow traceability of specimen activity

track_to
type: ObjectProperty
definition: A relation that is used to track specimen activity

has maximum capacity
type: ObjectProperty
domain: container
range: measurement datum
definition: A relation that relates a container to a measurement datum that specifies the maximum capacity of the container.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

has actual load
type: ObjectProperty
domain: container
range: measurement datum
definition: A relation that relates a container to a measurement datum that specifies the actual amount of material in the container.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

provides_service_consumer_with
type: ObjectProperty
sub property of: has part
editor preferred label: provides_service_consumer_with
example of usage: The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
definition: A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.

is_supported_by_data
type: ObjectProperty
range: data item
editor preferred label: is_supported_by_data
example of usage: 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.
definition: 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
definition editor: OBI
definition source: OBI
definition source: Philly 2011 workshop

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: trace_from
sub property of: has_participant
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
definition: 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.
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
editor preferred label: is_specified_input_of
example of usage: 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
has curation status: IAO_0000122
definition: 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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: trace_from
sub property of: has_participant
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
definition: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
imported from: obi.owl
imported from: omrse.owl

is_manufactured_by
type: ObjectProperty
domain: material entity
editor preferred label: is_manufactured_by
example of usage: http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
definition: c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
definition editor: Alan Ruttenberg
definition editor: Liju Fan
alternative term: has_make
alternative term: has_manufacturer

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: IAO_0000122
definition: 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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: obi.owl
imported from: omrse.owl

achieves_planned_objective
type: ObjectProperty
domain: planned process
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
definition: 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.
definition editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

is member of organization
type: ObjectProperty
inverse of: has organization member
range: organization
editor preferred label: is member of organization
definition: Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
editor note: 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
editor note: JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Helen Parkinson
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

has organization member
type: ObjectProperty
domain: organization
editor preferred label: has organization member
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
definition editor: Person: Jie Zheng

specifies value of
type: ObjectProperty
sub property of: is about
editor preferred label: specifies value of
definition: A relation between a value specification and an entity which the specification is about.

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
editor preferred label: has value specification
definition: A relation between an information content entity and a value specification that specifies its value.
definition editor: PERSON: James A. Overton
definition source: OBI

has performer
type: ObjectProperty
sub property of: trace_from
sub property of: has_participant
domain: planned process
editor preferred label: has performer
has curation status: IAO_0000428
definition editor: performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system)

owns
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is owned by
type: AsymmetricProperty
range: Class
  union of: material entity
  union of: information content entity
definition editor: Mathias Brochhausen
source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.

administrates
type: ObjectProperty
type: AsymmetricProperty
range: Class
  union of: material entity
  union of: information content entity
definition: a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
definition editor: Mathias Brochhausen
comment: A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl

is contact information about
type: ObjectProperty
sub property of: is about
type: AsymmetricProperty
type: IrreflexiveProperty
domain: information content entity
definition: a is contact information for b, if a is a information content entity, b is a human being or an organization and a identifies a physical location or electronic resource that allows to initiate communication with a.
definition editor: Mathias Brochhausen

is owned by
type: ObjectProperty
type: AsymmetricProperty
domain: Class
  union of: material entity
  union of: information content entity
definition: a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
definition source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.

is-aggregate-of
type: ObjectProperty
has obsolescence reason: BFO relation takes precedence.
imported from: omrse.owl
comment: We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
deprecated: true

inheres in
type: ObjectProperty
sub property of: topObjectProperty
inverse of: bearer of
type: FunctionalProperty
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: 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
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: 'inheres in at all times'
alternative term: inheres_in
imported from: ido.owl
imported from: omrse.owl

bearer of
type: ObjectProperty
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: 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
editor note: 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.
alternative term: bearer of
alternative term: bearer_of
alternative term: is bearer of
imported from: ido.owl
imported from: omrse.owl
label: bearer_of
label: is bearer of

participates in
type: ObjectProperty
inverse of: has_participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: ido.owl
imported from: omrse.owl

has_participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
alternative term: has_participant
imported from: ido.owl
imported from: omrse.owl
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
label: has participant

concretizes
type: ObjectProperty
sub property of: topObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
editor preferred label: concretizes
example of usage: 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).
example of usage: 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).
definition: 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.
imported from: omrse.owl
imported from: http://purl.obolibrary.org/obo/obi.owl
comment: 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.

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative term: function_of
alternative term: is function of

quality of
type: ObjectProperty
equivalent property:
  inverse of: has quality
sub property of: inheres in
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of

role of
type: ObjectProperty
equivalent property:
  inverse of: has_role
sub property of: inheres in
inverse of: has_role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative term: is role of
alternative term: role_of

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_function
imported from: ro.owl

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality
imported from: ro.owl

has_role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_role
imported from: ro.owl
label: has role

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
definition: 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
editor note: 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'.
alternative term: derives_into

location of
type: ObjectProperty
equivalent property:
  inverse of: located in
sub property of: located in
inverse of: located in
type: TransitiveProperty
editor preferred label: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: location_of
imported from: ro.owl
has db xref: RO:0001015
has_obo_namespace: uberon
id: location_of
shorthand: location_of
label: location_of

contained in
type: ObjectProperty
inverse of: contains
domain: material entity
range: independent continuant
editor preferred label: contained in
editor note: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
editor note: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
editor note: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
alternative term: contained_in
in subset: ro-eco

contains
type: ObjectProperty
inverse of: contained in
editor preferred label: contains
has db xref: RO:0001019
has_obo_namespace: uberon
id: contains
in subset: ro-eco
shorthand: contains

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
imported from: gaz.owl
imported from: ro.owl
source: http://www.obofoundry.org/ro/#OBO_REL:located_in
has db xref: RO:0001025
has_obo_namespace: uberon
shorthand: located_in
label: located_in
label: located_in (type level)

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

aligned with
type: ObjectProperty
type: TransitiveProperty
editor note: May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
definition editor: David Osumi-Sutherland

cell expresses
type: ObjectProperty
sub property of: expresses
definition: A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
definition editor: David Osumi-Sutherland
description: x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y

has component
type: ObjectProperty
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
imported from: ro.owl

has phenotype
type: ObjectProperty
sub property of: topObjectProperty
inverse of: phenotype of
definition: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
definition editor: Chris Mungall
in subset: ro-eco

phenotype of
type: ObjectProperty
sub property of: topObjectProperty
type: FunctionalProperty
definition: inverse of has phenotype
definition editor: Chris Mungall
in subset: RO_0002259
in subset: ro-eco

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: continuant
domain: Class
  union of: generically dependent continuant
  union of: material entity
example of usage: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
definition: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
definition editor: Chris Mungall

temporal relation
type: ObjectProperty
range: occurrent
editor preferred label: temporal relation
editor note: move to BFO?
definition source: Allen
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporal relation
editor preferred label: starts
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen

has input
type: ObjectProperty
sub property of: has_participant
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: consumes
imported from: ro.owl

has output
type: ObjectProperty
sub property of: has_participant
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
definition editor: Chris Mungall
alternative term: produces
imported from: ro.owl

related via exposure to
type: ObjectProperty
sub property of: causally related to
definition: Any relationship between an exposure event or process and any other entity.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.

over-expressed in
type: ObjectProperty
sub property of: expressed in
definition: g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.

under-expressed in
type: ObjectProperty
sub property of: expressed in
definition: g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.

ubiquitously expressed in
type: ObjectProperty
sub property of: expressed in
inverse of: ubiquitously expresses
definition: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
editor note: Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
definition editor: Chris Mungall

expresses
type: ObjectProperty
sub property of: genomically related to
definition: Inverse of 'expressed in'
definition editor: Chris Mungall

ubiquitously expresses
type: ObjectProperty
sub property of: expresses
definition: inverse of ubiquiotously expressed in
definition editor: Chris Mungall
in subset: RO_0002259

is treated by substance
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'is substance that treats'
creator: cjm
in subset: RO_0002259

genomically related to
type: ObjectProperty
domain: continuant
range: continuant
definition: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism

member of
type: ObjectProperty
equivalent property:
  inverse of: has member
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO

has member
type: ObjectProperty
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
imported from: ro.owl

output of
type: ObjectProperty
definition: inverse of has output
definition editor: Chris Mungall
imported from: ro.owl

causally related to
type: ObjectProperty
definition: This relation groups causal relations between material entities and causal relations between processes
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

has symptom
type: ObjectProperty
sub property of: has phenotype
domain: disease
definition: A relation that holds between a disease or an organism and a phenotype
definition editor: Chris Mungall

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causal relation between material entities
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: material entity
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: 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.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
definition editor: Chris Mungall
definition source: causal-relations

is marker for
type: ObjectProperty
sub property of: correlated with
definition: c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
editor note: May be ceded to OBI

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: causal-relations

correlated with
type: ObjectProperty
definition: A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
curator note: Groups both positive and negative correlation

causes or contributes to condition
type: ObjectProperty
sub property of: causally related to
example of usage: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
editor note: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

condition ameliorated by
type: ObjectProperty
sub property of: causally related to
definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.

condition exacerbated by
type: ObjectProperty
sub property of: causally related to
definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.

condition has genetic basis in
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: Class
  union of: process
  union of: quality
  union of: material entity
curator note: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: cjm
creation date: 2017-11-05T02:38:20Z

realizable has basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is basis for realizable
created by: cjm
creation date: 2017-11-05T03:20:01Z

is basis for realizable
type: ObjectProperty
sub property of: causally related to
created by: cjm
creation date: 2017-11-05T03:20:29Z

disease has basis in
type: ObjectProperty
sub property of: realizable has basis in
sub property of: causal relationship with disease as subject
domain: disease
created by: cjm
creation date: 2017-11-05T03:26:47Z

disease has basis in dysfunction of
type: ObjectProperty
sub property of: disease has basis in
definition: A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
OBO foundry unique label: disease has basis in dysfunction of (disease to anatomical structure)
created by: cjm
creation date: 2017-11-05T03:29:32Z

disease has basis in disruption of
type: ObjectProperty
sub property of: disease has basis in
range: process
definition: A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
OBO foundry unique label: disease has basis in disruption of (disease to process)
created by: cjm
creation date: 2017-11-05T03:37:52Z

disease has basis in feature
type: ObjectProperty
sub property of: has phenotype
sub property of: disease has basis in
domain: disease
definition: A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
created by: cjm
creation date: 2017-11-05T03:46:07Z

causal relationship with disease as subject
type: ObjectProperty
sub property of: causally related to
sub property of: disease relationship
domain: disease
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
created by: cjm
creation date: 2017-11-05T03:50:54Z

disease causes disruption of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: disease
range: process
definition: A relationship between a disease and a process where the disease process disrupts the execution of the process.
OBO foundry unique label: disease causes disruption of (disease to process)
created by: cjm
creation date: 2017-11-05T03:51:09Z

disease causes dysfunction of
type: ObjectProperty
sub property of: causal relationship with disease as subject
domain: disease
OBO foundry unique label: disease causes dysfunction of (disease to anatomical entity)
created by: cjm
creation date: 2017-11-05T03:58:20Z

disease has location
type: ObjectProperty
sub property of: disease relationship
domain: disease
range: independent continuant
definition: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
editor note: TODO: complete range axiom once more of CARO has been mireoted in to this ontology
curator note: This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
created by: cjm
creation date: 2017-11-05T04:06:02Z

disease has inflammation site
type: ObjectProperty
sub property of: disease has location
domain: disease
definition: A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
created by: cjm
creation date: 2017-12-26T19:37:31Z

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: material entity
definition: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: cjm
creation date: 2017-12-26T19:45:49Z

disease has feature
type: ObjectProperty
sub property of: disease relationship
domain: disease
definition: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
created by: cjm
creation date: 2017-12-26T19:50:53Z
has db xref: RO:0004029
id: disease_has_feature

disease arises from structure
type: ObjectProperty
sub property of: disease has basis in
definition: A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.
created by: cjm
creation date: 2017-12-26T19:58:44Z

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: process
example of usage: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
example of usage: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
example of usage: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
definition: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: Austin Meier
contributor: Chris Mungall
contributor: David Osumi-Sutherland
contributor: Marie Angelique Laporte
has exact synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: hasExactSynonym
annotated target: triggered by process
has db xref: RO:cjm

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: generically dependent continuant
range: independent continuant
example of usage: Genetic information generically depend on molecules of DNA.
example of usage: The novel *War and Peace* generically depends on this copy of the novel.
example of usage: The pattern shared by chess boards generically depends on any chess board.
example of usage: The score of a symphony g-depends on a copy of the score.
example of usage: This pdf file generically depends on this server.
definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
definition source: [072-ISO]
has exact synonym: g-depends on

is carrier of
type: ObjectProperty
domain: independent continuant
range: generically dependent continuant
example of usage: Molecules of DNA are carriers of genetic information.
example of usage: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
example of usage: This hard drive is carrier of these data items.
definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
definition source: [072-ISO]

disease relationship
type: ObjectProperty
definition: This relation groups relations between diseases and any other kind of entity.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
created by: cjm
creation date: 2018-09-26T00:00:32Z

executes
type: ObjectProperty
sub property of: trace_from
definition: relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes)
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: AGB

is related to
type: ObjectProperty
type: SymmetricProperty
comment: 'is related to' is the top level relation in SIO
subset: core
subset: relations+

has attribute
type: ObjectProperty
sub property of: is related to
inverse of: is attribute of
subset: core

is attribute of
type: ObjectProperty
sub property of: is related to

is annotation of
type: ObjectProperty
sub property of: is attribute of
inverse of: has annotation
domain: language entity

has annotation
type: ObjectProperty
sub property of: has attribute
range: language entity
example: document x is annotated with the keywords 'ontology','semantic web'

has identifier
type: ObjectProperty
sub property of: has attribute
inverse of: is identifier for
range: identifier

is identifier for
type: ObjectProperty
sub property of: is attribute of
domain: identifier

has unique identifier
type: ObjectProperty
sub property of: has identifier
inverse of: is unique identifier for
type: InverseFunctionalProperty
range: unique identifier

is unique identifier for
type: ObjectProperty
sub property of: is identifier for
type: FunctionalProperty
domain: unique identifier

has form
type: ObjectProperty

directly preceded by
type: ObjectProperty
sub property of: preceded by
sub property of:
  inverse of: followed by
example of usage: Microsoft version 2007 is directly preceded by Microsoft version 2003.
definition: Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software.
definition source: Allyson Lister
creator: OBO Foundry

directly followed by
type: ObjectProperty
sub property of: followed by
sub property of:
  inverse of: preceded by
definition: 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s.
definition source: Allyson Lister

has format specification
type: ObjectProperty
sub property of: SWO_0000741
domain: information content entity
definition: Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification.
definition source: Allyson Lister

userEmailId
type: DatatypeProperty
definition: A data property that set user email ID

userID
type: DatatypeProperty
definition: A data property that set user ID

userPassword
type: DatatypeProperty
definition: A data property that set user password

userName
type: DatatypeProperty
definition: A data property that set user name

Sequence accession
type: Class
subclass of: sequence identifier
created in: beta12orEarlier
definition: A persistent, unique identifier of a molecular sequence database entry.
definition editor: Damion Dooley
imported from: EDAM
has definition: A persistent, unique identifier of a molecular sequence database entry.
has exact synonym: Sequence accession number
in subset: data
in subset: edam
in subset: identifiers
label: sequence accession

entity
type: Class
subclass of: Thing
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
imported from: ido.owl
imported from: omrse.owl

Axiom
annotated source: entity
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
definition: 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.
editor note: 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
editor note: 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
imported from: ido.owl
imported from: omrse.owl
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: 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])
imported from: ido.owl
imported from: omrse.owl
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (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]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: 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.
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
editor note: 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
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

spatiotemporal region
type: Class
subclass of: occurrent
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

process
type: Class
subclass of: occurrent
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: 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])
editor note: 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)
has associated axiom(fol): (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]

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: 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.
has associated axiom(nl): 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])
has associated axiom(fol): (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]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
imported from: ido.owl
imported from: omrse.owl
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (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]
has associated axiom(fol): (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]

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

quality
type: Class
subclass of: specifically dependent continuant
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (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]

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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.
definition: 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])
definition: 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])
editor note: 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.
imported from: ido.owl
imported from: omrse.owl
has associated axiom(fol): (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]
has associated axiom(fol): (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]

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

role
type: Class
subclass of: realizable entity
example of usage: 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.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: 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.
editor note: 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.
imported from: omrse.owl
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object
type: Class
subclass of: material entity
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
label: fiat object part

Axiom
annotated source: fiat object
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
example of usage: an edge of a cube-shaped portion of space.
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

three-dimensional spatial region
type: Class
subclass of: spatial region
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

site
type: Class
subclass of: immaterial entity
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74

generically dependent continuant
type: Class
subclass of: continuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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.
definition: 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])
imported from: ido.owl
imported from: omrse.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: 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.
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

process boundary
type: Class
subclass of: occurrent
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: 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])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
imported from: ido.owl
imported from: omrse.owl
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (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]
has associated axiom(fol): (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]

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
editor note: 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

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

process profile
type: Class
subclass of: process
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
example of usage: 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.
example of usage: a marriage bond, an instance of love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]

Axiom
annotated source: relational quality
annotated property: definition
annotated target: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

infected cell
type: Class
subclass of: cell type
imported from: bto.owl
has_obo_namespace: BrendaTissueOBO
id: BTO:0000152

cerebrovascular endothelial cell
type: Class
subclass of: endothelial cell
subclass of: cell type
definition: Endothelial cell of or involving the cerebrum and the blood vessels supplying it.
imported from: bto.owl
has_obo_namespace: BrendaTissueOBO
id: BTO:0000238

erythroleukemia cell
type: Class
subclass of: disease cell type
definition: Cancer cell of the blood-forming tissues in which large numbers of immature, abnormal red blood cells are found in the blood and bone marrow.
imported from: bto.owl
has_obo_namespace: BrendaTissueOBO
id: BTO:0000426

lung cancer cell
type: Class
subclass of: cell type
definition: Cancer cell of the major organ of respiration the lung.

bone marrow cancer cell
type: Class
subclass of: disease cell type
imported from: bto.owl
has_obo_namespace: BrendaTissueOBO
id: BTO:0000583

prostate gland cancer cell
type: Class
subclass of: disease cell type
definition: A malignant tumour cell of glandular origin in the prostate. Over 95% are adenocarcinomas.
imported from: bto.owl
has_obo_namespace: BrendaTissueOBO
has related synonym: prostate cancer cell
has related synonym: prostate carcinoma cell
has related synonym: prostate tumor cell
has related synonym: prostate tumour cell
id: BTO:0001130

colorectal cancer cell
type: Class
subclass of: disease cell type
imported from: bto.owl
has_obo_namespace: BrendaTissueOBO
has related synonym: CRC cell
has related synonym: colorectal carcinoma cell
id: BTO:0001615

stationary phase culture
type: Class
subclass of: experimental cell
definition: A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die.

logarithmic phase culture
type: Class
subclass of: experimental cell
definition: A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes.

cholangioma cell
type: Class
subclass of: disease cell type
definition: A rare type of hepatocellular carcinoma arising from the cholangioles, composed of tumor cells resembling the epithelial cells of the cholangioles arranged in cords consisting of two layers of cells surrounding a minute lumen.

breast invasive ductal carcinoma cell
type: Class
subclass of: disease cell type
definition: Infiltrating ductal carcinoma is one of several recognized specific patterns of cancer of the breast. It is so named because it begins in the cells forming the ducts of the breast. It is the most common form of breast cancer, comprising 65-85% of all cases.

corneal epithelial cell
type: Class
subclass of: cell type

vascular smooth muscle cell
type: Class
subclass of: cell type
imported from: bto.owl
created by: mgr
creation date: 2010-04-11T12:13:16Z
has_obo_namespace: BrendaTissueOBO
has related synonym: VSMC cell
id: BTO:0004578

immaterial anatomical entity
type: Class
subclass of: immaterial entity

molecular entity
type: Class
subclass of: material entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: 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
alternative term: molecular entity
imported from: chebi.owl

immortal cell line cell
type: Class
subclass of: cell type
definition: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line.

early embryonic cell
type: Class
subclass of: embryonic cell
definition: A cell found in the embryo before the formation of all the gem layers is complete.

male germ cell
type: Class
subclass of: germ cell
definition editor: James Malone

oocyte
type: Class
subclass of: germ cell
definition: A female germ cell that has entered meiosis.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12598
SNOMEDCT definition citation: SNOMEDCT:86082002
ZFA definition citation: ZFA:0009008

stem cell
type: Class
subclass of: cell type
definition: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12662
SNOMEDCT definition citation: SNOMEDCT:419758009

hematopoietic stem cell
type: Class
subclass of: cell type
definition: A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system.
definition: 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, CD14, CD19, CD20, integrin alpha-M, neural cell adhesion molecule 1, lymphocyte antigen 6G, lymphocyte antigen 76.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12551
SNOMEDCT definition citation: SNOMEDCT:418318001

erythroid progenitor cell
type: Class
subclass of: erythroid lineage cell
subclass of: myeloid lineage restricted progenitor cell
subclass of: cell type
definition: A progenitor cell committed to the erythroid lineage.
definition: A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12526

monoblast
type: Class
subclass of: monopoietic cell
NCI thesaurus definition citation: NCIt:C13014
SNOMEDCT definition citation: SNOMEDCT:53945006

mature eosinophil
type: Class
subclass of: eosinophil

neutrophilic myeloblast
type: Class
subclass of: myeloblast

mature basophil
type: Class
subclass of: basophil

neuronal stem cell
type: Class
subclass of: stem cell
definition: 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.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12985

multipotent stem cell
type: Class
subclass of: stem cell
definition: A stem cell that can give rise to mulitple lineages of cells.
definition: A stem cell that can give rise to multiple lineages of cells.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C43419

common myeloid progenitor
type: Class
subclass of: hematopoietic oligopotent progenitor cell

megakaryocyte-erythroid progenitor cell
type: Class
subclass of: hematopoietic oligopotent progenitor cell

common lymphoid progenitor
type: Class
subclass of: hematopoietic oligopotent progenitor cell

blast cell
type: Class
subclass of: cell type
definition: A precursor cell with a limited number of potential fates.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12918
SNOMEDCT definition citation: SNOMEDCT:312256009

myoblast
type: Class
subclass of: cell type
definition: An embryonic (precursor) cell of the myogenic lineage that develops from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes.
definition: An embryonic cell that becomes a cell of muscle fiber.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C33151

fibroblast
type: Class
subclass of: cell type
definition: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
definition: 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.
definition: A connective-tissue cell of mesenchymal origin that secretes proteins and especially molecular collagen from which the extracellular fibrillar matrix of connective tissue forms.
definition: A large, flat, oval cell found in connective tissue and responsible for the formation of fibers.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12482
NIFSTD definition citation: NIFSTD:nlx_cell_20090201
SNOMEDCT definition citation: SNOMEDCT:52547004

osteoblast
type: Class
subclass of: cell type
definition: A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12568
SNOMEDCT definition citation: SNOMEDCT:48156001

ependymal cell
type: Class
subclass of: epithelial cell
definition: A neurectoderm derived cell that lines the neural lumen. [ JB:jb GOC:tfm PMID:9550134 ]

epithelial cell
type: Class
subclass of: cell type
definition: A cell that is usually found in a two-dimensional sheet with a free surface.
definition: 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.
definition: Cell that cover the surface of the body and line its cavities.
definition: Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH).
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12578
NIFSTD definition citation: NIFSTD:sao441624014
SNOMEDCT definition citation: SNOMEDCT:4212006

blood vessel endothelial cell
type: Class
subclass of: endothelial cell
definition: The endothelial cells that line the vasculature.
definition editor: James Malone

mesothelial cell
type: Class
subclass of: epithelial cell
definition: A flattened epithelial cell of mesenchymal origin that lines the serous cavity.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C33104
SNOMEDCT definition citation: SNOMEDCT:58966000

circulating cell
type: Class
subclass of: cell type
definition: A cell which moves among different tissues of the body, via blood, lymph, or other medium.
definition editor: Ele Holloway
definition editor: James Malone
ZFA definition citation: ZFA:0009043

blood cell
type: Class
subclass of: cell type
definition: A cell found predominately in the blood.
definition editor: Tomasz Adamusiak
SNOMEDCT definition citation: SNOMEDCT:63370004

exocrine pancreas cell
type: Class
subclass of: cell type
definition: An epithelial cell of the pancreas.
definition: Cells of the pancreas that secrete digestive enzymes, the archetypal secretory cell upon which much of the early work on the sequence of events in the secretory process was done.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C93173

Kupffer cell
type: Class
subclass of: tissue-resident macrophage
NCI thesaurus definition citation: NCIt:C12564
SNOMEDCT definition citation: SNOMEDCT:256002

osteoclast
type: Class
subclass of: myeloid leukocyte
NCI thesaurus definition citation: NCIt:C12570
SNOMEDCT definition citation: SNOMEDCT:27770000

granulocyte
type: Class
subclass of: myeloid leukocyte
subclass of: cell type
definition: A leukocyte with abundant granules in the cytoplasm.
definition: A polymorphonuclear white blood cell with granule-containing cytoplasm.
definition: A polymorphonuclear white blood cell with granule-containing cytoplasm.nIn humans the granulocytes are also classified as polymorphonuclear leucocytes and are subdivided according to the staining properties of the granules into eosinophils, basophils and neutrophils, some invertebrate blood cells are also referred to, not very helpfully, as granulocytes.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12530
SNOMEDCT definition citation: SNOMEDCT:256909001

mature neutrophil
type: Class
subclass of: neutrophil

mast cell
type: Class
subclass of: myeloid leukocyte
NCI thesaurus definition citation: NCIt:C12747
SNOMEDCT definition citation: SNOMEDCT:6445007

interneuron
type: Class
subclass of: neuron
definition: Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12625

motor neuron
type: Class
subclass of: neuron
definition: An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement.
definition: Neurons which activate muscle cells (MSH).
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12644
NIFSTD definition citation: NIFSTD:sao1460710779
SNOMEDCT definition citation: SNOMEDCT:31513005

sensory neuron
type: Class
subclass of: neuron
definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
definition editor: Ele Holloway
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12628

columnar neuron
type: Class
subclass of: cell type
definition editor: James Malone

endothelial cell
type: Class
subclass of: cell type
definition: An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
definition: The main type of cell found in the inside lining of blood vessels, lymph vessels, and the heart.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12865
SNOMEDCT definition citation: SNOMEDCT:45709008

glial cell
type: Class
subclass of: cell type
definition: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
definition: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. (Reichenbach and Wolburg)
definition: MERGED DEFINITION:nTARGET DEFINITION: The delicate network of branched cells and fibers that supports the tissue of the central nervous system.n--------------------nSOURCE DEFINITION: The cells of the supportive tissue of the central nervous system (neuroglia). These non-neural cells are of three kinds: astrocytes, oligodendrocytes (collectively termed macroglia) and microglia.
definition: The delicate network of branched cells and fibers that supports the tissue of the central nervous system.
definition editor: James Malone
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D009457
NCI thesaurus definition citation: NCIt:C12615
NIFSTD definition citation: NIFSTD:sao313023570
SNOMEDCT definition citation: SNOMEDCT:2156000

astrocyte
type: Class
subclass of: glial cell
definition: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from "star" cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and "reactive astrocytes" (along with microglia) respond to injury (MSH).
definition: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury.
definition: cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12477
NIFSTD definition citation: NIFSTD:sao1394521419
SNOMEDCT definition citation: SNOMEDCT:78399007
definition citation: http://purl.obolibrary.org/obo/BTO_0000099

oligodendrocyte
type: Class
subclass of: cell type
definition: A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.
definition: A class of large neuroglial (macroglial) cells in the central nervous system. Oligodendroglia may be called interfascicular, perivascular, or perineuronal (not the same as satellite cells, perineuronal of ganglia) according to their location. They form the insulating myelin sheath of axons in the central nervous system (MSH).
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D009836
NCI thesaurus definition citation: NCIt:C12618
NIFSTD definition citation: NIFSTD:sao844118448
SNOMEDCT definition citation: SNOMEDCT:66254009

microglial cell
type: Class
subclass of: central nervous system macrophage
subclass of: cell type
definition: A central nervous system macrophage found in the parenchyma of the central nervous system.
definition: A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.
definition: A small, migratory, phagocytic, interstitial cell of hematopoietic origin found in the central nervous system. Microglial cells are of various forms and may have slender branched processes.
definition: MERGED DEFINITION:nTARGET DEFINITION: The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system. They are of various forms and may have slender branched processes. They are migratory and act as phagocytes to waste products of nerve tissue. n--------------------nSOURCE DEFINITION: One of the small interstitial phagocytic cells of the microglia.
definition: The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system. They are of various forms and may have slender branched processes. They are migratory and act as phagocytes to waste products of nerve tissue.
definition editor: James Malone
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D017628
NCI thesaurus definition citation: NCIt:C12616
NIFSTD definition citation: NIFSTD:sao789292116
SNOMEDCT definition citation: SNOMEDCT:63483002

fat cell
type: Class
subclass of: cell type
definition: A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
definition: A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of tryglycerides.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12556
NCI thesaurus definition citation: NCIt:C32991
SNOMEDCT definition citation: SNOMEDCT:24826007

chondrocyte
type: Class
subclass of: cell type
definition: Polymorphic cell that form cartilage.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12557
SNOMEDCT definition citation: SNOMEDCT:433180002
SNOMEDCT definition citation: SNOMEDCT:81272008

melanocyte
type: Class
subclass of: cell type
definition: A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
definition: An epidermal cell that produces melanin.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12591
SNOMEDCT definition citation: SNOMEDCT:9683001

secretory cell
type: Class
subclass of: cell type
definition: A cell that specializes in controlled release of one or more substances.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13055

goblet cell
type: Class
subclass of: epithelial cell
subclass of: secretory cell
definition: A cell of the epithelial lining that produce and secrete mucins.
MSH definition citation: MESH:A03.492.411.369.320
has_obo_namespace: cell

parietal cell
type: Class
subclass of: secretory cell
definition: A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12594

endocrine cell
type: Class
subclass of: secretory cell
definition: A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
MSH definition citation: MESH:A06.407
has_obo_namespace: cell

neuroendocrine cell
type: Class
subclass of: cell type
definition: A neuron that has the specialized function to produce and secrete hormones, and that constitutes, in whole or in part, an endocrine organ or system.
definition: Neuroendocrine cells are cells that receive neuronal input (neurotransmitters released by nerve cells) and, as a consequence of this input, release message molecules (hormones) to the blood. An example of a neuroendocrine cell is the cell of the adrenal medulla which releases adrenalin to the blood. The major center of neuroendocrine integration in the body is found in the hypothalamus and the pituitary gland. Here hypothalamic neurosecretory cells release factors to the blood.
definition: Neuroendocrine cells are cells that receive neuronal input (neurotransmitters released by nerve cells) and, as a consequence of this input, release message molecules (hormones) to the blood. In this way they bring about and integration between the nervous system and the endocrine system, a process known as neuroendocrine integration. An example of a neuroendocrine cell is the cell of the adrenal medulla (innermost part of the adrenal gland) which releases adrenalin to the blood. The adrenal medullary cells are controlled by the sympathetic division of the autonomic nervous system. These cells are modified postganglionic neurons. Autonomic nerve fibers lead directly to them from the central nervous system. The major center of neuroendocrine integration in the body is found in the hypothalamus and the pituitary gland. Here hypothalamic neurosecretory cells release factors to the blood. Some of these these factors, release at the median eminence, control the secretion of pituitary hormones, while others (the hormones oxytocin and vasopressin) are released directly to the peripheral circulation.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12485

beta cell
type: Class
subclass of: endocrine pancreas
definition: A cell that composes the bulk of the islets of Langerhans and secretes insulin.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C32199

type B pancreatic cell
type: Class
subclass of: pancreatic cell
definition: A cell that secretes insulin and is located towards the center of the islets of Langerhans.
GOC definition citation: GOC:tfm
ISBN definition citation: ISBN:0517223651
NCI thesaurus definition citation: NCIT:C32199

pancreatic A cell
type: Class
subclass of: epithelial cell
subclass of: cell type
definition: A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C32052

pancreatic D cell
type: Class
subclass of: pancreatic cell
definition: A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
GOC definition citation: GOC:tfm
has_obo_namespace: cell

Leydig cell
type: Class
subclass of: cell type
definition: A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12609

hepatocyte
type: Class
subclass of: cell type
definition: A liver cell.
definition: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules.
definition: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12588

myoepithelial cell
type: Class
subclass of: epithelial cell
definition: Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament. [ GOC:tfm ISBN:0721662544 ]

muscle cell
type: Class
subclass of: cell type
definition: A mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle.
definition: A mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle. This cell has as part of its cytoplasm myofibrils organized in various patterns.
definition: Mature contractile cells, commonly known as myocytes, that form one of three kinds of muscle. The three types of muscle cells are skeletal (muscle fibers), cardiac (myocytes, cardiac), and smooth (myocytes, smooth muscle). They are derived from embryonic (precursor) muscle cells called myoblasts (MSH).
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12612
NIFSTD definition citation: NIFSTD:sao519252327

smooth muscle cell
type: Class
subclass of: muscle cell
definition: A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
definition: Non-striated, elongated, spindle-shaped cells found lining the digestive tract, uterus, and blood vessels. They are derived from specialized myoblasts (myoblasts, smooth muscle) (MSH).
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13001
NIFSTD definition citation: NIFSTD:sao676858164

cochlear hair cell
type: Class
subclass of: cell type
definition: A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
definition: A mechanoreceptor cell located in the organ of Corti that is sensitive to auditory stimuli and in the vestibular apparatus that is sensitive to movement of the head. In each case the accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NIFSTD definition citation: NIFSTD:sao630986029

electrically active cell
type: Class
subclass of: cell type
definition: A cell whose function is determined by the generation or the reception of an electric signal.
imported from: cl.owl
has_obo_namespace: cell

Sertoli cell
type: Class
subclass of: secretory cell
definition: A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12595

Schwann cell
type: Class
subclass of: cell type
definition: A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12620

mesodermal cell
type: Class
subclass of: cell type
definition: A cell of the middle germ layer of the embryo.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C33936

erythrocyte
type: Class
subclass of: erythroid lineage cell
subclass of: cell type
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
definition: A red blood cell. In mammals, mature erythrocytes are non-nucleated, biconcave disks containing hemoglobin whose function is to transport oxygen.
definition: Any of the hemoglobin-containing cells that carry oxygen to the tissues and are responsible for the red color of vertebrate blood.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12521
SNOMEDCT definition citation: SNOMEDCT:41898006

platelet
type: Class
subclass of: myeloid cell
subclass of: fetal blood cell
definition: A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
definition editor: James Malone
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D001792
NCI thesaurus definition citation: NCIt:C12520
SNOMEDCT definition citation: SNOMEDCT:16378004
gwas trait: true

macrophage
type: Class
subclass of: myeloid leukocyte
subclass of: cell type
definition: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
definition: A mononuclear phagocyte which differentiates from monocytes, is typically resident in a particular tissue, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells (Cell Ontology).
definition: Relatively long-lived phagocytic cell of mammalian tissues, derived from blood monocyte. Macrophages from different sites have distinctly different properties. Main types are peritoneal and alveolar macrophages, tissue macrophages (histiocytes), Kuppfer cells of the liver, and osteoclasts. In response to foreign materials may become stimulated or activated. Macrophages play an important role in killing of some bacteria, protozoa, and tumour cells, release substances that stimulate other cells of the immune system, and are involved in antigen presentation. May further differentiate within chronic inflammatory lesions to epithelioid cells or may fuse to form foreign body giant cells or Langhans' giant cells.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12558
NIFSTD definition citation: NIFSTD:sao185843373
SNOMEDCT definition citation: SNOMEDCT:58986001

B cell
type: Class
subclass of: cell type
definition: A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
definition: A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive.
definition: Immunologically important lymphocyte that is not thymus-dependent, is either short-lived and naive or long-lived and of memory phenotype, and resembles the bursa-derived lymphocyte of birds in that it is responsible for the production of immunoglobulins.
definition editor: James Malone
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D001402
NCI thesaurus definition citation: NCIt:C12474
SNOMEDCT definition citation: SNOMEDCT:112130006

hyphal cell
type: Class
subclass of: cell type
definition: A cell of a filament of a fungal mycelium.
imported from: cl.owl
has_obo_namespace: cell

guard cell
type: Class
subclass of: cell type
definition: One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor.
definition editor: Tomasz Adamusiak

neural crest cell
type: Class
subclass of: cell type
definition: A cell of the strip of specialized ectoderm flanking each side of the embryonal neural plate, which after the closure of the neural tube, forms a column of isolated cells along the dorsal aspect of the neural tube. Most of the cranial and all of the spinal sensory ganglion cells arise by differentiation of neural crest cells.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C33937

neuroblast (sensu Vertebrata)
type: Class
subclass of: neuronal stem cell
definition: An embryonic cell that develops into a nerve cell or neuron.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12991

hair follicle dermal papilla cell
type: Class
subclass of: cell type
definition: 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.
definition editor: Helen Parkinson

extraembryonic cell
type: Class
subclass of: cell type
definition: A cell which is part of an extraembryonic structure 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.
has exact synonym: extra-embryonic cell

trophoblast cell
type: Class
subclass of: extraembryonic cell
definition: A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface.
has exact synonym: trophoblastic cell

epiblast cell
type: Class
subclass of: embryonic stem cell
definition: A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
definition editor: James Malone

epidermal cell
type: Class
subclass of: epithelial cell
definition: An epithelial cell of the integument (the outer layer of an organism).

protoplast
type: Class
subclass of: cell type
definition: The cell protoplasm after removal of the cell wall.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12659

ligament cell
type: Class
subclass of: cell type
definition editor: Tomasz Adamusiak

hemocyte
type: Class
subclass of: cell type
definition: A blood cell especially of an invertebrate animal.
definition editor: Tomasz Adamusiak

blood cell (sensu Nematoda and Protostomia)
type: Class
subclass of: blood cell

polygonal cell
type: Class
subclass of: cell type
has_obo_namespace: cell

diploid cell
type: Class
subclass of: cell type
definition: A cell whose nucleus has two haploid genomes.
imported from: cl.owl
has_obo_namespace: cell

coelomocyte
type: Class
subclass of: cell type
definition: A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids.
imported from: cl.owl
has_obo_namespace: cell

follicular dendritic cell
type: Class
subclass of: cell type
definition: A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response.
imported from: cl.owl
ISBN definition citation: ISBN:127520252
NCI thesaurus definition citation: NCIt:C12622
SNOMEDCT definition citation: SNOMEDCT:56685008
has_obo_namespace: cell
comment: Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451.

dendritic cell
type: Class
subclass of: leukocyte
subclass of: cell type
definition: A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.
definition: A special type of cell that is a key regulator of the immune system, acting as a professional antigen-presenting cell, APC, capable of activating naive T cells and stimulating the growth and differentiation of B cells. Dendritic cells are found, for example, in the lymph nodes and spleen. As an APC, a dendritic cell can retain antigen for long periods on its surface, present the antigen to a T or B cell and so influence their behavior.
definition: Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12583
SNOMEDCT definition citation: SNOMEDCT:127942009
SNOMEDCT definition citation: SNOMEDCT:24333000
SNOMEDCT definition citation: SNOMEDCT:37510001

Langerhans cell
type: Class
subclass of: conventional dendritic cell
NCI thesaurus definition citation: NCIt:C12584

follicle cell
type: Class
subclass of: cell type
definition editor: James Malone

connective tissue type mast cell
type: Class
subclass of: mast cell

mucosal type mast cell
type: Class
subclass of: mast cell

stromal cell
type: Class
subclass of: cell type
definition: A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12571

granulosa cell
type: Class
subclass of: cell type
definition: A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors.
NCI thesaurus definition citation: NCIt:C12587

paneth cell
type: Class
subclass of: epithelial cell
subclass of: secretory cell
subclass of: cell type
definition: An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix.
NCI thesaurus definition citation: NCIt:C12593
SNOMEDCT definition citation: SNOMEDCT:84907006

smooth muscle myoblast
type: Class
subclass of: muscle cell
definition: A precursor cell destined to differentiate into smooth muscle myocytes.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C33516

skeletal muscle myoblast
type: Class
subclass of: myoblast
definition: A myoblast that differentiates into skeletal muscle fibers.
definition editor: Helen Parkinson

prokaryotic cell
type: Class
subclass of: cell type
imported from: cl.owl
has_obo_namespace: cell

fungal cell
type: Class
subclass of: cell type
imported from: cl.owl
has_obo_namespace: cell

syncytiotrophoblast cell
type: Class
subclass of: cell type
definition: A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo. It It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.
definition editor: Tomasz Adamusiak

neuron
type: Class
subclass of: cell type
definition: A grayish or reddish granular cell with specialized processes that is the fundamental functional unit of nervous tissue.
definition: 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.
definition: The basic cellular units of nervous tissue. Neurons are polarized cells with defined regions consisting of the cell body, an axon, and dendrites, although some types of neurons lack axons or dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12623
NIFSTD definition citation: NIFSTD:sao1417703748
SNOMEDCT definition citation: SNOMEDCT:47220008

proerythroblast
type: Class
subclass of: erythroid lineage cell
subclass of: cell type
definition: An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells.
definition: An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13129
SNOMEDCT definition citation: SNOMEDCT:16671004

basophilic erythroblast
type: Class
subclass of: erythroblast
definition: A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared.
definition: A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13130
SNOMEDCT definition citation: SNOMEDCT:115610004
SNOMEDCT definition citation: SNOMEDCT:464005

polychromatophilic erythroblast
type: Class
subclass of: erythroblast
NCI thesaurus definition citation: NCIt:C13131
SNOMEDCT definition citation: SNOMEDCT:16779009

orthochromatic erythroblast
type: Class
subclass of: erythroblast

megakaryocyte progenitor cell
type: Class
subclass of: myeloid lineage restricted progenitor cell
subclass of: cell type
definition: The earliest cytologically identifiable precursor in the thrombocytic series.
definition: The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13122
SNOMEDCT definition citation: SNOMEDCT:27852005
SNOMEDCT definition citation: SNOMEDCT:50284009

megakaryocyte
type: Class
subclass of: myeloid cell
subclass of: cell type
definition: A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm.
definition: A large cell that has a lobulated nucleus, is found especially in the bone marrow, and is the source of blood platelets.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12553
SNOMEDCT definition citation: SNOMEDCT:23592000

granulocyte monocyte progenitor cell
type: Class
subclass of: hematopoietic oligopotent progenitor cell
subclass of: cell type
definition: A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata-1, Gata2 but do express C/EBPa, and Pu.1.
definition: A progenitor cell that has plasma membrane part CD123, CD34, and CD45RA, lacks plasma membrane part CD19 and CD3, and is committed to the granulocyte and monocyte lineages.
definition editor: Tomasz Adamusiak

reticulocyte
type: Class
subclass of: erythroid lineage cell
subclass of: cell type
definition: An immature erythrocyte showing a basophilic reticulum under vital staining.
definition: An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12528
SNOMEDCT definition citation: SNOMEDCT:52802009

promonocyte
type: Class
subclass of: monopoietic cell
NCI thesaurus definition citation: NCIt:C13121
SNOMEDCT definition citation: SNOMEDCT:1075005

band form neutrophil
type: Class
subclass of: immature neutrophil

nucleate erythrocyte
type: Class
subclass of: erythrocyte

neutrophilic promyelocyte
type: Class
subclass of: promyelocyte
SNOMEDCT definition citation: SNOMEDCT:34254002

monocyte
type: Class
subclass of: myeloid leukocyte
subclass of: cell type
definition: A mononuclear phagocytic leukocyte, 13 to 25 mm in diameter, with an ovoid or kidney-shaped nucleus, containing lacy, linear chromatin and abundant gray-blue cytoplasm filled with fine reddish and azurophilic granules. Formed in the bone marrow from promonocytes, monocytes are transported to tissues such as the lung and liver, where they develop into macrophages.
definition: Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
definition editor: James Malone
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D009000
NCI thesaurus definition citation: NCIt:C12547
SNOMEDCT definition citation: SNOMEDCT:55918008
gwas trait: true

border follicle cell
type: Class
subclass of: cell type
definition: A follicle cell that migrates from the anterior pole of the egg chamber, between the nurse cells, to the anterior of the oocyte where they participate in formation of the micropyle. About 6-10 border cells per egg chamber migrate as a tightly associated cluster.
definition editor: Tomasz Adamusiak

neutrophilic myelocyte
type: Class
subclass of: immature neutrophil
subclass of: myelocyte
SNOMEDCT definition citation: SNOMEDCT:4717004

peritoneal macrophage
type: Class
subclass of: tissue-resident macrophage
NCI thesaurus definition citation: NCIt:C12566

neutrophilic metamyelocyte
type: Class
subclass of: immature neutrophil
subclass of: metamyelocyte
SNOMEDCT definition citation: SNOMEDCT:50134008

alveolar macrophage
type: Class
subclass of: tissue-resident macrophage
NCI thesaurus definition citation: NCIt:C12565
SNOMEDCT definition citation: SNOMEDCT:33956004

enterocyte
type: Class
subclass of: intestinal epithelial cell
definition: An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen.
has db xref: SANBI:mhl
has_obo_namespace: cell

germ cell
type: Class
subclass of: cell type
definition: The reproductive cell in multicellular organisms.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12597

odontoclast
type: Class
subclass of: osteoclast

enucleate erythrocyte
type: Class
subclass of: erythrocyte

pyramidal cell
type: Class
subclass of: neuron
definition: A projection neuron in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region.
imported from: cl.owl
GOC definition citation: GOC:tfm
NCI thesaurus definition citation: NCIt:C12652
NIF cell definition citation: NIF_Cell:sao862606388
SNOMEDCT definition citation: SNOMEDCT:17522008
has_obo_namespace: cell

conidium
type: Class
subclass of: cell type
definition: An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm.
imported from: cl.owl
FAO definition citation: FAO:0000024
SNOMEDCT definition citation: SNOMEDCT:14127004
has_obo_namespace: cell

eosinophil progenitor cell
type: Class
subclass of: granulocytopoietic cell

eosinophilic myelocyte
type: Class
subclass of: immature eosinophil
subclass of: myelocyte
SNOMEDCT definition citation: SNOMEDCT:90961003

basophil progenitor cell
type: Class
subclass of: granulocytopoietic cell

basophilic myelocyte
type: Class
subclass of: immature basophil
SNOMEDCT definition citation: SNOMEDCT:17295002

GABAergic neuron
type: Class
subclass of: neuron
definition: A neuron that uses GABA as a vesicular neurotransmitter
definition editor: James Malone

acinar cell
type: Class
subclass of: secretory cell
definition: A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13077

photosynthetic cell
type: Class
subclass of: cell type
definition: A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source.
imported from: cl.owl
has_obo_namespace: cell
comment: see PMID:21177950, The making of a photosynthetic animal.

hepatic stellate cell
type: Class
subclass of: cell type
definition: A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver.
imported from: cl.owl
NCI thesaurus definition citation: NCIt:C32734
has exact synonym: Ito cell
has exact synonym: hepatic perisinusoidal cell
has exact synonym: perisinusoidal cell
has_obo_namespace: cell
has related synonym: fat-storing cell
has related synonym: lipocyte
has related synonym: vitamin A-storing cells
comment: Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen.

basal cell
type: Class
subclass of: stem cell
definition: Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C12475

multinucleated giant cell
type: Class
subclass of: myeloid leukocyte

pericyte
type: Class
subclass of: cell type
definition: *Slender, contractile, mesenchymal-like cell found in close association with capillary walls. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. (From OBO Cell Type Ontology). *A flattened, or elongated, stellate-shaped solitary cell with multiple cytoplasmic processes encircling the capillary endothelium and contacting a large abluminal vessel area. It may be equivalent to the vascular smooth muscle cell, although this identify has not been conclusively determined yet (Armulik et al., Circ Res 97: 512, 2005).
definition: A slender, contractile, mesenchymal-like cell found in close association with capillary walls. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. (From Stedman, 26th ed).
definition: An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12656
NIFSTD definition citation: NIFSTD:nifext_171
SNOMEDCT definition citation: SNOMEDCT:34773004

primordial germ cell
type: Class
subclass of: germ cell
definition: A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C33401

glutamatergic neuron
type: Class
subclass of: neuron
definition editor: James Malone

dopaminergic neuron
type: Class
subclass of: neuron
definition: A neuron that releases dopamine as a neurotransmitter.
NCI thesaurus definition citation: NCIt:C26454

cumulus cell
type: Class
subclass of: granulosa cell
subclass of: cell type
definition: Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle.
imported from: cl.owl
has_obo_namespace: cell

somatic stem cell
type: Class
subclass of: stem cell
subclass of: somatic cell
definition: A stem cell that can give rise to cell types of the body other than those of the germ-line.
SNOMEDCT definition citation: SNOMEDCT:417904004
has_obo_namespace: cell

leukocyte
type: Class
subclass of: cell type
definition: A nucleated cell of the myeloid or lymphoid lineages, found in blood or other tissue.
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
definition: Any of the blood cells that are colorless, lack hemoglobin, contain a nucleus, and include the lymphocytes, monocytes, neutrophils, eosinophils, and basophils.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12529
SNOMEDCT definition citation: SNOMEDCT:52501007

cardiac muscle cell
type: Class
subclass of: muscle cell
definition: A heart muscle cell.
definition: A myocyte located in the heart. The contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
definition: A striated muscle cell found in the heart. They develop from cardiac myoblasts.
definition: Striated muscle cells found in the heart. They are derived from cardiac myoblasts (myoblasts, cardiac (MSH).
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13002
NIFSTD definition citation: NIFSTD:sao658938043
SNOMEDCT definition citation: SNOMEDCT:86441007

nucleated thrombocyte
type: Class
subclass of: myeloid cell

myeloid cell
type: Class
subclass of: cell type
definition: A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
definition: Any of the immature blood cells that develop in the bone marrow, such as those involved in hematopoiesis.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12549

erythroid lineage cell
type: Class
subclass of: myeloid cell
definition: A immature or mature cell in the lineage leading to and including erythrocytes.

erythroblast
type: Class
subclass of: erythroid lineage cell
subclass of: cell type
definition: A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
definition: A nucleated precursor of an erythrocyte.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12527
SNOMEDCT definition citation: SNOMEDCT:84227004

myeloid leukocyte
type: Class
subclass of: leukocyte

basophil
type: Class
subclass of: granulocyte
definition: Granular leukocytes characterized by a relatively pale-staining, lobate nucleus and cytoplasm containing coarse dark-staining granules of variable size and stainable by basic dyes.
definition editor: Dani Welter
MSH definition citation: MSH:D001491
NCI thesaurus definition citation: NCIt:C12531
SNOMEDCT definition citation: SNOMEDCT:30061004
gwas trait: true

immature basophil
type: Class
subclass of: basophil

basophilic metamyelocyte
type: Class
subclass of: immature basophil
subclass of: metamyelocyte
SNOMEDCT definition citation: SNOMEDCT:63369000

band form basophil
type: Class
subclass of: immature basophil

eosinophil
type: Class
subclass of: granulocyte
definition: Granular leukocytes with a nucleus that usually has two lobes connected by a slender thread of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and stainable by eosin.
definition editor: Dani Welter
MSH definition citation: MSH:D004804
NCI thesaurus definition citation: NCIt:C12532
SNOMEDCT definition citation: SNOMEDCT:14793004
gwas trait: true

immature eosinophil
type: Class
subclass of: eosinophil

eosinophilic metamyelocyte
type: Class
subclass of: immature eosinophil
subclass of: metamyelocyte
SNOMEDCT definition citation: SNOMEDCT:80036001

band form eosinophil
type: Class
subclass of: immature eosinophil

neutrophil
type: Class
subclass of: granulocyte
definition: A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
definition: A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
definition editor: Ele Holloway
definition editor: James Malone
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D009504
NCI thesaurus definition citation: NCIt:C12533
SNOMEDCT definition citation: SNOMEDCT:116712007
gwas trait: true

immature neutrophil
type: Class
subclass of: neutrophil

mesangial phagocyte
type: Class
subclass of: tissue-resident macrophage
subclass of: cell type
definition: A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling.
definition: A tissue-resident macrophage of the renal glomerular mesangium.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13159
SNOMEDCT definition citation: SNOMEDCT:24259000

mononuclear osteoclast
type: Class
subclass of: osteoclast

multinuclear osteoclast
type: Class
subclass of: osteoclast

myeloid dendritic cell
type: Class
subclass of: conventional dendritic cell

plasmacytoid dendritic cell
type: Class
subclass of: dendritic cell
subclass of: cell type
definition: A dendritic cell type of distinct morphology, localization, and surface marker expression from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C45236

mature B cell
type: Class
subclass of: B cell
definition: A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C33058

plasma cell
type: Class
subclass of: secretory cell
definition: A terminally differentiated cell of the B lymphocyte lineage that produces antibodies; plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern.
definition: A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12486
SNOMEDCT definition citation: SNOMEDCT:113335003

memory B cell
type: Class
subclass of: mature B cell

naive B cell
type: Class
subclass of: mature B cell

immature B cell
type: Class
subclass of: precursor B cell
subclass of: cell type
definition: An immature B cell is a precursor B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C32766

precursor B cell
type: Class
subclass of: B cell
definition: A precursor B cell is a B cell with the phenotype CD10-positive (P08473/NEP_HUMAN; PIRSF001194).
definition: A precursor B cell is a B cell with the phenotype CD10-positive.
definition editor: James Malone
definition editor: Tomasz Adamusiak

transitional stage B cell
type: Class
subclass of: B cell

B-1 B cell
type: Class
subclass of: mature B cell

B-1a B cell
type: Class
subclass of: B-1 B cell

B-1b B cell
type: Class
subclass of: B-1 B cell

B-2 B cell
type: Class
subclass of: B cell
subclass of: mature B cell
definition: A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative.
definition editor: James Malone
definition editor: Tomasz Adamusiak

thromboblast
type: Class
subclass of: myeloid lineage restricted progenitor cell

basophilic myeloblast
type: Class
subclass of: myeloblast

basophilic promyelocyte
type: Class
subclass of: promyelocyte
SNOMEDCT definition citation: SNOMEDCT:71170001

mast cell progenitor
type: Class
subclass of: myeloid lineage restricted progenitor cell

eosinophilic myeloblast
type: Class
subclass of: myeloblast
SNOMEDCT definition citation: SNOMEDCT:259719000

eosinophilic promyelocyte
type: Class
subclass of: promyelocyte
SNOMEDCT definition citation: SNOMEDCT:4029003

neutrophil progenitor cell
type: Class
subclass of: granulocytopoietic cell

myeloblast
type: Class
subclass of: granulocytopoietic cell
NCI thesaurus definition citation: NCIt:C13015
SNOMEDCT definition citation: SNOMEDCT:15622002

promyelocyte
type: Class
subclass of: granulocytopoietic cell
NCI thesaurus definition citation: NCIt:C13114
SNOMEDCT definition citation: SNOMEDCT:43446009

hematopoietic multipotent progenitor cell
type: Class
subclass of: cell type
definition: A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
definition: A progenitor cell of any hematopoietic lineage, potentially multipotent.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak

lymphoid lineage restricted progenitor cell
type: Class
subclass of: hematopoietic lineage restricted progenitor cell

myeloid lineage restricted progenitor cell
type: Class
subclass of: hematopoietic lineage restricted progenitor cell
subclass of: cell type
definition: A progenitor cell of any myeloid lineage, potentially multipotent.
definition: A progenitor cell restricted to the myeloid lineage.
definition editor: Tomasz Adamusiak

immature conventional dendritic cell
type: Class
subclass of: conventional dendritic cell

mature conventional dendritic cell
type: Class
subclass of: conventional dendritic cell

follicular B cell
type: Class
subclass of: mature B cell

germinal center B cell
type: Class
subclass of: mature B cell

marginal zone B cell
type: Class
subclass of: mature B cell

classical monocyte
type: Class
subclass of: monocyte

elicited macrophage
type: Class
subclass of: macrophage

suppressor macrophage
type: Class
subclass of: elicited macrophage

inflammatory macrophage
type: Class
subclass of: elicited macrophage

tissue-resident macrophage
type: Class
subclass of: macrophage

gastrointestinal tract (lamina propria) macrophage
type: Class
subclass of: gut-associated lymphoid tissue macrophage

thymic macrophage
type: Class
subclass of: tissue-resident macrophage

secondary lymphoid organ macrophage
type: Class
subclass of: tissue-resident macrophage

lymph node macrophage
type: Class
subclass of: secondary lymphoid organ macrophage

tonsillar macrophage
type: Class
subclass of: mucosa-associated lymphoid tissue macrophage

Peyer's patch macrophage
type: Class
subclass of: gut-associated lymphoid tissue macrophage

splenic macrophage
type: Class
subclass of: secondary lymphoid organ macrophage

splenic marginal zone macrophage
type: Class
subclass of: splenic macrophage

splenic metallophillic macrophage
type: Class
subclass of: splenic macrophage

splenic red pulp macrophage
type: Class
subclass of: splenic macrophage

non-classical monocyte
type: Class
subclass of: monocyte

splenic white pulp macrophage
type: Class
subclass of: splenic macrophage

central nervous system macrophage
type: Class
subclass of: tissue-resident macrophage

meningeal macrophage
type: Class
subclass of: central nervous system macrophage

choroid-plexus macrophage
type: Class
subclass of: central nervous system macrophage

perivascular macrophage
type: Class
subclass of: central nervous system macrophage

thymic medullary macrophage
type: Class
subclass of: thymic macrophage

thymic cortical macrophage
type: Class
subclass of: thymic macrophage

mucosa-associated lymphoid tissue macrophage
type: Class
subclass of: secondary lymphoid organ macrophage

gut-associated lymphoid tissue macrophage
type: Class
subclass of: mucosa-associated lymphoid tissue macrophage

nasal and broncial associated lymphoid tissue macrophage
type: Class
subclass of: mucosa-associated lymphoid tissue macrophage

lymph node subcapsular sinus macrophage
type: Class
subclass of: lymph node macrophage

lymph node tingible body macrophage
type: Class
subclass of: lymph node macrophage

myeloid suppressor cell
type: Class
subclass of: myeloid leukocyte

alternatively activated macrophage
type: Class
subclass of: elicited macrophage

early lymphoid progenitor
type: Class
subclass of: hematopoietic multipotent progenitor cell

thymic conventional dendritic cell
type: Class
subclass of: conventional dendritic cell

thymic plasmacytoid dendritic cell
type: Class
subclass of: plasmacytoid dendritic cell

Be1 Cell
type: Class
subclass of: Be cell

Be2 cell
type: Class
subclass of: Be cell

IgE plasma cell
type: Class
subclass of: long lived plasma cell

IgE memory B cell
type: Class
subclass of: class switched memory B cell

IgD plasmablast
type: Class
subclass of: plasmablast

IgE plasmablast
type: Class
subclass of: plasmablast

IgE short lived plasma cell
type: Class
subclass of: short lived plasma cell

Bm1 B cell
type: Class
subclass of: follicular B cell

Bm2 B cell
type: Class
subclass of: follicular B cell

Bm3-delta B cell
type: Class
subclass of: germinal center B cell

Bm2' B cell
type: Class
subclass of: germinal center B cell

Bm3 B cell
type: Class
subclass of: germinal center B cell

Bm4 B cell
type: Class
subclass of: germinal center B cell

Bm5 B cell
type: Class
subclass of: memory B cell

Be cell
type: Class
subclass of: mature B cell

regulatory B cell
type: Class
subclass of: mature B cell
NCI thesaurus definition citation: NCIt:C113502

unswitched memory B cell
type: Class
subclass of: memory B cell

IgM memory B cell
type: Class
subclass of: unswitched memory B cell

class switched memory B cell
type: Class
subclass of: memory B cell

IgA memory B cell
type: Class
subclass of: class switched memory B cell

long lived plasma cell
type: Class
subclass of: plasma cell

short lived plasma cell
type: Class
subclass of: plasma cell

IgA short lived plasma cell
type: Class
subclass of: short lived plasma cell

IgG short lived plasma cell
type: Class
subclass of: short lived plasma cell

IgM short lived plasma cell
type: Class
subclass of: short lived plasma cell

IgG memory B cell
type: Class
subclass of: class switched memory B cell

plasmablast
type: Class
subclass of: mature B cell
NCI thesaurus definition citation: NCIt:C37082
SNOMEDCT definition citation: SNOMEDCT:2579009

double negative memory B cell
type: Class
subclass of: memory B cell

IgG plasmablast
type: Class
subclass of: plasmablast

IgM plasmablast
type: Class
subclass of: plasmablast

IgA plasmablast
type: Class
subclass of: plasmablast

IgG plasma cell
type: Class
subclass of: long lived plasma cell

IgM plasma cell
type: Class
subclass of: long lived plasma cell

IgA plasma cell
type: Class
subclass of: long lived plasma cell

hematopoietic cell
type: Class
subclass of: cell type
definition: A blood cell.
definition: A cell found predominately in the blood.
definition: A cell of a hematopoietic lineage.
definition editor: Tomasz Adamusiak

CD11c-low plasmacytoid dendritic cell
type: Class
subclass of: plasmacytoid dendritic cell

conventional dendritic cell
type: Class
subclass of: dendritic cell

CD11c-negative plasmacytoid dendritic cell
type: Class
subclass of: plasmacytoid dendritic cell

immature CD11c-low plasmacytoid dendritic cell
type: Class
subclass of: CD11c-low plasmacytoid dendritic cell

mature CD11c-low plasmacytoid dendritic cell
type: Class
subclass of: CD11c-low plasmacytoid dendritic cell

immature CD11c-negative plasmacytoid dendritic cell
type: Class
subclass of: CD11c-negative plasmacytoid dendritic cell

CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor
type: Class
subclass of: hematopoietic oligopotent progenitor cell

mature CD11c-negative plasmacytoid dendritic cell
type: Class
subclass of: CD11c-negative plasmacytoid dendritic cell

CD8_alpha-negative CD11b-negative dendritic cell
type: Class
subclass of: conventional dendritic cell

CD4-positive CD11b-positive dendritic cell
type: Class
subclass of: CD11b-positive dendritic cell

CD8_alpha-positive CD11b-negative dendritic cell
type: Class
subclass of: conventional dendritic cell

immature CD8_alpha-negative CD11b-negative dendritic cell
type: Class
subclass of: CD8_alpha-negative CD11b-negative dendritic cell

mature CD8_alpha-negative CD11b-negative dendritic cell
type: Class
subclass of: CD8_alpha-negative CD11b-negative dendritic cell

immature CD8_alpha-positive CD11b-negative dendritic cell
type: Class
subclass of: CD8_alpha-positive CD11b-negative dendritic cell

mature CD8_alpha-positive CD11b-negative dendritic cell
type: Class
subclass of: CD8_alpha-positive CD11b-negative dendritic cell

dermal dendritic cell
type: Class
subclass of: conventional dendritic cell

interstitial dendritic cell
type: Class
subclass of: conventional dendritic cell

Kit and Sca1-positive hematopoietic stem cell
type: Class
subclass of: hematopoietic stem cell

immature dermal dendritic cell
type: Class
subclass of: dermal dendritic cell

mature dermal dendritic cell
type: Class
subclass of: dermal dendritic cell

immature interstitial dendritic cell
type: Class
subclass of: interstitial dendritic cell

CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor
type: Class
subclass of: hematopoietic oligopotent progenitor cell

mature interstitial dendritic cell
type: Class
subclass of: interstitial dendritic cell

CD1a-positive Langerhans cell
type: Class
subclass of: Langerhans cell

CD8_alpha-low Langerhans cell
type: Class
subclass of: Langerhans cell

CD115-positive monocyte OR common dendritic progenitor
type: Class
subclass of: hematopoietic lineage restricted progenitor cell

CD115-positive monocyte
type: Class
subclass of: monocyte

CD34-positive, CD38-negative hematopoietic stem cell
type: Class
subclass of: hematopoietic stem cell

common dendritic progenitor
type: Class
subclass of: hematopoietic lineage restricted progenitor cell

CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor
type: Class
subclass of: hematopoietic oligopotent progenitor cell

neoplastic cell
type: Class
subclass of: cell type
definition: An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism.
GOC definition citation: GOC:add
GOC definition citation: GOC:cg
GOC definition citation: GOC:wdd
NCI thesaurus definition citation: NCIt:C12922
has_obo_namespace: cell

Kit-positive erythroid progenitor cell
type: Class
subclass of: erythroid progenitor cell

CD34-positive, CD38-positive granulocyte monocyte progenitor
type: Class
subclass of: granulocyte monocyte progenitor cell

Kit-positive granulocyte monocyte progenitor
type: Class
subclass of: granulocyte monocyte progenitor cell

CD34-positive, GlyA-negative erythroid progenitor cell
type: Class
subclass of: erythroid progenitor cell

CD34-negative, GlyA-negative proerythroblast
type: Class
subclass of: proerythroblast

Kit-low, CD34-positive eosinophil progenitor cell
type: Class
subclass of: eosinophil progenitor cell

CD34-positive, CD38-positive eosinophil progenitor cell
type: Class
subclass of: eosinophil progenitor cell

macrophage dendritic cell progenitor
type: Class
subclass of: hematopoietic oligopotent progenitor cell

pre-conventional dendritic cell
type: Class
subclass of: hematopoietic lineage restricted progenitor cell

Kit-low proerythroblast
type: Class
subclass of: proerythroblast

GlyA-positive basophillic erythroblast
type: Class
subclass of: basophilic erythroblast

Kit-negative, Ly-76 high basophilic erythroblast
type: Class
subclass of: basophilic erythroblast

Kit-negative, Ly-76 high polychromatophilic erythroblast
type: Class
subclass of: polychromatophilic erythroblast

CD71-low, GlyA-positive polychromatic erythroblast
type: Class
subclass of: polychromatophilic erythroblast

Kit-negative, Ly-76 high orthochromatophilic erythroblasts
type: Class
subclass of: orthochromatic erythroblast

CD71-negative, GlyA-positive orthochromatic erythroblast
type: Class
subclass of: orthochromatic erythroblast

Ly-76 high reticulocyte
type: Class
subclass of: enucleated reticulocyte

GlyA-positive reticulocytes
type: Class
subclass of: enucleated reticulocyte

GlyA-positive erythrocyte
type: Class
subclass of: enucleate erythrocyte

Ly-76 high positive erythrocyte
type: Class
subclass of: enucleate erythrocyte

CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell
type: Class
subclass of: megakaryocyte progenitor cell

Kit-positive megakaryocyte progenitor cell
type: Class
subclass of: megakaryocyte progenitor cell

CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell
type: Class
subclass of: megakaryocyte progenitor cell

CD34-negative, CD41-positive, CD42-positive megakaryocyte cell
type: Class
subclass of: megakaryocyte

CD9-positive, CD41-positive megakaryocyte cell
type: Class
subclass of: megakaryocyte

basophil mast progenitor cell
type: Class
subclass of: myeloid lineage restricted progenitor cell

Fc-epsilon RIalpha-low mast cell progenitor
type: Class
subclass of: mast cell progenitor

Fc-epsilon RIalpha-high basophil progenitor cell
type: Class
subclass of: basophil progenitor cell

hematopoietic lineage restricted progenitor cell
type: Class
subclass of: cell type

hematopoietic oligopotent progenitor cell
type: Class
subclass of: cell type

Slamf1-negative multipotent progenitor cell
type: Class
subclass of: hematopoietic multipotent progenitor cell

Slamf1-positive multipotent progenitor cell
type: Class
subclass of: hematopoietic multipotent progenitor cell

CD34-positive, CD38-negative multipotent progenitor cell
type: Class
subclass of: hematopoietic multipotent progenitor cell

Kit-positive, integrin beta7-high basophil mast progenitor cell
type: Class
subclass of: basophil mast progenitor cell

Fraction F mature B cell
type: Class
subclass of: mature B cell

CD14-positive, CD16-negative classical monocyte
type: Class
subclass of: classical monocyte

Gr1-low non-classical monocyte
type: Class
subclass of: non-classical monocyte

CD8alpha-positive thymic conventional dendritic cell
type: Class
subclass of: thymic conventional dendritic cell

melanophage
type: Class
subclass of: tissue-resident macrophage

pancreatic ductal cell
type: Class
subclass of: pancreatic cell
definition: Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH.
GOC definition citation: GOC:tfm
PMID definition citation: PMID:14740223
has_obo_namespace: cell

nongranular leukocyte
type: Class
subclass of: leukocyte

bone marrow cell
type: Class
subclass of: cell type
definition: A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. [ GOC:tfm ISBN:0618947256 ]
comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.

CD38-positive naive B cell
type: Class
subclass of: naive B cell

CD38-negative naive B cell
type: Class
subclass of: naive B cell

IgG-positive double negative memory B cell
type: Class
subclass of: double negative memory B cell

IgG-negative double negative memory B cell
type: Class
subclass of: double negative memory B cell

CD38-positive IgG memory B cell
type: Class
subclass of: IgG memory B cell

IgD-positive CD38-positive IgG memory B cell
type: Class
subclass of: CD38-positive IgG memory B cell

IgD-negative CD38-positive IgG memory B cell
type: Class
subclass of: CD38-positive IgG memory B cell

CD38-negative IgG memory B cell
type: Class
subclass of: IgG memory B cell

B220-positive CD38-positive naive B cell
type: Class
subclass of: CD38-positive naive B cell

B220-low CD38-positive naive B cell
type: Class
subclass of: CD38-positive naive B cell

CD38-negative unswitched memory B cell
type: Class
subclass of: unswitched memory B cell

B220-positive CD38-negative unswitched memory B cell
type: Class
subclass of: CD38-negative unswitched memory B cell

B220-low CD38-negative unswitched memory B cell
type: Class
subclass of: CD38-negative unswitched memory B cell

CD38-positive unswitched memory B cell
type: Class
subclass of: unswitched memory B cell

B220-positive CD38-positive unswitched memory B cell
type: Class
subclass of: CD38-positive unswitched memory B cell

B220-low CD38-positive unswitched memory B cell
type: Class
subclass of: CD38-positive unswitched memory B cell

IgG-negative class switched memory B cell
type: Class
subclass of: class switched memory B cell

CD38-negative IgG-negative class switched memory B cell
type: Class
subclass of: IgG-negative class switched memory B cell

CD38-positive IgG-negative class switched memory B cell
type: Class
subclass of: IgG-negative class switched memory B cell

CD24-positive CD38-negative IgG-negative class switched memory B cell
type: Class
subclass of: CD38-negative IgG-negative class switched memory B cell

CD24-negative CD38-negative IgG-negative class switched memory B cell
type: Class
subclass of: CD38-negative IgG-negative class switched memory B cell

B220-positive CD38-positive IgG-negative class switched memory B cell
type: Class
subclass of: CD38-positive IgG-negative class switched memory B cell

B220-low CD38-positive IgG-negative class switched memory B cell
type: Class
subclass of: CD38-positive IgG-negative class switched memory B cell

capillary endothelial cell
type: Class
subclass of: cell type
definition: An endothelial cell found in capillaries.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-24T10:15:00Z
has_obo_namespace: cell

epitheloid cell
type: Class
subclass of: myeloid leukocyte

late promyelocyte
type: Class
subclass of: promyelocyte

early promyelocyte
type: Class
subclass of: promyelocyte

echinocyte
type: Class
subclass of: enucleate erythrocyte

granulocytopoietic cell
type: Class
subclass of: myeloid lineage restricted progenitor cell

metamyelocyte
type: Class
subclass of: granulocytopoietic cell
NCI thesaurus definition citation: NCIt:C13116
SNOMEDCT definition citation: SNOMEDCT:83321009

myelocyte
type: Class
subclass of: granulocytopoietic cell
subclass of: cell type
definition: A cell derived from a promyelocyte. It differentiates into a metamyelocyte. It has a diameter of 10-18 micrometer, and an oval or round nucleus with finely granulated chromatin.
definition: A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13115
SNOMEDCT definition citation: SNOMEDCT:127915008

monopoietic cell
type: Class
subclass of: myeloid lineage restricted progenitor cell

tuft cell
type: Class
subclass of: epithelial cell
definition: A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known.
GOC definition citation: GOC:tfm
ISBN definition citation: ISBN:0517223651
PMID definition citation: PMID:15817800
has_obo_namespace: cell

epithelial cell of prostate
type: Class
subclass of: epithelial cell
definition: An epithelial cell of the prostate.
imported from: cl.owl
GOC definition citation: GOC:tfm
has_obo_namespace: cell

peripheral blood stem cell
type: Class
subclass of: hematopoietic stem cell
NCI thesaurus definition citation: NCIt:C12946
SNOMEDCT definition citation: SNOMEDCT:419583006

pleural macrophage
type: Class
subclass of: tissue-resident macrophage

pluripotent stem cell
type: Class
subclass of: somatic stem cell
definition: 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.
NCI thesaurus definition citation: NCIt:C12977
created by: tmeehan
creation date: 2010-09-07T04:26:06Z
has_obo_namespace: cell

epithelial cell of large intestine
type: Class
subclass of: intestinal epithelial cell
definition: An epithelial cell of the large intestine.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-08T09:28:22Z
has alternative id: CL:1000292
has_obo_namespace: cell
has related synonym: epithelial cell of colon

pancreatic PP cell
type: Class
subclass of: pancreatic cell
definition: A PP cell located in the islets of the pancreas.
GOC definition citation: GOC:tfm
has_obo_namespace: cell

periperhal blood mesothelial cell
type: Class
subclass of: blood cell

neural cell
type: Class
subclass of: cell type

embryonic cell
type: Class
subclass of: cell type
definition: A cell of the embryo.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C13054

embryonic stem cell
type: Class
subclass of: stem cell
definition: Totipotent cell cultured from early embryo. Have the advantage that following modification in vitrothey can be used to produce chimeric embryos and thus transgenic animals.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12935
SNOMEDCT definition citation: SNOMEDCT:419965008

mammary epithelial cell
type: Class
subclass of: epithelial cell
definition: An epithelial cell of the mammary gland.
imported from: cl.owl
GOC definition citation: GOC:tfm
PMID definition citation: PMID:19022771
has_obo_namespace: cell

preadipocyte
type: Class
subclass of: cell type
definition: A precursor to an adipocyte.
definition: An undifferentiated fibroblast that can be stimulated to form a fat cell.
definition editor: James Malone
definition editor: Tomasz Adamusiak

circulating endothelial cell
type: Class
subclass of: endothelial cell
definition: A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage.
imported from: cl.owl
PMID definition citation: PMID:19022771
has_obo_namespace: cell

progenitor cell of endocrine pancreas
type: Class
subclass of: cell type
definition: 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.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
definition citation: http://en.wikipedia.org/wiki/Pancreas

gestational hematopoietic stem cell
type: Class
subclass of: hematopoietic stem cell

fetal liver hematopoietic progenitor cell
type: Class
subclass of: gestational hematopoietic stem cell
subclass of: cell type
definition: 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.
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak

primitive red blood cell
type: Class
subclass of: primitive erythroid lineage cell

primitive reticulocyte
type: Class
subclass of: primitive erythroid lineage cell

fetal derived definitive erythrocyte
type: Class
subclass of: enucleate erythrocyte

pyrenocyte
type: Class
subclass of: primitive erythroid lineage cell

primitive erythroid progenitor
type: Class
subclass of: primitive erythroid lineage cell

keratocyte
type: Class
subclass of: fibroblast
definition: A keratocyte is a specialized fibroblast residing in the stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate.
definition editor: Ele Holloway
definition editor: James Malone
definition editor: Tomasz Adamusiak
SNOMEDCT definition citation: SNOMEDCT:397052000

cortical thymic epithelial cell
type: Class
subclass of: epithelial cell
definition: An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. [ PMID:18403190 GOC:tfm ]

medullary thymic epithelial cell
type: Class
subclass of: cell type
definition: An epithelial cell located in the inner portion of the thymus where the T lymphocytes become mature and are released into the circulation.
definition: An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C45702

respiratory epithelial cell
type: Class
subclass of: epithelial cell
definition: An endo-epithelial cell of the respiratory tract.
definition: Epithelium of the respiratory portion of the bronchial tree.
definition editor: Tomasz Adamusiak

somatic cell
type: Class
subclass of: cell type
definition: 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).
definition: One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells.
definition editor: James Malone
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12949

intermediate monocyte
type: Class
subclass of: monocyte

CD141-positive myeloid dendritic cell
type: Class
subclass of: myeloid dendritic cell

Gr1-high classical monocyte
type: Class
subclass of: classical monocyte

CD14-low, CD16-positive monocyte
type: Class
subclass of: non-classical monocyte

CD14-positive, CD16-positive monocyte
type: Class
subclass of: intermediate monocyte

Gr1-positive, CD43-positive monocyte
type: Class
subclass of: intermediate monocyte

CD1c-positive myeloid dendritic cell
type: Class
subclass of: myeloid dendritic cell

Peyer's patch B cell
type: Class
subclass of: mature B cell

pancreatic stellate cell
type: Class
subclass of: fibroblast
subclass of: pancreatic cell
definition: A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast.
GOC definition citation: GOC:mah
GOC definition citation: GOC:tfm
PMID definition citation: PMID:17200706
has_obo_namespace: cell

primitive erythroid lineage cell
type: Class
subclass of: erythroid lineage cell

nucleated reticulocyte
type: Class
subclass of: reticulocyte

enucleated reticulocyte
type: Class
subclass of: reticulocyte

mammary stem cell
type: Class
subclass of: stem cell
definition: 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. [ PMID:16397499 GOC:tfm PMID:17851544 GOC:hjd PMID:15987436 ]

oligodendrocyte precursor cell
type: Class
subclass of: oligodendrocyte
definition: The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons.
GOC definition citation: GOC:tfm
PMID definition citation: PMID:2014242
has_obo_namespace: cell

Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell
type: Class
subclass of: CD11b-positive dendritic cell

CD8_alpha-negative plasmactyoid dendritic cell
type: Class
subclass of: CD11c-low plasmacytoid dendritic cell

CD8_alpha-positive plasmactyoid dendritic cell
type: Class
subclass of: CD11c-low plasmacytoid dendritic cell

epidermal Langerhans cell
type: Class
subclass of: Langerhans cell
SNOMEDCT definition citation: SNOMEDCT:127854005

langerin-positive dermal dendritic cell
type: Class
subclass of: dermal dendritic cell

langerin-negative dermal dendritic cell
type: Class
subclass of: dermal dendritic cell

CD8alpha-negative thymic conventional dendritic cell
type: Class
subclass of: thymic conventional dendritic cell

CD103-positive dendritic cell
type: Class
subclass of: conventional dendritic cell

adipose dendritic cell
type: Class
subclass of: conventional dendritic cell

CD11b-positive dendritic cell
type: Class
subclass of: conventional dendritic cell

small intestine serosal dendritic cell
type: Class
subclass of: CD11b-positive dendritic cell

Gr1-high myeloid suppressor cell
type: Class
subclass of: myeloid suppressor cell

Gr1-low myeloid suppressor cell
type: Class
subclass of: myeloid suppressor cell

MHC-II-negative classical monocyte
type: Class
subclass of: Gr1-high classical monocyte

MHC-II-positive classical monocyte
type: Class
subclass of: Gr1-high classical monocyte

MHC-II-negative non-classical monocyte
type: Class
subclass of: Gr1-low non-classical monocyte

MHC-II-low non-classical monocyte
type: Class
subclass of: Gr1-low non-classical monocyte

MHC-II-high non-classical monocyte
type: Class
subclass of: Gr1-low non-classical monocyte

lymphoid MHC-II-negative classical monocyte
type: Class
subclass of: MHC-II-negative classical monocyte

lymphoid MHC-II-negative non-classical monocyte
type: Class
subclass of: MHC-II-negative non-classical monocyte

bone marrow macrophage
type: Class
subclass of: tissue-resident macrophage

adipose macrophage
type: Class
subclass of: tissue-resident macrophage

F4/80-negative adipose macrophage
type: Class
subclass of: adipose macrophage

F4/80-positive adipose macrophage
type: Class
subclass of: adipose macrophage

langerin-positive lymph node dendritic cell
type: Class
subclass of: conventional dendritic cell

langerin-negative, CD103-negative lymph node dendritic cell
type: Class
subclass of: conventional dendritic cell

CD103-positive, langerin-positive lymph node dendritic cell
type: Class
subclass of: langerin-positive lymph node dendritic cell

CD103-negative, langerin-positive lymph node dendritic cell
type: Class
subclass of: langerin-positive lymph node dendritic cell

CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell
type: Class
subclass of: langerin-negative, CD103-negative lymph node dendritic cell

CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell
type: Class
subclass of: langerin-negative, CD103-negative lymph node dendritic cell

CD14-positive dermal dendritic cell
type: Class
subclass of: dermal dendritic cell

CD1a-positive dermal dendritic cell
type: Class
subclass of: dermal dendritic cell

CD16-positive myeloid dendritic cell
type: Class
subclass of: myeloid dendritic cell

mesenchymal stem cell of the bone marrow
type: Class
subclass of: mesenchymal stem cell
definition: A mesenchymal stem cell that is part of the bone marrow. [ GOC:tfm ]

fibroblast of dermis
type: Class
subclass of: fibroblast
definition: fibroblast that is part of dermis
definition editor: Sirarat Sarntivijai
created by: tmeehan
creation date: 2011-02-28T05:05:33Z
has_obo_namespace: cell

lung fibroblast
type: Class
subclass of: fibroblast
definition: A fibroblast that is part of lung

intestinal epithelial cell
type: Class
subclass of: cell type
definition: An epithelial cell of the intestine. [ GOC:tfm ]
created by: tmeehan
has_obo_namespace: cell

bronchial smooth muscle cell
type: Class
subclass of: smooth muscle cell
created by: tmeehan
creation date: 2011-03-06T05:46:39Z
has_obo_namespace: cell

uterine smooth muscle cell
type: Class
subclass of: cell type
definition: A smooth muscle cell of the uterus.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-06T05:53:28Z
has_obo_namespace: cell

hippocampal neuron
type: Class
subclass of: neuron
definition: A neuron of the hippocampus.

adipocyte of breast
type: Class
subclass of: fat cell
definition: A fat cell that is part of the breast.

endothelial cell of umbilical vein
type: Class
subclass of: blood vessel endothelial cell
definition: An endothelial cell of the umbilical vein. [ GOC:tfm ]

adult endothelial progenitor cell
type: Class
subclass of: mesenchymal stem cell
definition: 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. [ GOC:tfm PMID:20807818 PMID:9020076 ]

repiratory basal cell
type: Class
subclass of: basal cell
subclass of: Restriction
  on property: part of
  some values from: respiratory epithelial cell
definition: A basal cell in the respiratory tract. [ PMID:20699479 GOC:tfm ]

pancreatic epsilon cell
type: Class
subclass of: secretory cell
subclass of: pancreatic cell
definition: Ghrelin secreting cells found in the found in the exocrine pancreas.
PMID definition citation: PMID:14970313
has_obo_namespace: cell

retinal cell
type: Class
subclass of: cell type
definition: Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
PMID definition citation: PMID:10702418

cholangiocyte
type: Class
subclass of: epithelial cell
definition: An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. [ PMID:18356246 PMID:16550043 GOC:tfm ]

kidney cell
type: Class
subclass of: cell type
imported from: cl.owl
KUPO definition citation: KUPO:0001010
has_obo_namespace: cell

endothelial cell of coronary artery
type: Class
subclass of: blood vessel endothelial cell
definition: Any endothelial cell of artery that is part of a coronary artery. [ GOC:TermGenie ]

calvarial osteoblast
type: Class
subclass of: osteoblast
definition: Any osteoblast that is part of a skull. [ GOC:TermGenie ]

splenocyte
type: Class
subclass of: leukocyte
definition: Any leukocyte that is part of a spleen. [ GOC:TermGenie ]
comment: Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology.

cancer
type: Class
subclass of: disease
definition: A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
alternative term: malignant neoplasm
alternative term: malignant tumor
alternative term: primary cancer
imported from: doid.owl

specimen barcode
type: Class
subclass of: specimen identifier
definition: A specimen barcode is a specimen identification number formatted as an optical machine-readable representation.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Barcode
imported from: flu.owl

geographic location
type: Class
subclass of: site
editor preferred label: geographic location
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: gaz.owl

reference genome identifier
type: Class
subclass of: sequence identifier
subclass of: reference genome datum
definition: Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community
definition editor: Damion Dooley
in subset: GENEPIO

de-identified data
type: Class
subclass of: data item
GENEPIO_0001763: help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users.
has curation status: IAO_0000428
definition: A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them.
editor note: Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature.
definition editor: Damion Dooley
IAO_0000600: Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/

sequence identifier
type: Class
subclass of: centrally registered identifier symbol

Canada postal code
type: Class
subclass of: Postal Code
GENEPIO 1919: /^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ])) ?(:<LDU>[0-9][ABCEGHJKLMNPRSTVWXYZ][0-9])$/i, $FSA $LDU
has curation status: IAO_0000428
definition: A Canadian postal code is a postal code that pertains to a geographic region of Canada.
editor note: Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account.

sequence feature location
type: Class
subclass of: generically dependent continuant
definition: The location of a sequence feature as defined by its start and end position on some reference coordinate system.
comment: 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.

genomic feature location
type: Class
subclass of: sequence feature location
definition: The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system
editor note: In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences.
editor note: In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus).
alternative term: genomic location
alternative term: genomic locus
has db xref: VMC:Location
comment: 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: IAO_0000122
definition: 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.
editor note: 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."
editor note: 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.
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

software
type: Class
subclass of: plan specification
editor preferred label: software
has curation status: IAO_0000120
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition source: GROUP: OBI

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
definition: 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.
editor note: 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.
editor note: 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.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
definition editor: PERSON: James A. Overton
definition editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary

numeral
type: Class
subclass of: symbol
editor preferred label: numeral
definition: A symbol that denotes a number.
definition editor: PERSON: Jonathan Rees

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition: A generically dependent continuant that is about some thing.
editor note: 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).
editor note: 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.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: ido.owl
imported from: omrse.owl

scalar measurement datum
type: Class
subclass of: measurement datum
example of usage: 10 feet. 3 ml.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

directive information entity
type: Class
subclass of: information content entity
has curation status: IAO_0000122
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 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.
editor note: 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.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: IAO_0000120
definition: 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.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

software interpreter
type: Class
subclass of: algorithm
editor preferred label: software interpreter
example of usage: R program, Perl interpreter, Java virtual machine
has curation status: IAO_0000120
definition: A software interpreter is a software application that executes some specified input software.
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000199
definition source: group:OBI

report
type: Class
subclass of: document
editor preferred label: report
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
has curation status: IAO_0000125
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Chris Stoeckert
definition source: GROUP: OBI
definition source: OBI_0000099
imported from: obi.owl

data set
type: Class
subclass of: data item
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

plan specification
type: Class
subclass of: directive information entity
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000122
definition: 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.
editor note: 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.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 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

measurement datum
type: Class
subclass of: data item
editor preferred label: measurement datum
example of usage: 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,}.
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: obi.owl
has db xref: http://www.ebi.ac.uk/efo/EFO_0001444

version number
type: Class
subclass of: symbol
editor preferred label: version number
has curation status: IAO_0000123
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
definition editor: GROUP: IAO

lot number
type: Class
subclass of: symbol
editor preferred label: lot number
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
alternative term: batch number

material information bearer
type: Class
subclass of: material entity
editor preferred label: material information bearer
example of usage: 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.
example of usage: a brain
example of usage: a hard drive
definition: A material entity in which a concretization of an information content entity inheres.
definition editor: GROUP: IAO

textual entity
type: Class
subclass of: language entity
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
definition editor: PERSON: Lawrence Hunter
alternative term: text

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
definition: A collection of information content entities intended to be understood together as a whole
definition editor: PERSON: Lawrence Hunter

document part
type: Class
subclass of: information content entity
editor preferred label: document part
example of usage: An abstract, introduction, method or results section.
definition: an information content entity that is part of a document
definition editor: PERSON: Lawrence Hunter

methods section
type: Class
subclass of: document part
editor preferred label: methods section
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: experimental
alternative term: experimental procedures
alternative term: experimental section
alternative term: methods

results section
type: Class
subclass of: document part
editor preferred label: results section
example of usage: The section labelled 'results' in a typical scientific journal article
definition: A part of a publication about an investigation that is about a study design execution
definition editor: PERSON: Lawrence Hunter
alternative term: results

time measurement datum
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
imported from: obi.owl
comment: Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards

documenting
type: Class
subclass of: planned process
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
definition: a planned process in which a document is created or added to by including the specified input in it.
editor note: 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
definition editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting

centrally registered identifier symbol
type: Class
subclass of: symbol
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls

software method
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software module
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software module is software composed of a collection of software methods.
definition editor: PERSON: Melanei Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software library
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software application
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software application is software that can be directly executed by some processing unit.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software script
type: Class
subclass of: software
has curation status: IAO_0000123
definition: A software script is software whose instructions can be executed using a software interpreter.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

case report section
type: Class
subclass of: document part
editor preferred label: case report section
example of usage: The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
definition: A part of a document about the medical history of a specific patient as it relates to the topic of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: case presentation
alternative term: case report

consent section
type: Class
subclass of: document part
editor preferred label: consent section
example of usage: The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
definition: A part of a document about the consent process that was used to enroll patients in a study.
definition editor: PERSON: Bill Baumgartner
alternative term: consent

ethical approval section
type: Class
subclass of: document part
editor preferred label: ethical approval section
example of usage: The section labelled 'ethical approval' in a typical scientific journal article.
definition: A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
definition editor: PERSON: Bill Baumgartner
alternative term: ethical approval

materials section
type: Class
subclass of: document part
editor preferred label: materials section
example of usage: The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
definition: A part of a document about the materials required to reproduce the content of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: materials

requirements section
type: Class
subclass of: document part
editor preferred label: requirements section
example of usage: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
definition: A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
definition editor: PERSON: Bill Baumgartner
alternative term: requirements

statistical analysis section
type: Class
subclass of: document part
editor preferred label: statistical analysis section
example of usage: The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
definition: A part of the document used to describe the statistical methodologies employed in the work presented in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: statistical analysis

identifier
type: Class
subclass of: specifically dependent continuant
definition: A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
definition editor: Mathias Brochhausen
label: proper name

personal name
type: Class
subclass of: identifier
definition: A personal name is a proper name identifying an individual person.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Personal_name
comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)

informed consent form
type: Class
subclass of: document
definition: A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject.
definition editor: AK, FM, YH, YL, MH, EE
definition source: NCIt C16468
imported from: ico.owl

completely filled informed consent form
type: Class
subclass of: informed consent form
definition: an informed consent form that has been filled with all required contents.
definition editor: YH
imported from: ico.owl

partially filled informed consent form
type: Class
subclass of: informed consent form
definition: an informed consent form that has been partically filled with required contents.
definition editor: YH
imported from: ico.owl

informed consented study period
type: Class
subclass of: one-dimensional temporal region
definition: a one-dimensional temporal region that is a period of an informed consented study
definition editor: YH

participation duration
type: Class
subclass of: one-dimensional temporal region
definition: a temporal interval that represent the time of someone (for example the study subject) participating the study or the research.
definition editor: YL, MH, AK, EE, YH

actual duration of study subject participation
type: Class
subclass of: participation duration
definition: Total length of time of subject's participation in a clinical study; from the time of enrollment to the completion of follow-up.
editor note: This duration is different with the 'planned duration of study subject participation'
definition editor: YL

storage duration of signed informed consent form
type: Class
subclass of: one-dimensional temporal region
definition: a termporal interval that represents a period of time during which a signed informed consent form is stored.
definition editor: YH, EE, YL, AK, MH
definition source: WEB: http://answers.hhs.gov/ohrp/questions/7223

planned duration of study subject participation
type: Class
subclass of: participation duration
definition: a participation time that is the total length of time of subject's participation in a research study; from the time of enrollment to the completion of follow-up.
editor note: The term definition is adapted from NCIt definition of "Planned Duration of Study Subject Participation" (C70707) with modification. Compared to the NCIt definition, the ICO definition specifies research research study instead of a clinical study.
editor note: This duration is different with the 'planned duration of study subject participation'
definition editor: YL

eligibility of candidate participation
type: Class
subclass of: realizable entity
definition: A realizable entity that represents the eligibility of a candidate according to a study protocol.
definition editor: Frank Manion, Oliver He
imported from: ico.owl

immunosuppressive disposition
type: Class
subclass of: disposition
definition: A disposition whose realization negatively regulates an immune response.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
imported from: ido.owl

Euteleostomi
type: Class
subclass of: Vertebrata <Metazoa>
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred label: Bilateria
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: mammals
imported from: ncbitaxon.owl

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
editor preferred label: Vertebrata <Metazoa>
alternative term: Vertebrata
alternative term: vertebrates
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred label: Homo sapiens
alternative term: human
alternative term: human being
alternative term: man
imported from: ncbitaxon.owl

Postal Code
type: Class
subclass of: centrally registered identifier symbol
subclass of: personally identifiable information
definition: Any system designed to expedite the sorting and delivery of mail by assigning a series of alphanumeric codes to each delivery area. Also used to refer to any individual delivery area code.
imported from: ncit.owl

Street Address
type: Class
subclass of: address
definition: The street name and building number where a person or organization can be found.
imported from: ncit.owl

Zip Code
type: Class
subclass of: Postal Code
GENEPIO 1919: /^(:<zip>\d{5}(-\d{4})?)/, $zip
definition: A system designed to expedite the sorting and delivery of mail by assigning a series of numbers to each delivery area in the United States. Also used to refer to any individual delivery area code.
imported from: ncit.owl

Smoking History
type: Class
subclass of: history
definition: A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others.
alternative term: Smoking History
imported from: ncit.owl

Telephone Number
type: Class
subclass of: centrally registered identifier symbol
subclass of: personally identifiable information
definition: A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network.
imported from: ncit.owl

E-mail Address
type: Class
subclass of: centrally registered identifier symbol
subclass of: personally identifiable information
definition: A text string identifier for a location to which e-mail can be delivered.
editor note: Damion Dooley's note: It can also be used as an authorization token in some identification processes.
imported from: ncit.owl

Alcohol Use History
type: Class
subclass of: history
definition: A description of an individual's current and past experience with alcoholic beverage consumption.
alternative term: Alcohol Use History
imported from: ncit.owl

SIFT score impact
type: Class
subclass of: data item
definition: Data item which represents a normalized probability of observing the new amino acid at that position and ranges from 0 to 1.

DNA processed specimen
type: Class
subclass of: processed specimen
definition: A processed specimen which is the output of preparing a DNA sample for further analysis.
definition editor: Dalia Alghamdi

PS1 criteria
type: Class
subclass of: ACMG strong variants classification
definition: Same amino acid change as a previously established pathogenic variant regardless of nucleotide change

PS2 criteria
type: Class
subclass of: ACMG strong variants classification
definition: De novo (both maternity and paternity confirmed) in a patient with the disease and no family history

PS4 criteria
type: Class
subclass of: ACMG strong variants classification
definition: The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls

PM1 criteria
type: Class
subclass of: ACMG moderate classification criteria
definition: Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation

PM2 criteria
type: Class
subclass of: ACMG moderate classification criteria
definition: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or ExAC

PM6 criteria
type: Class
subclass of: ACMG moderate classification criteria
definition: Assumed de novo, but without confirmation of paternity and maternity

PM3 criteria
type: Class
subclass of: ACMG moderate classification criteria
definition: For recessive disorders, detected in trans with a pathogenic variant

PM4 criteria
type: Class
subclass of: ACMG moderate classification criteria
definition: Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants

ACMG strong variants classification
type: Class
subclass of: ACMG guidelines for classification of variants
definition: ACMG guidelines for classification of variants of strong variants classification

PS3 criteria
type: Class
subclass of: ACMG strong variants classification
definition: Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product

ACMG moderate classification criteria
type: Class
subclass of: ACMG guidelines for classification of variants
definition: ACMG guidelines for classification of variants of moderate classification

ACMG very strong classification criteria
type: Class
subclass of: ACMG guidelines for classification of variants
definition: ACMG guidelines for classification of variants of very strong classification

ACMG supporting classification criteria
type: Class
subclass of: ACMG guidelines for classification of variants
definition: ACMG guidelines for classification of variants of spporting classification

data file format
type: Class
subclass of: information content entity
term source: inferred from the College of American Pathologists (CAP) requirements
definition: Information content entity that is a standard way that information is encoded for storage in a computer file.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/File_format

VCF format
type: Class
subclass of: data file format
term source: inferred from https://en.wikipedia.org/wiki/Variant_Call_Format
definition: A file format which represent represent the format of a text file used in bioinformatics for storing gene sequence variations
definition editor: Dalia Alghamdi

SAM format
type: Class
subclass of: data file format
definition: A file format which represent a text-based format for storing biological sequences aligned to a reference sequence
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/SAM_(file_format)

FASTA format
type: Class
subclass of: data file format
definition: A file format which represent represent a text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes
definition editor: Dalia Alghamdi
definition source: https://zhanglab.ccmb.med.umich.edu/FASTA/

FASTQ format
type: Class
subclass of: data file format
definition: A file format which represent text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/FASTQ_format

unstained fixed tissue slide
type: Class
subclass of: fixed tissue slide specimen
definition: A fixed tissue slide specimen that is contain unstained tissue section(s)
definition editor: inferred from KFMC SOP

2bit format
type: Class
subclass of: data file format
definition: A file format which represent a binary file format designed for storing a genome consists of multiple chromosomal sequences
definition editor: Dalia Alghamdi
definition source: https://biojulia.net/BioSequences.jl/stable/io/twobit.html

bed graph format
type: Class
subclass of: data file format
definition: A file format which represent a data format allows display of continuous-valued data in track format
definition editor: Dalia Alghamdi
definition source: https://genome.ucsc.edu/goldenPath/help/bedgraph.html

bed format
type: Class
subclass of: data file format
definition: A file format which represent represent format provides a flexible way to define the data lines that are displayed in an annotation track
definition editor: Dalia Alghamdi
definition source: https://genome.ucsc.edu/FAQ/FAQformat.html

BAM format
type: Class
subclass of: data file format
definition: A file format which represent binary format for storing sequence data.
definition editor: Dalia Alghamdi
definition source: https://genome.sph.umich.edu/wiki/BAM

shipping and receiving of samples SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for shipping and receiving of sample

reference genome version number
type: Class
subclass of: version number
subclass of: reference genome datum
definition: A reference genome datum which represent reference genome edition

reference genome URI
type: Class
subclass of: reference genome datum
subclass of: URL
term source: inferred from College of American Pathologists (CAP) requirments
definition: A reference genome datum which represent a location where reference genome can be accessed online
definition editor: Dalia Alghamdi

information about local data storage
type: Class
subclass of: information about data storage location
definition: Information about data storage location information content entity which represent any physical hardware such as external hard drives, flash drives, and CD
definition citation: https://www.kelsercorp.com/blog/pros-and-cons-of-local-and-cloud-data-storage

information about cloud storage bucket
type: Class
subclass of: information about data storage location
definition: Information about data storage location information content entity which represent information about the basic containers that hold your data in cloud storage
definition editor: Dalia Alghamdi
definition source: https://cloud.google.com/storage/docs/key-terms

name of specimen donor
type: Class
subclass of: personal name
definition: A personal name that designates the human being donated specimen

material transfer agreement
type: Class
subclass of: document
definition: A document which represent a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Material_transfer_agreement

data transfer agreement
type: Class
subclass of: document
term source: inferred from ISBER
definition: A document information content entity established between organisations that governs the transfer of one or more data sets from the owner/provider to a third party
definition editor: Dalia Alghamdi
definition source: https://www.medschl.cam.ac.uk/research/information-governance/information-governance-data-transfer-agreements/

specimen collection kit
type: Class
subclass of: assay kit
definition: An assay kit processed material comprises a sterile device for collecting a sample, a collection and dispersing device for depositing and holding the sample, a device for transferring the sample, and a container for storing the sample to be tested. There may also be a labeling system for identifying the sample and for diluting the sample
definition editor: Dalia Alghamdi

insulated shipping container
type: Class
subclass of: container
definition: A container which used to ship temperature sensitive products such as foods, pharmaceuticals, organs, blood, biologic materials, and chemicals. They are used as part of a cold chain to help maintain product freshness and efficacy.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Insulated_shipping_container

standard operating procedure actual use duration
type: Class
subclass of: one-dimensional temporal region
definition: A one-dimensional temporal region that is a period of an duration of standard operation procedure
definition editor: Dalia Alghamdi
description: When a procedure is discontinued or replaced, a paper or electronic copy is maintained for at least 2 years, recording initial date of use, and retirement date.

adapter ligation process
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: processed material
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: executes
  some values from: adapter ligation protocol
term source: inferred from the College of American Pathologists (CAP) requirements
definition: A material processing process which attaches synthetic oligonucleotides of a known sequence to one or both ends of cDNA fragments
definition editor: Dalia Alhgamdi
definition source: https://www.ebi.ac.uk/training/online/glossary/adapter-ligation

specimen derivative
type: Class
subclass of: processed material
subclass of: specimen
definition: A specimen which is a recognizable part or product taken from specimen
definition editor: Dalia Alghamdi

bioinformatics analysis
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: executes
  some values from: plan specification
definition: A data transformation which involeves curation, processing and analysis of complex biological data
definition editor: Dalia Alghamdi

gene expression level analysis
type: Class
subclass of: bioinformatics analysis
definition: A gene expression level analysis is a bioinformatics analysis that compares the RNA expression levels of multiple genes (profiling) and/or multiple samples (screening)
definition editor: Dalia Alghamdi
definition source: inferred from https://www.thermofisher.com/ca/en/home/life-science/gene-expression-analysis-genotyping/gene-expression-profiling.html

variant calling assay
type: Class
subclass of: bioinformatics analysis
definition: Variant calling is the process by which we identify variants from sequence data.
definition editor: Dalia Alghamdi
definition source: https://www.ebi.ac.uk/training/online/course/human-genetic.../variant.../what-variant

variant classification assay
type: Class
subclass of: genetic variantion analysis
subclass of: Restriction
  on property: has_specified_output
  some values from: clinical variant interpretation
subclass of: Restriction
  on property: executes
  some values from: interpretation of clinical variant protocol
definition: A genetic variation analysis which assign a formal classification to a detected genetic variant.
has synonym: variant interpretation

sequence clustring
type: Class
subclass of: sequence analysis data transformation
definition: A bioinformatics analysis which attempt to group biological sequences that are somehow related
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Sequence_clustering

axt file format
type: Class
subclass of: data file format
definition: A file format which represent alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent at UCSC
definition editor: Dalia Alghamdi
definition source: http://genome.ucsc.edu/goldenPath/help/axt.html

paraffin embedding and Fixation quality check report
type: Class
subclass of: quality assesment report
definition: required quality check list for the procedure of paraffin embedding and/or fixation.
definition editor: Dalia Alghamdi

remnant specimen
type: Class
subclass of: specimen
definition: a specimen which represent remaining portion of a specimen obtained for clinical purposes that is no longer needed for its original purpose and that would otherwise be discarded
definition editor: Dalia Alghamdi
definition source: CAP accreditation program, Biorepository checklist

specimen with potentially infectious materials
type: Class
subclass of: specimen
definition: A specimen that derives from an organism and might contain infectious materials.

training manual
type: Class
subclass of: document
definition: A training manual is a book or booklet of instructions, designed to improve the quality of a performed task.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Training_manual

personally identifiable information
type: Class
subclass of: data item
definition: A data item infromation content entity that represent any data that could potentially identify a specific individual. Any information that can be used to distinguish one person from another and can be used for de-anonymizing anonymous data can be considered PII.
definition editor: Dalia Alghamdi
definition source: https://searchfinancialsecurity.techtarget.com/definition/personally-identifiable-information

protein sequencing
type: Class
subclass of: sequencing assay
definition: A sequencing assay which involves the determination of the arrangement of the amino acid sequence of a protein.
definition editor: Dalia Alghamdi

biological database
type: Class
subclass of: database
term source: inferred from College of American Pathologists (CAP) requirments
definition: A database which represent libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Biological_database

alignment
type: Class
subclass of: bioinformatics analysis
definition: A bioinformatics analysis data transformation which two or more things are positioned in a straight line or parallel to each other
definition source: https://dictionary.cambridge.org/dictionary/english/alignment

database index
type: Class
subclass of: data transformation
definition: A bioinformatics analysis that produces data structure that improves the speed of data retrieval operations on a database table at the cost of additional writes and storage space to maintain the index data structure
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Database_index

genome indexing
type: Class
subclass of: bioinformatics analysis
definition: A bioinformatics analysis which referes to the process of compressing to reduze the size of genome file
definition editor: Dalia Alghamdi

Allele-specific expression data
type: Class
subclass of: measured expression level
definition: A measured expression level which refers to the characteristic of preferentially expressing a parental allele in the hybrid due to variations in regulatory sequences from the parental genomes.
definition editor: Dalia Alghamdi
definition source: https://www.pnas.org/content/116/12/5653
has synonym: ASE_SNP_CNV_Expression, Allele-Specific Expression

microarray CNV genotypes data
type: Class
subclass of: measured expression level
definition: A measured expression level measurement datum which represent copy number variation (CNV) obtained by microarray
definition editor: Dalia Alghamdi

microRNA expression data
type: Class
subclass of: measured expression level
definition: A measured expression level measurement datum which refers to represent small non-coding RNAs of 19-24 nucleotides in length that downregulate gene expression during various crucial cell processes such as apoptosis, differentiation and development.
definition editor: Dalia Alghamdi

gene expression profile data
type: Class
subclass of: measured expression level
definition: A measured expression level which refers to activity (the expression) of thousands of genes at once, to create a global picture of cellular function.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Gene_expression_profiling

whole exome sequence data
type: Class
subclass of: DNA sequence data
term source: inferred from the College of American Pathologists (CAP) requirements.
definition: A mesurement datum that represent all of the protein-coding regions of genes in a genome (known as the exome)
definition editor: Dalia Alghamdi

single molecule real time sequencing data
type: Class
subclass of: DNA sequence data
definition: A single molecule real time sequencing data is DNA sequence data generated from parallelized single molecule DNA sequencing method.
definition editor: Dalia Alghamdi
definition source: inferred from https://en.wikipedia.org/wiki/Single-molecule_real-time_sequencing

whole genome sequence data
type: Class
subclass of: DNA sequence data
term source: inferred from the College of American Pathologists (CAP) requirements
definition: A DNA sequence data which represent the the complete DNA sequence of an organism's genome at a single time
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Whole_genome_sequencing

metagenomics sequence data
type: Class
subclass of: DNA sequence data
definition: DNA sequence data which represent genomic DNA obtained from environmental samples
definition editor: Dalia Alghamdi

whole transcriptome sequence data
type: Class
subclass of: RNA sequence data
definition: RNA sequence data which represent the complete complement of transcripts in a sample, at a given time
definition editor: Dalia Alghamdi
definition source: inferred from https://sequencing.roche.com/en/

16s RNA sequence data
type: Class
subclass of: RNA sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of RNA molecule
term source: Inffered from clinical lab standard operating procedure
example of usage: 16s RNA sequence data is used to identify bacteria at the species level in order to differentiate between closely related species.
definition: RNA sequence data which is about the 16s gene of one or more organisms.
definition editor: Dalia Alghamdi
definition citation: https://www.sciencedirect.com/topics/neuroscience/16s-ribosomal-rna

variant prioritisation
type: Class
subclass of: genetic variantion analysis
definition: A genetic variation analysis which involves identifying biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.
definition editor: Dalia Alghamdi
definition source: Bioinformatics operations, data types, formats, identifiers and topics ontology (operation_3226)

genetic variants filtration assay
type: Class
subclass of: genetic variantion analysis
definition: An assay which attempt to select highly confident variants and remove the ones that are falsely called
definition editor: Dalia Alghamdi
definition source: https://www.sevenbridges.com/smart-variant-filtering/

global sequence alignment
type: Class
subclass of: sequence alignment
definition: A sequence alignment which align every residue in every sequence
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Sequence_alignment

local sequence alignment
type: Class
subclass of: sequence alignment
definition: A sequence alignment which align dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Sequence_alignment#Global_and_local_alignments

multiple sequence alignment
type: Class
subclass of: sequence alignment
definition: A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Multiple_sequence_alignment
comment: replace with OBIws

pairwise sequence alignment
type: Class
subclass of: sequence alignment
definition: A sequence alignment bioinformatics analysis which identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid)
definition editor: Dalia Alghamdi
definition source: https://www.ebi.ac.uk/Tools/psa/

sequence similarity search
type: Class
subclass of: bioinformatics analysis
definition: A bioinformatics analysis which attempt to searching sequence databases by using alignment to a query sequence
definition editor: Dalia Alghamdi
definition source: https://www.ebi.ac.uk/Tools/sss/

command line flag
type: Class
subclass of: symbol
term source: inferred from College of American Pathologists (CAP) requirments
example of usage: appropriate command line flags for running bioinformatics pipline, for example, bwa - Burrows-Wheeler Alignment Tool options found here: http://bio-bwa.sourceforge.net/bwa.shtml
definition: A symbol that is used to specify options for command line programs.
has synonym: command line argument command line parameter

functional annotation
type: Class
subclass of: sequence annotation
definition: Functional annotation is a bioinformatics analysis consists of attaching biological information to genomic elements such as: biochemical function, biological function, involved regulation and interactions and expression
definition editor: Dalia Alghamdi

data validation
type: Class
subclass of: planned process
definition: A planned process which ensure data have undergone data cleansing to ensure they have data quality, that is, that they are both correct and useful.
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Data_validation

format validation
type: Class
subclass of: data validation
definition: A data validation process that checks that the data is in a specified format (template), e.g., dates have to be in the format DD/ MM/YYYY is correct
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Data_validation

sequence data quality validation
type: Class
subclass of: data validation
term source: inferred from College of American Pathologists (CAP) requirments
definition: A data validating whech validate sequencing quality scores and measure the probability that a base is called incorrectly.
definition editor: Dalia alghamdi

assay kit
type: Class
subclass of: processed material
term source: inffered from the College of American Pathologists (CAP) requirments
definition: A processed material which contain a set of articles or equipment needed for a specific purpose.
definition editor: Dalia Alghamdi

DNA library
type: Class
subclass of: processed material
definition: A process material which contains DNA fragments that represent the entire genome of an organism.
definition editor: Dalia Alghamdi
definition source: https://www.thermofisher.com/ca/en/home/life-science/cloning/cloning-applications/library-construction.html

DNA extraction assay kit
type: Class
subclass of: assay kit
term source: inffered from the College of American Pathologists (CAP) requirments
definition: An assay kit used for the technique of isolating DNA in a biological sample
definition editor: Dalia Alghamdi

reference genome datum
type: Class
subclass of: data item
definition: A data item which represent datum related to reference genome used as a standard for comparison in basic research and clinical settings
definition editor: Dalia Alghamdi

data file URL
type: Class
subclass of: data storage datum
subclass of: URL
term source: inferred from College of American Pathologists (CAP) requirments
definition: A URL at which the data file file is stored.

database
type: Class
subclass of: information content entity
definition: A database is an information content entity that describe a structured set of data held in a computer, especially one that is accessible in various ways.
definition editor: Dalia Alghamdi
definition source: https://en.oxforddictionaries.com/definition/database

library construction kit
type: Class
subclass of: assay kit
term source: inferred from College of American Pathologists (CAP) requirments
definition: An assay kit processed material that include a set of articles or equipment needed for library construction
definition editor: Dalia Alghamdi

quality assesment report
type: Class
subclass of: report
definition: A report that represent the process of data collection and analysis through which the degree of conformity to predetermined standards and criteria are exemplified
definition editor: Dalia Alghamdi
definition source: https://pubmed.ncbi.nlm.nih.gov/1604740/

sample derivative from specimen creation process
type: Class
subclass of: material processing
definition: A material processing that has as its input a specimen and as its output a sample derivative.
definition editor: Dalia Alghamdi

compressed file
type: Class
subclass of: data item
definition: A data item that represent sort of archive that contains one or more files that have been reduced in size through file compression process
definition source: inferred from https://support.microsoft.com/en-us/windows/zip-and-unzip-files-8d28fa72-f2f9-712f-67df-f80cf89fd4e5

genetic variantion analysis
type: Class
subclass of: bioinformatics analysis
definition: A bioinformatics analysis which analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
definition editor: Dalia Alghamdi
definition source: Bioinformatics operations, data types, formats, identifiers and topics EDAM

validation of known variant assay
type: Class
subclass of: assay
definition: An assay which represent the process of targeting detected known disease causing genetic variant for validation purposes

allele specific PCR
type: Class
subclass of: validation of known variant assay
term source: inferred from the College of American Pathologists (CAP) requirements
definition: A validation of known variant assay which permits the direct detection of any point mutation in human DNA by analyzing the PCR products in an ethidium bromide-stained agarose or polyacrylamide gel
definition source: https://www.sciencedirect.com/science/article/pii/S1046202305801240

copy number variation
type: Class
subclass of: data item
definition: A molecular quality that represent the number of copies of a particular gene varies from one individual to the next (germline mutation)
definition editor: Dalia Alghamdi
definition source: inferred from https://www.genome.gov/genetics-glossary/Copy-Number-Variation

copy number alteration
type: Class
subclass of: data item
definition: A molecular quality that describe changes in copy number that have arisen in somatic tissues.
definition editor: Dalia Alghamdi
definition source: Li, W., Lee, A. & Gregersen, P.K. Copy-number-variation and copy-number-alteration region detection by cumulative plots. BMC Bioinformatics 10, S67 (2009). https://doi.org/10.1186/1471-2105-10-S1-S67

secure file transfer process
type: Class
subclass of: planned process
definition: Secure file transfer is a planned process that represent data sharing via a secure, reliable delivery method. It is used to safeguard proprietary and personal data in transit and at rest. Most secure file sharing methods use standard protocols, including: Secure File Transfer Protocol (SFTP)
definition source: https://www.globalscape.com/solutions/secure-file-transfer

secure file transfer protocol
type: Class
subclass of: data transfer protocol
definition: A data transfer protocol is a network protocol that provides file access, file transfer, and file management over any reliable data stream
definition source: https://en.wikipedia.org/wiki/SSH_File_Transfer_Protocol

data transfer protocol
type: Class
subclass of: protocol
definition: A protocol plan specification which describes the process of data transfer between two entities

hypertext transfer protocol secure
type: Class
subclass of: data transfer protocol
definition: A data transfer protocol, and extension of the Hypertext Transfer Protocol (HTTP). It is used for secure communication over a computer network, and is widely used on the Internet
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/HTTPS

library preparation protocol
type: Class
subclass of: protocol
definition: A protocol plan specification which describes the process of generating a collection of DNA fragments for sequencing

result acceptance or rejection protocol
type: Class
subclass of: protocol
definition: Protocol for acceptence or rejcetion must be based on metrics and quality control parameters established during test optimization and utilized during validation

specimen acceptance or rejection protocol
type: Class
subclass of: protocol
definition: A protocol which describe the criteria for acceptance or rejection of a specimen

sequencing quality scores
type: Class
subclass of: symbol
definition: Sequencing quality scores measure the probability that a base is called incorrectly.
comment: to review

HUGO gene nomenclature committee gene name
type: Class
subclass of: biological database
term source: inferred from the College of American Pathologists (CAP) requirements
definition: A biological database that contains genes nomenclature created by the HUGO Gene Nomenclature Committee (HGNC) that sets the standards for human gene nomenclature.
definition editor: Dalia Alghamdi

aliquot
type: Class
subclass of: processed specimen
definition: A specimen that is divided into separate parts which are typically stored in separate containers as individual samples

specimen tracking protocol
type: Class
subclass of: protocol
term source: inferred from ISBER
definition: A protocol that ensure that biospecimens can be tracked accurately from the collection site through biospecimen arrival and subsequent

storage unit identifier
type: Class
subclass of: identifier
definition: Each freezer, refrigerator, room temperature stor- age cabinet, or other unit appropriate to the collec- tions should have a unique identifier.

Availability of other specimen from the same donor
type: Class
subclass of: data item
definition: A data item which represent the availability of other specimen from the same donor

specimen shipment identifier
type: Class
subclass of: identifier
term source: inferred from ISBER
definition: An identifier which denotes number assigned by a shipper of specimen.
definition editor: Dalia Alghamdi

standard operating procedure version number
type: Class
subclass of: version number
definition: A version number denotes standard operating procedure
definition editor: Dalia Alghamdi
definition editor: inferred from College of American Pathologists (CAP) requirments

standard operating procedure title
type: Class
subclass of: name
definition: A unique SOP name which captures the essence of the practice described.

specimen shipping temperature
type: Class
subclass of: temperature
definition: A temperature which represent specimen temperature during shipment.

refrigerated specimen temperature
type: Class
subclass of: specimen shipping temperature
subclass of: temperature
definition: A specimen shipping tempruture which represent a Refrigerated temperature (2 to 8°C) - wet ice or gel packs (conditioned at –15°C, designed for refrigerated temperatures, or phase change material rated for refrigerated transport).
definition editor: Dalia Alghamdi

specimen destruction assay
type: Class
subclass of: planned process
term source: inferred from ISBER
definition: A planned process with the objective to destroy an entire collection or specific specimen.

specimen culling
type: Class
subclass of: planned process
term source: inferred from ISBER
definition: A specimen culling is the process of reviewing and eliminating specimens in a collection or an entire collection either by destruction or transfer to a new custodian

clinical variant interpretation
type: Class
subclass of: data item
definition: A data item representing a variant’s significance in relation to a disease or phenotype.

pathogenic variant
type: Class
subclass of: clinical variant interpretation
term source: inferred from College of American Pathologists (CAP) requirments
definition: A clinical variant interpretation that represents a sequence variant that is previously reported and is a recognized cause of the disorder.
has synonym: disease causing mutation predisposing variant sasceptibility gene susceptibility gene mutation

likely pathogenic variant
type: Class
equivalent class: Class
  union of: Class
    intersection of: Restriction
      on property: derives from
      some values from: ACMG strong variants classification
    intersection of: Restriction
      on property: derives from
      min qualified cardinality: 1
      on class: ACMG very strong classification criteria
  union of: Class
    intersection of: Restriction
      on property: derives from
      some values from: ACMG strong variants classification
    intersection of: Restriction
      on property: derives from
      min qualified cardinality: 2
      on class: ACMG supporting classification criteria
  union of: Class
    intersection of: Restriction
      on property: derives from
      min qualified cardinality: 1
      on class: ACMG moderate classification criteria
    intersection of: Restriction
      on property: derives from
      min qualified cardinality: 4
      on class: ACMG supporting classification criteria
  union of: Class
    intersection of: Restriction
      on property: derives from
      min qualified cardinality: 2
      on class: ACMG moderate classification criteria
    intersection of: Restriction
      on property: derives from
      min qualified cardinality: 2
      on class: ACMG supporting classification criteria
  union of: Restriction
    on property: derives from
    min qualified cardinality: 3
    on class: ACMG moderate classification criteria
  union of: Restriction
    on property: derives from
    qualified cardinality: 1
    on class: ACMG very strong classification criteria
subclass of: clinical variant interpretation
term source: inferred from College of American Pathologists (CAP) requirments
definition: A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which is expected to cause the disorder.

variant of unknown significance
type: Class
subclass of: clinical variant interpretation
term source: inferred from College of American Pathologists (CAP) requirments
definition: A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which may or may not be causative of the disorder.
has synonym: VUS variant of uncertain significance

likely benign variant
type: Class
subclass of: clinical variant interpretation
term source: inferred from College of American Pathologists (CAP) requirments
definition: A clinical variant interpretation that represents a sequence variant that is previously unreported and is probably not causative of disease

benign variant
type: Class
subclass of: clinical variant interpretation
term source: inferred from College of American Pathologists (CAP) requirements
definition: A clinical variant interpretation that represents a sequence variant previously classified or reported as a recognized neutral variant

expression quantitative trait loci
type: Class
subclass of: genomic feature location
definition: A genomic feature location which represent the expression quantitative trait loci are genomic loci that explain all or a fraction of variation in expression levels of mRNAs
definition editor: Dalia Alghamdi
definition source: https://en.wikipedia.org/wiki/Expression_quantitative_trait_loci

messenger RNA sequence data
type: Class
subclass of: RNA sequence data
definition: RNA sequence data that represent the sequence of single-stranded RNA molecule that is complementary to one of the DNA strands of a gene. The mRNA is an RNA version of the gene that leaves the cell nucleus and moves to the cytoplasm where proteins are made.
definition source: https://www.genome.gov/genetics-glossary/messenger-rna

measurement datum availability statement
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: measurement datum
term source: inferred from use case discussion
definition: A data item which indicates availability of specimen associated data
definition editor: Dalia Alghamdi

target region enrichment assay
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: target enrichment kit
subclass of: Restriction
  on property: has_specified_input
  some values from: DNA extract
subclass of: Restriction
  on property: has_specified_output
  some values from: processed specimen
subclass of: Restriction
  on property: has performer
  some values from: PCR instrument
subclass of: Restriction
  on property: executes
  some values from: target enrichment protocol
definition: A material processing which capture specific regions of interest after library preparation for next generation sequencing.
definition citation: https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/target-enrichment.html#:~:text=Target%20enrichment%20is%20a%20cost,reduced%20cost%20and%20simplified%20analysis.

raw sequence file editing
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: measurement datum
definition: A bioinformatics analysis which involves any edit or change to a molecular sequence file.
definition editor: Dalia Alghamdi

omics data generation assay
type: Class
subclass of: planned process
subclass of: sequencing assay
subclass of: Restriction
  on property: has_specified_input
  some values from: assay kit
subclass of: Restriction
  on property: has_specified_input
  some values from: processed specimen
subclass of: Restriction
  on property: has_specified_input
  some values from: reagent
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: has performer
  some values from: device
definition: An assay which generate OMICS data through a wet bench process such as sequencing techniques.
definition editor: Dalia Alghamdi

interpretation of clinical variant protocol
type: Class
subclass of: protocol
definition: A protocol that describe the process of assigning a formal classification to the detected variant
definition editor: Dalia Alghamdi

ACMG guidelines for classification of variants
type: Class
subclass of: interpretation of clinical variant protocol
term source: inffered from College of American Pathologists (CAP) requirment
definition: A protocol which describes the guidance for the interpretation of sequence variants suggested by The American College of Medical Genetics and Genomics (ACMG).
definition editor: Dalia Alghamdi
definition citation: https://pubmed.ncbi.nlm.nih.gov/25741868/

Burrows-Wheeler Aligner algorithm
type: Class
subclass of: algorithm
term source: inffered from whole exome sequencing clinical report
definition: An algorithm which perform mapping of low-divergent sequences against a large reference genome, such as the human genome.
definition editor: Dalia Alghamdi
definition source: http://bio-bwa.sourceforge.net/#:~:text=It%20consists%20of%20three%20algorithms,ranged%20from%2070bp%20to%201Mbp.&text=BWA%2DMEM%20also%20has%20better,for%2070%2D100bp%20Illumina%20reads.

adapter ligation protocol
type: Class
subclass of: protocol
subclass of: Restriction
  on property:
    inverse of: executes
  some values from: adapter ligation process
term source: inferred from the College of American Pathologists (CAP) requirements
has curation status: http://purl.obolibrary.org/obo/IAO_0000428
definition: A protocol which describes the process of attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments as a prepration for sequencing
editor note: rev
definition editor: Dalia Alghamdi

validation of known variant protocol
type: Class
subclass of: protocol
term source: inferred from College of American Pathologists (CAP) requirments
definition: A protocol which describe the process of validation of known variant
definition editor: Dalia Alghamdi
definition source: inferred from Rodenburg RJ. The functional genomics laboratory: functional validation of genetic variants. J Inherit Metab Dis. 2018;41(3):297-307. doi:10.1007/s10545-018-0146-7

allele specific PCR protocol
type: Class
subclass of: protocol
term source: inferred from the College of American Pathologists (CAP) requirements
definition: A protocol which describes the process of Allele-specific polymerase chain reaction (PCR)
definition editor: Dalia Alghamdi

data anonymization protocol
type: Class
subclass of: protocol
term source: inferred from ISBER
definition: A protocol plan specification which describes the process of reducing the likelihood that the data can identify an individual.
definition editor: Dalia Alghamdi

BWA assembly process
type: Class
subclass of: bioinformatics analysis
subclass of: Restriction
  on property: has_specified_input
  some values from: command line flag
definition: Bioinformatics analysis which performs gapped alignment for single-end reads, supports paired-end mapping, generates mapping quality, and gives multiple hits if required
definition source: inferred from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/

bioinformatics analysis software
type: Class
subclass of: software
definition: A software designed to extract meaningful information from the mass of molecular biology data

data storage datum
type: Class
subclass of: data item
term source: inferred from College of American Pathologists (CAP) requirments
definition: A data item that represent information on data storage.
definition editor: Dalia Alghamdi

ligation objective
type: Class
subclass of: material combination objective
definition: An objective specification to determine attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments
definition editor: Dalia Alghamdi
definition editor: inferred from the College of American Pathologists (CAP) requirements
definition source: inferred from https://www.cytivalifesciences.com/en/us/solutions/genomics/knowledge-center/glossary/adapter-ligation

target enrichment protocol
type: Class
subclass of: protocol
term source: inferred from the College of American Pathologists (CAP) requirements
definition: A protocol which describes the workflow to capture specific regions of interest after library preparation for NGS and has many advantages over whole genome sequencing (WGS).
definition editor: Dalia Alghamdi

target sequence information
type: Class
subclass of: plan specification
term source: inferred from the College of American Pathologists (CAP) requirements use case clinial report
definition: A data item that which represent information about subset of genes or specific regions of interest of the genome.
definition citation: inferred from https://www.bgi.com/us/sequencing-services/dna-sequencing/target-region-sequencing/

information about data storage location
type: Class
subclass of: information content entity
subclass of: data storage datum
definition: An information content entity that is about the location of data storage

in-bead tagmentation library prepration
type: Class
subclass of: library preparation
term source: inferred from use case
definition: A library preparation material processing which uses bead-linked transposomes for a more uniform tagmentation reaction compared to in-solution tagmentation reactions
definition editor: Dalia Alghamdi
definition source: https://www.illumina.com/techniques/sequencing/ngs-library-prep/tagmentation.html

name of data generation assay executor
type: Class
subclass of: personal name
definition: A personal name that designates the person who executed the sequencing run.
creator: Dalia Alghamdi

assay kit version
type: Class
subclass of: version number
definition: A version number of assay kit.

name of bioinformatics analysis executor
type: Class
subclass of: personal name
term source: inffered from whole exome sequencing clinical report
definition: A personal name that designates the person who executed the bioinformatics analysis.

output data file
type: Class
subclass of: data file
definition: A data file which contain the output of data transformation process
creator: Dalia Alghamdi

input data file
type: Class
subclass of: data file
definition: A data file which contain the input for data transformation process
creator: Dalia Alghamdi

information about software
type: Class
subclass of: information content entity
definition: Information content entity about bioinformatics software

bioinformatics software name
type: Class
subclass of: information about software
definition: Information about software includes software name

software version number
type: Class
subclass of: information about software
definition: Information about software includes information on software version number.

software parameter value
type: Class
subclass of: information about software
definition: Information about software includes information on software parameter value.

bioinformatics software parameter name
type: Class
subclass of: information about software
definition: Information about software includes information on software parameter name.

bioinformatics analysis execution date
type: Class
subclass of: time measurement datum
definition: A time measurement datum of the bioinformatics analysis execution date.

software description
type: Class
subclass of: information about software
definition: Information about software includes software description.

software Documentation URI
type: Class
subclass of: information about software
definition: Information about software includes software documentation URI

software run identifier
type: Class
subclass of: identifier
definition: An identifier which denotes the bioinformatics analysis ID.

data file description
type: Class
subclass of: description
definition: A description of the file that contain raw data generated by a measurement device.

assay execution note
type: Class
subclass of: document part
definition: A document part of relevant notes or instructions regarding data generation assay execution

detected gene mutation
type: Class
subclass of: conclusion based on data
definition: A conclusion based on data about a permanent change in the DNA sequence that makes up a gene

data file
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has format specification
  some values from: data file format
definition: Any data file as generated by some acquisition computer or console.
definition source: http://nmrML.org/nmrCV#NMR:1400267

amino acid substitution
type: Class
subclass of: data item
definition: A data item which represents the substitution of one or more amino acids.

data transfer agreement document act
type: Class
subclass of: document editing
definition: A planned process of making the decision of the data transfer.

probe ID
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is about
  some values from: oligonucleotide probe
definition: An Identifier of an oligonucleotide probe.

oligonucleotide probe
type: Class
subclass of: region
definition: A region of short stretches of single-stranded DNA or RNA used to detect the presence of complementary nucleic acid sequences (target sequences) by hybridization.

expression quantitative trait loci data
type: Class
subclass of: data item
definition: A data item that describe expression quantitative trait loci.

target enrichment kit
type: Class
subclass of: assay kit
definition: An assay kit used for the technique of target enrichment

bioinformatics pipeline
type: Class
subclass of: software pipeline
definition: A software pipeline that is composed of a wide array of software algorithms to process biological raw data.
definition editor: Dalia Alghamdi
definition source: https://www.sciencedirect.com/science/article/pii/S1525157817303732

user information
type: Class
subclass of: information content entity
definition: An information content entity about user authentication information.
comment: This term is used for to store users information registered in a federated service https://github.com/Dalalghamdi/NGBOSemanticWebApplication

medication material
type: Class
subclass of: material entity
definition: A material entity that is bearer of a medication role.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: Penn Group

specimen receiving
type: Class
subclass of: sample handling
definition: A planned process for receiving specimens such as into a laboratory.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

adding specimen into a container
type: Class
subclass of: adding a material entity into a target
definition: An adding a material entity into a target process where a collected specimen is added to a specimen container. (note, not used for other specimen process that produce new specimens)
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

blood spotting
type: Class
subclass of: adding specimen into a container
definition: An adding specimen into a container process that spots the blood from an organism on the blood spot card.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

buffy coat specimen
type: Class
subclass of: processed specimen
definition: A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Buffy_coat

blood specimen on blood spot card
type: Class
subclass of: blood specimen
subclass of: processed specimen
definition: A blood specimen that is located on a blood spot card.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group
comment: A specimen that located in a blood spot card via blood spotting process.

duration time of smoking regularly
type: Class
subclass of: duration time of smoking
definition: A duration time of smoking about how long a person has been smoking regularly. (better to have criteria of regularly mean, such as smoke everyday)
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

smoking start date
type: Class
subclass of: time measurement datum
definition: A time measurement datum which is the start date of a smoking behavior.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

duration time of smoking
type: Class
subclass of: time measurement datum
definition: A time measurement datum about how long a person has been smoking.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

smoking end date
type: Class
subclass of: time measurement datum
definition: A time measurement datum which is the end date of a smoking behavior.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

time in fixative measurement
type: Class
subclass of: time measurement datum
definition: A time measurement datum that states the duration during which a specimen was submerged in fixative.
editor note: more general than time in formalin
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

collection packet identifier
type: Class
subclass of: identifier
definition: An identifier that refers to a collection packet used in a specimen collection process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: Kit ID
definition source: OBIB
ontology term requester: NCI BBRB

standard operating procedure
type: Class
subclass of: document
subclass of: protocol
subclass of: Restriction
  on property: is about
  some values from: planned process
definition: A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: SOP
definition source: https://en.wikipedia.org/wiki/Standard_operating_procedure
ontology term requester: NCI BBRB

specimen transport SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the transportation of specimens.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

tissue procurement SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for collecting specimens from organism.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

case report form completion SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for properly and completely filling out a case report form.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: CRF completion protocol
definition source: OBIB
ontology term requester: NCI BBRB

specimen collected with specific collection packet
type: Class
subclass of: specimen from organism
example of usage: specimen collected with GTEx Pink Kit
definition: A specimen from organism that is collected with a collection packet that is designed to collect specimens of a particular type for a particular purpose.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: specimen collected with specific kit
definition source: OBIB
ontology term requester: NCI BBRB

time donor body refrigerated measurement
type: Class
subclass of: time measurement datum
definition: A time measurement datum that states the duration during which the specimen donor's body was refrigerated.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

in vivo intraoperative ischemic period
type: Class
subclass of: time measurement datum
definition: A time measurement datum of the period between organ resection and the time of first clamping perfomed in vivo.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

Duration of fasting by specimen donor prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum of the duration of fasting by the specimen donor prior to surgery.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

receipt and dissection of surgical specimen SOP
type: Class
subclass of: standard operating procedure
example of usage: BPV SOP governing receipt and dissection of surgical tissue in the Tissue Bank
definition: A standard operating procedure for the receipt and dissection of surgical tissue in a biobank.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of biobank person receiving specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who received a specimen in the biobank.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

parent specimen ID
type: Class
subclass of: specimen identifier
example of usage: Parent Tissue Specimen ID of required study tumor tissue received in Tissue Bank from the Pathology Gross Room
definition: A specimen ID denoting a specimen that is used to create a specimen family.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of dissector of parent specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the dissection of a surgical specimen to create a specimen family.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

buffered formalin condition
type: Class
subclass of: quality
definition: A quality that inheres in buffered formalin by virtue of its usage and processing.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

blood specimen collection and processing SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for collection and processing of blood specimens.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person performing blood draw
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the collection of a blood specimen.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person receiving blood specimen in laboratory
type: Class
subclass of: personal name
definition: A personal name that designates the person who received a blood specimen in the laboratory.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

vacutainer specimen barcode
type: Class
subclass of: specimen barcode
example of usage: DNA PAXgene tube Specimen Barcode ID
definition: A specimen barcode that is associated with a vacutainer.
editor note: need specimen barcode
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person storing specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who stored a specimen.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

conical centrifuge tube identifier
type: Class
subclass of: identifier
definition: An identifier that specifically identifies a particular conical centrifuge tube.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: Conical centrifuge Tube code
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

blood plasma specimen barcode
type: Class
subclass of: specimen barcode
definition: A specimen barcode that is associated with a blood plasma specimen.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

cryovial specimen barcode
type: Class
subclass of: specimen barcode
definition: A specimen barcode that is associated with a cryovial.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person processing blood plasma specimen aliquots
type: Class
subclass of: personal name
definition: A personal name that designates the person who processed a blood specimen to generate aliquots of blood plasma specimens.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person transferring blood plasma specimens to freezer
type: Class
subclass of: personal name
definition: A personal name that designates the person who transferred blood plasma specimens to freezer.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

cell pellet specimen barcode
type: Class
subclass of: specimen barcode
example of usage: Whole Cell Pellet Aliquot Specimen Barcode ID
definition: A specimen barcode that is associated with a cell pellet specimen.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person processing blood cell pellet specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed processing of the blood cell pellet specimen.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

specimen transporting organization
type: Class
subclass of: role
definition: A role borne by an organization that is the provider of a specimen that is transported to another organization.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: specimen shipping organization
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen receiving organization
type: Class
subclass of: role
definition: A role borne by an organization that is the recipient of a specimen that is transported from another organization.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person responsible for specimen transport
type: Class
subclass of: personal name
definition: A personal name that designates the person who is responsible for the transport of a specimen to another organization.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: name of person responsible for specimen shipment
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of IATA-trained person verifying specimen transport
type: Class
subclass of: personal name
definition: A personal name that designates the person who verified the specimen transport was according to best practice, international standards, and industry regulations as trained by the IATA.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: name of IATA-trained person verifying specimen shipment
definition source: http://www.iata.org/training/pages/index.aspx
ontology term requester: NCI BBRB

name of quality control inspector of specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed a quality control inspection of the specimen that is to be transported to another organization.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of data entry person for tissue recovery form
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the data entry process for filling in a tissue recovery case report form.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of team leader for filling out tissue recovery form
type: Class
subclass of: personal name
definition: A personal name that designates the person who is the leader of the team responsible for entering the tissue recovery form data.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue processing SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for fixation of a tissue to the state where it is completely infiltrated with a suitable histological wax and can be embedded ready for section cutting on the microtome for a formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.leicabiosystems.com/pathologyleaders/an-introduction-to-specimen-processing/
ontology term requester: NCI BBRB

adherence of alcohol stage duration to FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether duration of the alcohol stage followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE alcohol stage duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of the alcohol stage in a formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence of dehydration process duration to FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether duration of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE dehydration process duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of the dehydration process in the formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence of dehydration process temperature to FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether temperature of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence of stage and replicate numbers to FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether the number of stages and replicates followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence of duration in clearing agent to FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether the duration in clearing agent followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE clearing agent duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration in clearing agent in the formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence of temperature of clearing agent to FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether the temperature of clearing agent followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence to paraffin impregnation method in FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether the paraffin impregnation method followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence of paraffin temperature to FFPE tissue processing SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether the paraffin temperature followed that prescribed in the FFPE tissue processing SOP.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue paraffin embedding SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

total time FFPE freshly poured blocks were cooled
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the total time that freshly poured blocks were cooled in the formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue block handling, tracking, and storage SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the handling, tracking, and storing of a formalin-fixed paraffin-embedded (FFPE) tissue block.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence to FFPE tissue block storage SOP
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that indicates whether the FFPE tissue block storage SOP was followed.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of specimen slide preparation technician
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed a specimen slide preparation.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: Slide Prep Technician Name
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section preparation SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

microtome blade age
type: Class
subclass of: age
definition: An age that inheres in a microtome blade.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

fresh microtome blade
type: Class
subclass of: microtome blade age
definition: A microtome blade age that indicates that the microtome blade is as new as possible.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E staining and mounting SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the hematoxylin and eosin (H&E) staining and slide mounting of a formalin-fixed paraffin-embedded (FFPE) tissue section.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E staining in oven duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration in an oven for the hematoxylin and eosin staining of a formalin-fixed paraffin-embedded (FFPE) tissue section.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E deparaffinization
type: Class
subclass of: fixation
definition: A planned process involving the manual performance of the FFPE tissue section H&E deparaffinization protocol.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E staining
type: Class
subclass of: fixation
definition: A planned process involving the manual performance of the FFPE tissue section H&E staining protocol.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E clearing
type: Class
subclass of: fixation
definition: A planned process involving the manual performance of the FFPE tissue section H&E clearing protocol.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E cover slipping
type: Class
subclass of: fixation
definition: A planned process involving the manual performance of the FFPE tissue section H&E cover slip protocol.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

specimen randomization key ID
type: Class
subclass of: specimen barcode
definition: A specimen barcode associated with the specific chart (key) used to randomly assign specimens to one of several distinct experimental protocols.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

collection packet component ID
type: Class
subclass of: identifier
definition: An identifier that specifically identifies a particular component of a collection packet.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: kit component ID
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue cassette ID
type: Class
subclass of: specimen identifier
definition: A specimen ID that specifically identifies a particular tissue cassete used in a formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

placement of tissue cassette in FFPE fixative delay duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of the the planned delay of placing the tissue cassette in fixative in the formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

measurement of time between FFPE tissue processor cycle completion and embedding
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time between FFPE tissue processor cycle completion and embedding in a formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of dissector of normal adjacent tissue to tumor for FFPE
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the dissection of a normal tissue adjacent to a tumor for a formalin-fixed paraffin-embedded (FFPE) process.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen image ID
type: Class
subclass of: identifier
definition: An identifier that specifically identifies a particular specimen image.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of submitter of pathology case summary report.
type: Class
subclass of: personal name
definition: name of submitter of pathology case summary report.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: name of submitting pathologist
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of reviewer of pathology case summary report.
type: Class
subclass of: personal name
definition: A personal name that designates the person who served as the reviewer for quality assurance purposes of a pathology case summary report.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: name of submitting pathologist
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

confirmation of histologic type of FFPE H&E tumor slide
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that is an indicator of whether the local pathology review of a formalin-fixed paraffin-embedded (FFPE) hematoxylin and eosin (H&E)-stained tumor tissue slide confirmed the histological type.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of reviewing pathologist at organization conducting specimen collection
type: Class
subclass of: personal name
definition: A personal name that designates the person who served as the pathologist reviewing a specimen slide at an organization conducting specimen collection from organisms.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of data entry person for local pathology review form
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the data entry process for filling in a local pathology review form.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person in gross room receiving OR specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who received a specimen in a pathology gross room from an associated operating room (OR).
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen transport from OR to gross room SOP
type: Class
subclass of: specimen transport SOP
definition: A specimen transport SOP governing the transport of tissue from the operating room (OR) to the pathology gross room.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of performer of gross evaluation of resected tissue specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the gross evaluation of a resected tissue specimen.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

additional tumor specimen was obtained and processed with a particular FFPE fixation delay protocol
type: Class
subclass of: paraffin embedding and Fixation quality check report
definition: An information content entity that is an indicator of whether a tumor specimen was obtained and processed with a particular FFPE fixation delay protocol other than meeting the top priority for tissue procurement.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

identification number of a protocol at a particular site
type: Class
subclass of: centrally registered identifier symbol
definition: An centrally registered identifier symbol assigned by an Institutional Review Board (IRB) that identifies a particular protocol at a given site.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: protocol number at a site
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person screening specimen donors
type: Class
subclass of: personal name
definition: A personal name that designates who performed the screening of a potential specimen donor for a research study.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: specimen donor screener
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person obtaining authorization from legally authorized representative for post-mortem specimen donation
type: Class
subclass of: personal name
definition: A personal name of an individual with research obtainer role who approaches a person's legal representative and informs them of key facts about potential risks and benefits, and asks them for authorization for post-mortem specimen donation for research for the person they legally represent.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: Research authorization obtainer for post-mortem specimen donation
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

identifier for legally authorized representative
type: Class
subclass of: identifier
definition: An identifier that uniquely identifies a particular legally authorized representative in a research study.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: legal representative identifier
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

relationship between person signing research authorization and specimen donor
type: Class
subclass of: specifically dependent continuant
definition: A relationship that may be biological or legal, between the specimen donor and the legally authorized representative who signed the research authorization.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time since radiation therapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since radiation therapy prior to surgery.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time since chemotherapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since chemotherapy prior to surgery.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time since immunotherapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since immunotherapy prior to surgery.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time since hormonal therapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since hormonal therapy prior to surgery.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

lifelong non-drinker of alcohol
type: Class
subclass of: Alcohol Use History
definition: An Alcohol Use History in which there is no alcohol consumption.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current non-drinker of alcohol
type: Class
subclass of: Alcohol Use History
definition: An Alcohol Use History in which there was alcohol consumption in the past but is currently a non-drinker of alcohol.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

moderate alcohol consumption history
type: Class
subclass of: Alcohol Use History
definition: An Alcohol Use History in which alcohol consumption was equal to or less than 2 drinks per day for men and 1 drink or less per day for women.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

greater than moderate alcohol consumption history
type: Class
subclass of: Alcohol Use History
definition: An Alcohol Use History in which alcohol consumption was more than 2 drinks per day for men and more than 1 drink per day for women.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

duration of greater than moderate alcohol consumption prior to enrollment
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of greater than moderate alcohol consumption (more than 2 drinks per day for a man or more than 1 drink per day for a woman) prior to study enrollment.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

lifelong non-smoker history
type: Class
subclass of: Smoking History
example of usage: Less than 100 cigarettes smoked in lifetime
definition: A Smoking History in which there was no or an insignificant level of smoking.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current smoker history
type: Class
subclass of: Smoking History
definition: A Smoking History in which there is current smoking either on a daily or non-daily basis.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current reformed smoker for more than 15 years history
type: Class
subclass of: Smoking History
definition: A Smoking History in which there is no current smoking and has not been smoking for more than 15 years.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current reformed smoker for less than 15 years history
type: Class
subclass of: Smoking History
definition: A Smoking History in which there is no current smoking and has not been smoking for less than 15 years.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

duration of hormonal birth control use prior to enrollment
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of use of hormonally based birth control prior to enrollment in a study.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time since last usage of hormonal birth control
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally based birth control.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

duration of hormone replacement therapy prior to enrollment
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of hormone replacement therapy prior to enrollment in a study.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time since last usage of hormone replacement therapy
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally replacement therapy.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

clinical history of sepsis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of sepsis.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of pneumonia
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of pneumonia.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of open wounds
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of open wounds.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of high unexplained fever
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of a high unexplained fever .
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of positive blood cultures
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of positive blood cultures.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of abnormal white blood cell levels
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of abnormal white blood cell levels.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of fungal infections
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of fungal infections.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of ascites
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of the presence of ascites fluid.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of cellulitis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of cellulitis.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of blood transfusion in foreign country
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of receiving a blood transfusion while in another country.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of human tissue transplant
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of receiving a human tissue or organ transplant .
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of animal tissue xenotransplant
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of receiving an animal tissue or organ xenotransplant.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of smallpox vaccination
type: Class
subclass of: clinical history
definition: A clinic history in which there is a history of a recent of smallpox vaccination.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

a clinical history of contact with someone with smallpox
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of contact with someone who recently had smallpox.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of dialysis
type: Class
subclass of: clinical history
example of usage: The patient had a clinical history of dialysis treatment three times a week for longer than one month.
definition: A clinical history in which there is a history of significant regular dialysis treatment.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of cancer at death
type: Class
subclass of: clinical history
definition: A clinical history in which there is a current diagnosis of cancer at death.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of cancer within a time period before death
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of cancer diagnosis in the preceding five years.
definition: A clinical history in which there is a history of cancer diagnosis within a specified time frame.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of tuberculosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of tuberculosis .
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of meningitis at death
type: Class
subclass of: clinical history
definition: A clinical history in which there was active meningitis at death.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of encephalitis
type: Class
subclass of: clinical history
definition: A clinical history in which there was active encephalitis at death.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of long term steroid use
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of long term steroid use.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of osteomyelitis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of osteomyelitis.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained seizures
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of unexplained seizures.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained weakness and fatigue
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of unexplained weakness and fatigue described as flu-like symptoms.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of exposure to toxins
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of exposure to toxic substances that may have led to chronic conditions.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of exposure to rabies
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of an animal bite in the last 12 months, from an animal suspected to have rabies.
definition: A clinical history in which there is a history of an animal bite in recent past, from an animal suspected to have rabies.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of clotting disorders
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of clotting disorders, such as hemophilia, requiring treatment with human-derived clotting factors.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of growth hormone use
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of growth hormone use.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of inability to have Human Immunodeficiency Virus testing due to hemodilution
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of the donor not being able to be tested for Human Immunodeficiency Virus (HIV) because of hemodilution.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained weight loss
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of unexplained weight loss.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of night sweats
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of night sweats.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of blue or purple spots on skin or mucous membranes
type: Class
subclass of: clinical history
definition: A clinical history in which there is a of blue or purple spots on the skin or mucus membranes (typical of Kaposi's sarcoma).
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained lymphadenopathy
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of unexplained lymphadenopathy lasting more than one month.
definition: A clinical history in which there is a history of unexplained lymphadenopathy of a specific duration.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of a prolonged fever
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of fever of at least 38.6 Celsius for more than 10 days.
definition: A clinical history in which there is a history of fever of at least 38.6 Celsius for a specified duration.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of an unexplained cough or shortness of breath
type: Class
subclass of: clinical history
definition: A clinical history in which there is are active signs of unexplained persistent cough and/or shortness of breath.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of opportunistic infections
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of opportunistic infections.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of sexually transmitted disease
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of sexually transmitted diseases
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of drug abuse
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of drug abuse.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Severe Acute Respiratory Syndrome
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of a Severe Acute Respiratory Syndrome (SARS) diagnosis.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of exposure to Severe Acute Respiratory Syndrome
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of recent contact with someone who has Severe Acute Respiratory Syndrome (SARS).
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of West Nile Virus
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of West Nile Virus (WNV) infection.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of West Nile Virus exposure
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of contact with a human or animal who has West Nile Virus (WNV).
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of gonorrhea
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of current gonorrhea infection or treatment for gonorrhea in the last 12 months.
definition: A clinical history in which there is a history of active gonorrhea infection or treatment for gonorrhea in the recent past.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of syphilis
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of current syphilis infection or treatment for syphilis in the last 12 months.
definition: A clinical history in which there is a history of active syphilis infection or treatment for syphilis in the recent past.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Hepatitis B
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Hepatitis B infection.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Hepatitis C
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Hepatitis C infection.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Human Immunodeficiency Virus
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Human Immunodeficiency Virus (HIV).
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of lupus
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of systemic lupus
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of sarcoidosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of sarcoidosis.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of scleroderma
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of scleroderma.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Reye's Syndrome
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Reye's Syndrome.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of rheumatoid arthritis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of rheumatoid arthritis.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of idiopathic heart disease
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of idiopathic heart disease.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Alzheimer's disease
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Alzheimer's Disease.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of dementia of unknown cause
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of dementia with unknown cause that is not caused by a previous Cerebrovascular Accident (CVA) infection, head trauma or brain tumor).
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Multiple Sclerosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Multiple Sclerosis (MS).
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Amyotrophic Lateral Sclerosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Amyotrophic Lateral Sclerosis (ALS)
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

planned process
type: Class
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: '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.)
editor note: 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.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: 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)
imported from: obi.owl

biological feature identification objective
type: Class
subclass of: objective specification
editor preferred label: biological feature identification objective
has curation status: IAO_0000123
definition: Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
definition editor: Jennifer Fostel

material supplier role
type: Class
subclass of: service provider role
editor preferred label: material supplier role
example of usage: Jackson Labs is an organization which provide mice as experimental material
has curation status: IAO_0000120
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor note: Supplier role is a special kind of service, e.g. biobank
definition editor: PERSON:Jennifer Fostel
alternative term: material provider role
alternative term: supplier
imported from: obi.owl

chromatography column
type: Class
subclass of: material separation device
editor preferred label: chromatography column
definition: Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
definition editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Column_chromatography
curator note: open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178

processed material
type: Class
subclass of: material entity
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
definition: Is a material entity that is created or changed during material processing.
definition editor: PERSON: Alan Ruttenberg

liquid chromatography mass spectrometry platform
type: Class
subclass of: measurement device
subclass of: material separation device
editor preferred label: liquid chromatography mass spectrometry platform
definition: A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
definition editor: OBI instrument branch
definition source: OBI Instrument branch

software optimization objective
type: Class
subclass of: software testing objective
editor preferred label: software optimization objective
has curation status: IAO_0000123
definition: Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
definition editor: Jennifer Fostel

assay
type: Class
subclass of: planned process
disjoint with: data transformation
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: IAO_0000122
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 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.
definition editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
OBI_0001847: study assay
OBI_9991118: any method

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: IAO_0000120
definition: 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.
definition editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator note: 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.
comment: (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 t…

patient role
type: Class
subclass of: role
editor preferred label: patient role
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has curation status: IAO_0000120
definition: a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
definition editor: GROUP:Role Branch
alternative term: patient
definition source: OBI, CDISC
curator note: CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
imported from: obi.owl

material processing
type: Class
subclass of: planned process
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: IAO_0000122
definition: A planned process which results in physical changes in a specified input material
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived

protocol testing objective
type: Class
subclass of: methodology testing objective
editor preferred label: protocol testing objective
has curation status: IAO_0000123
definition: Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
definition editor: Jennifer Fostel

measured expression level
type: Class
subclass of: measurement datum
editor preferred label: measured expression level
example of usage: Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
has curation status: IAO_0000120
definition: 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.
definition editor: person:Chris Stoeckert
definition source: OBI Data Transformation branch

specimen role
type: Class
subclass of: role
editor preferred label: specimen role
example of usage: 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.
has curation status: IAO_0000122
definition: 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
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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.
definition editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

sequence feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: sequence feature identification objective
has curation status: IAO_0000123
definition: Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
definition editor: Jennifer Fostel

molecular feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: molecular feature identification objective
has curation status: IAO_0000123
definition: Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
definition editor: Jennifer Fostel

hardware testing objective
type: Class
subclass of: methodology testing objective
editor preferred label: hardware testing objective
has curation status: IAO_0000123
definition: Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
definition editor: Jennifer Fostel

filter paper
type: Class
subclass of: material separation device
editor preferred label: filter paper
definition: a device manufacture with the intent to provide a porous unsized paper used for filtering.
definition editor: Frank Gibson
definition source: sep:00107

protocol optimization objective
type: Class
subclass of: protocol testing objective
editor preferred label: protocol optimization objective
has curation status: IAO_0000123
definition: Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
definition editor: Jennifer Fostel

microtiter plate
type: Class
subclass of: container
editor preferred label: microtiter plate
example of usage: A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
definition: A microtiter_plate is a flat plate with multiple wells used as small test tubes.
definition editor: Melanie Courtot
alternative term: microplate
definition source: http://en.wikipedia.org/wiki/Microtiter_plate

methodology testing objective
type: Class
subclass of: objective specification
editor preferred label: methodology testing objective
has curation status: IAO_0000123
definition: Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
definition editor: Jennifer Fostel

cellular feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: cellular feature identification objective
has curation status: IAO_0000123
definition: Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
definition editor: Jennifer Fostel

hardware optimization objective
type: Class
subclass of: hardware testing objective
editor preferred label: hardware optimization objective
has curation status: IAO_0000123
definition: Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
definition editor: Jennifer Fostel

software testing objective
type: Class
subclass of: methodology testing objective
editor preferred label: software testing objective
has curation status: IAO_0000123
definition: Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
definition editor: Jennifer Fostel

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: 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.
has curation status: IAO_0000122
definition: 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.
definition: 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.
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: obi.owl
imported from: omrse.owl

DNA extraction
type: Class
subclass of: nucleic acid extraction
editor preferred label: DNA extraction
has curation status: IAO_0000123
definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

plan
type: Class
subclass of: realizable entity
editor preferred label: plan
example of usage: The plan of researcher X to perform an experiment according to a protocol.
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
editor note: This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
definition editor: AR, BP, JM, MC, PRS
definition source: branch derived

organism feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: organism feature identification objective
has curation status: IAO_0000123
definition: Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
definition editor: Jennifer Fostel

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: 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.
has curation status: IAO_0000122
definition: 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.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
OBI_0001847: study protocol

adding a material entity into a target
type: Class
subclass of: material combination
editor preferred label: adding a material entity into a target
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
definition editor: BP
definition source: branch derived

drawing a conclusion based on data
type: Class
subclass of: bioinformatics analysis
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
editor preferred label: interpreting data
example of usage: 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.
has curation status: IAO_0000122
definition: 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
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters

mass analyzer
type: Class
subclass of: measurement device
subclass of: material separation device
editor preferred label: mass analyzer
example of usage: The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
definition: A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
definition editor: Frank Gibson
definition editor: PERSON: Daniel Schober
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer

contain function
type: Class
subclass of: function
editor preferred label: contain function
example of usage: A syringe, a beaker
definition: A contain function is a function to constrain a material entities location in space
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot

heat function
type: Class
subclass of: function
editor preferred label: heat function
definition: A heat function is a function that increases the internal kinetic energy of a material
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot

material separation function
type: Class
subclass of: function
editor preferred label: material separation function
definition: A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot

mechanical function
type: Class
subclass of: function
editor preferred label: mechanical function
definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot
definition source: http://en.wikipedia.org/wiki/Mechanical_work

cool function
type: Class
subclass of: function
editor preferred label: cool function
definition: A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot

solid support function
type: Class
subclass of: function
editor preferred label: solid support function
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
definition: A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot

environment control function
type: Class
subclass of: function
editor preferred label: environment control function
definition: An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot

primer role
type: Class
subclass of: complementary nucleotide probe role
subclass of: Restriction
  on property: realized in
  all values from: polymerase chain reaction
editor preferred label: primer role
has curation status: IAO_0000123
definition: a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
definition source: (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer

viral RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: viral RNA extraction
example of usage: The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
has curation status: IAO_0000123
definition: The extraction of RNA from an input material that specifically isolates viral RNA
definition editor: Person:Bjoern Peters

polymerase chain reaction
type: Class
subclass of: enzymatic amplification
editor preferred label: polymerase chain reaction
example of usage: Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
has curation status: IAO_0000123
definition: PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
definition editor: OBI Plan
alternative term: PCR
definition source: adapted from wikipedai

extract
type: Class
subclass of: processed material
editor preferred label: extract
example of usage: Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
has curation status: IAO_0000120
definition: an extract is a material entity which results from an extraction process
definition editor: PERSON: Philippe Rocca-Serra
alternative term: extracted material
definition source: GROUP: OBI Biomatrial Branch

transcription profiling assay
type: Class
subclass of: omics data generation assay
subclass of: assay
editor preferred label: transcription profiling assay
example of usage: Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
has curation status: IAO_0000120
definition: An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity.
editor note: This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term.
definition editor: Philippe Rocca-Serra
alternative term: gene expression profiling
alternative term: transcription profiling
definition source: OBI

averaging objective
type: Class
subclass of: data transformation objective
editor preferred label: averaging objective
example of usage: A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
has curation status: IAO_0000122
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition source: PERSON: Elisabetta Manduchi

DNA sequence feature detection assay
type: Class
subclass of: sequence analysis data transformation
editor preferred label: DNA sequence feature detection assay
example of usage: genotyping using an Affymetrix chip
has curation status: IAO_0000123
definition: An assay with the objective to determine a sequence feature of DNA
definition editor: Bjoern Peters
definition editor: Philippe Rocca-Serra
definition source: OBI

adding material objective
type: Class
subclass of: material combination objective
editor preferred label: adding material objective
example of usage: creating a mouse infected with LCM virus
has curation status: IAO_0000122
definition: is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
definition editor: BP

needle
type: Class
subclass of: device
editor preferred label: needle
example of usage: Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
definition: a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
definition editor: Philippe Rocca-Serra
definition source: OBI Instrument

analyte measurement objective
type: Class
subclass of: assay objective
editor preferred label: analyte measurement objective
example of usage: The objective to measure the concentration of glucose in a blood sample
has curation status: IAO_0000122
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
definition editor: PERSON: Bjoern Peters
definition source: PPPB branch

DNA sequence variation detection assay
type: Class
subclass of: sequence analysis data transformation
editor preferred label: DNA sequence variation detection assay
example of usage: Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
has curation status: IAO_0000122
definition: An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule.
definition editor: Philippe Rocca-Serra
definition source: OBI Biomaterial

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: IAO_0000122
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
definition editor: PPPB branch
definition source: PPPB branch

target of material addition role
type: Class
subclass of: role
editor preferred label: target of material addition role
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
has curation status: IAO_0000120
definition: target of material addition role is a role realized by an entity into which a material is added in a material addition process
editor note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
definition editor: GROUP: Role Branch
definition source: OBI

packed column
type: Class
subclass of: chromatography column
editor preferred label: packed column
definition: A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube.
definition editor: PERSON:Daniel Schober
definition source: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218

regulatory agency
type: Class
subclass of: organization
editor preferred label: regulatory agency
example of usage: The US Environmental Protection Agency
has curation status: IAO_0000122
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator

measure function
type: Class
subclass of: function
editor preferred label: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
definition: 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.
definition editor: PERSON: Daniel Schober
definition editor: PERSON: Helen Parkinson
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Frank Gibson

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: IAO_0000122
definition: an objective specifiction that creates an specific output object from input materials.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing
type: Class
subclass of: material processing
editor preferred label: manufacturing
definition: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred label: manufacturing objective
has curation status: IAO_0000122
definition: is the objective to manufacture a material of a certain function (device)
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

organic acid column
type: Class
subclass of: chromatography column
editor preferred label: organic acid column
definition: An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099

protein column
type: Class
subclass of: chromatography column
editor preferred label: protein column
definition: A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
curator note: refactor as defined class

normal phase column
type: Class
subclass of: chromatography column
editor preferred label: normal phase column
definition: A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097

chromatography instrument
type: Class
subclass of: material separation device
editor preferred label: chromatography instrument
definition: Any instrument that is used to carry out a chromatography experiment.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262
curator note: chromatography device, defined class?

cation exchange column
type: Class
subclass of: ion exchange column
editor preferred label: cation exchange column
definition: A cation exchange column is a chromatography column that is used in cation exchange chromatography.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096

capillary column
type: Class
subclass of: chromatography column
editor preferred label: capillary column
definition: A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066

reversed phase column
type: Class
subclass of: chromatography column
editor preferred label: reversed phase column
definition: A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106

chromatofocusing column
type: Class
subclass of: chromatography column
editor preferred label: chromatofocusing column
definition: A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind.
definition editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209

trap column
type: Class
subclass of: chromatography column
editor preferred label: trap column
definition: A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261

affinity column
type: Class
subclass of: chromatography column
editor preferred label: affinity column
definition: An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094

gel filtration column
type: Class
subclass of: size exclusion column
editor preferred label: gel filtration column
definition: A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104

ion exchange column
type: Class
subclass of: chromatography column
editor preferred label: ion exchange column
definition: An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105

spin column
type: Class
subclass of: chromatography column
editor preferred label: spin column
definition: A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232

high temperature column
type: Class
subclass of: chromatography column
editor preferred label: high temperature column
definition: A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233

anion exchange column
type: Class
subclass of: ion exchange column
editor preferred label: anion exchange column
definition: An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095

plunger column
type: Class
subclass of: chromatography column
editor preferred label: plunger column
definition: A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108

liquid chromatography column
type: Class
subclass of: chromatography column
editor preferred label: liquid chromatography column
definition: A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227

open tubular column
type: Class
subclass of: chromatography column
editor preferred label: open tubular column
definition: An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube.
definition editor: PERSON:Daniel Schober
definition source: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219

glass column
type: Class
subclass of: chromatography column
editor preferred label: glass column
definition: A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101

size exclusion column
type: Class
subclass of: chromatography column
editor preferred label: size exclusion column
definition: A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100

custom made column
type: Class
subclass of: chromatography column
editor preferred label: custom made column
definition: A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234

gel permeation column
type: Class
subclass of: chromatography column
editor preferred label: gel permeation column
definition: A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size.
definition editor: PERSON:Daniel Schober
definition source: WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103

DNA sequencing assay
type: Class
subclass of: sequencing assay
editor preferred label: DNA sequencing assay
example of usage: Illumina (Solexa) sequencing is an example of DNA sequencing
has curation status: IAO_0000123
definition: A sequencing assay which determines information on the sequence of a DNA molecule.
definition editor: Philippe Rocca-Serra
alternative term: nucleotide sequencing
definition source: url:https://en.wikipedia.org/wiki/DNA_sequencing
imported from: obi.owl

carbon nanotube column
type: Class
subclass of: chromatography column
editor preferred label: carbon nanotube column
definition: Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well.
definition editor: PERSON:Daniel Schober
definition source: WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107

acquisition computer
type: Class
subclass of: computer
editor preferred label: acquisition computer
definition: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
definition editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
curator note: NMR instrument

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000122
definition: is an objective to transform a material entity into spatially separated components.
definition editor: PPPB branch
definition source: PPPB branch

urine specimen
type: Class
subclass of: specimen from organism
editor preferred label: urine specimen
definition: a portion of urine collected from an organism
editor note: 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
editor note: This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
editor note: are we happy calling collection of urine a material separation?

material combination
type: Class
subclass of: material processing
editor preferred label: material combination
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
definition editor: bp
definition source: bp

fuzzy clustering objective
type: Class
subclass of: data transformation objective
editor preferred label: fuzzy clustering objective
has curation status: IAO_0000122
definition: A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori.
definition editor: James Malone
definition source: PERSON: James Malone
definition source: PERSON: Ryan Brinkman

blood specimen
type: Class
subclass of: specimen from organism
editor preferred label: blood specimen
example of usage: blood drawn from a human for glucose assay
definition: a material entity derived from a portion of blood collected from an organism
definition editor: Bjoern Peters
definition source: Bjoern Peters

specimen collection process
type: Class
subclass of: planned process
editor preferred label: specimen collection process
example of usage: 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
definition: A planned process with the objective of collecting a specimen.
editor note: 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.
editor note: 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.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
definition editor: Bjoern Peters
alternative term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop

sample from organism
type: Class
subclass of: material sample
subclass of: specimen from organism
editor preferred label: sample from organism
definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.

statistical hypothesis test objective
type: Class
subclass of: data transformation objective
editor preferred label: statistical hypothesis test objective
has curation status: IAO_0000123
definition: is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
definition editor: James Malone
definition editor: Person:Helen Parkinson
alternative term: hypothesis test objective
definition source: WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing

portioning objective
type: Class
subclass of: material separation objective
disjoint with: separation into different composition objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: IAO_0000123
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.

average value
type: Class
subclass of: data item
editor preferred label: average value
has curation status: IAO_0000125
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
definition editor: PERSON: James Malone
definition editor: PERSON: Monnie McGee
alternative term: arithmetic mean

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000120
definition: 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).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: IAO_0000122
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
definition editor: Bjoern Peters
definition source: Bjoern Peters

material combination objective
type: Class
subclass of: material transformation objective
editor preferred label: material combination objective
has curation status: IAO_0000122
definition: is an objective to obtain an output material that contains several input materials.
definition editor: PPPB branch
definition source: bp

454 Genome Sequence 20
type: Class
subclass of: DNA sequencer
editor preferred label: 454 Genome Sequence 20
example of usage: PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
definition: is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
definition editor: Philippe Rocca-Serra
alternative term: GS 20

ABI 377 automated sequencer
type: Class
subclass of: DNA sequencer
editor preferred label: ABI 377 automated sequencer
definition: is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
definition editor: Philippe Rocca-Serra
definition source: Applied Biosystems

AB SOLiD System
type: Class
subclass of: DNA sequencer
editor preferred label: AB SOLiD System
example of usage: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
definition: is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
definition editor: Philippe Rocca-Serra
definition source: Applied Biosystems

454 Genome Sequencer FLX
type: Class
subclass of: DNA sequencer
editor preferred label: 454 Genome Sequencer FLX
example of usage: PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10.
definition: is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
definition editor: Philippe Rocca-Serra
alternative term: 454 GS FLX
alternative term: GS-FLX
definition source: adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay

Illumina Genome Analyzer II
type: Class
subclass of: DNA sequencer
editor preferred label: Illumina Genome Analyzer II
example of usage: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
definition: is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
definition editor: Philippe Rocca-Serra
definition source: Illumina Corporation

decision tree induction objective
type: Class
subclass of: data transformation objective
editor preferred label: decision tree induction objective
has curation status: IAO_0000123
definition: A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
definition editor: James Malone

Li-Cor 4300 DNA Analysis System
type: Class
subclass of: DNA sequencer
editor preferred label: Li-Cor 4300 DNA Analysis System
definition: is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
definition editor: Philippe Rocca-Serra
definition source: OBI and Li-Cor

library preparation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: library preparation
example of usage: PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
has curation status: IAO_0000120
definition: is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
definition editor: Philippe Rocca-Serra
alternative term: library construction

GenePattern software
type: Class
subclass of: software
editor preferred label: GenePattern software
has curation status: IAO_0000120
definition: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
definition editor: James Malone
definition editor: Person:Helen Parkinson
definition source: WEB: http://www.broadinstitute.org/cancer/software/genepattern/

HeliScope Single Molecule Sequencer
type: Class
subclass of: DNA sequencer
editor preferred label: HeliScope Single Molecule Sequencer
definition: is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
definition editor: Philippe Rocca-Serra

paired-end library
type: Class
subclass of: processed material
editor preferred label: paired-end library
example of usage: PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
has curation status: IAO_0000123
definition: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
definition editor: Philippe Rocca-Serra
alternative term: mate-paired library
alternative term: paired-end tag (PET) library
definition source: adapted from information provided by Solid web site

DNA sequencing by ligation assay
type: Class
subclass of: DNA sequencing assay
editor preferred label: DNA sequencing by ligation assay
example of usage: ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing).
has curation status: IAO_0000123
definition: A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase
definition editor: Philippe Rocca-Serra
definition source: url:https://en.wikipedia.org/wiki/Sequencing_by_ligation

DNA sequencing by synthesis assay
type: Class
subclass of: DNA sequencing assay
editor preferred label: DNA sequencing by synthesis assay
example of usage: Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing
has curation status: IAO_0000123
definition: A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
definition editor: Philippe Rocca-Serra
definition source: url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html

single fragment library
type: Class
subclass of: processed material
editor preferred label: single fragment library
has curation status: IAO_0000123
definition: is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
definition editor: Philippe Rocca-Serra
alternative term: fragment library

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: IAO_0000125
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
imported from: obi.owl

material sample
type: Class
subclass of: specimen
editor preferred label: material sample
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
definition: A material entity that has the material sample role
definition editor: OBI: workshop
alternative term: sample population
OBI_0001847: sample

multiple testing correction objective
type: Class
subclass of: error correction objective
editor preferred label: multiple testing correction objective
example of usage: Application of the Bonferroni correction
has curation status: IAO_0000120
definition: A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
alternative term: multiple comparison correction objective
definition source: http://en.wikipedia.org/wiki/Multiple_Testing_Correction

purification objective
type: Class
subclass of: separation into different composition objective
editor preferred label: purification objective
example of usage: the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
has curation status: IAO_0000120
definition: The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
definition editor: PERSON:Bjoern Peters
alternative term: isolation objective
definition source: BP
curator note: 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: IAO_0000122
definition: An objective specification maintains some or all of the qualities of a material over time.
definition editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters

informed consent process
type: Class
subclass of: planned process
editor preferred label: informed consent process
definition: A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
editor note: 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
definition editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

primary structure of DNA macromolecule
type: Class
subclass of: region
editor preferred label: primary structure of DNA macromolecule
has curation status: IAO_0000123
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
definition editor: BP et al

research organization
type: Class
subclass of: organization
editor preferred label: research organization
example of usage: The SALK institute is a research organization.
has curation status: IAO_0000123
definition: An organization formed with a goal to have its members conduct investigations
definition editor: Person:Bjoern Peters

measurement device
type: Class
subclass of: device
editor preferred label: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
definition: A device in which a measure function inheres.
definition editor: GROUP:OBI Philly workshop
definition source: OBI

manufacturer
type: Class
subclass of: material entity
editor preferred label: manufacturer
definition: A person or organization that has a manufacturer role

labeled oligonucleotide
type: Class
subclass of: molecular-labeled material
editor preferred label: labeled oligonucleotide
has curation status: IAO_0000123
definition: a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide
editor note: 2010-01-31: Philippe Rocca-Serra placeholder
definition editor: Person: Philippe Rocca-Serra

hospital
type: Class
subclass of: organization
editor preferred label: hospital
example of usage: human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
has curation status: IAO_0000120
definition: A medical organization at which sick or injured people are given clinical care
definition editor: Person:Alan Ruttenberg
definition editor: Person:Helen Parkinson
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
definition source: modified from the wording of the wordnet definition
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

primary structure of RNA molecule
type: Class
subclass of: region
editor preferred label: primary structure of RNA molecule
has curation status: IAO_0000123
definition: The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
definition editor: Person:Bjoern Peters

polyA RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: polyA RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group

organellar RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: organellar RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which the desired output material is RNA in the organelle(s).
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group

total RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: total RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which total cellular and organelle RNA are extracted.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group

complementary nucleotide probe role
type: Class
subclass of: role
editor preferred label: complementary nucleotide probe role
example of usage: A primer in a PCR reaction. A probe on an Affymetrix chip.
has curation status: IAO_0000120
definition: A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
definition editor: PERSON:Bjoern Peters

cytoplasmic RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: cytoplasmic RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which the desired output material is RNA in the cytoplasm.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group

pattern matching objective
type: Class
subclass of: data transformation objective
editor preferred label: pattern matching objective
has curation status: IAO_0000123
definition: A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees.
definition editor: Tina Boussard
definition source: http://en.wikipedia.org/wiki/Pattern_matching

RNA extract
type: Class
subclass of: specimen derivative
subclass of: nucleic acid extract
editor preferred label: RNA extract
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: Group: UPenn Group

nuclear RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: nuclear RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which the desired output material is RNA in the nucleus.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group

real time polymerase chain reaction assay
type: Class
subclass of: validation of known variant assay
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: polymerase chain reaction
editor preferred label: real time polymerase chain reaction assay
has curation status: IAO_0000120
definition: An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
definition editor: Bjoern Peters
definition editor: Melanie Courtot
alternative term: Q-PCR
alternative term: kinetic polymerase chain reaction
alternative term: qPCR
alternative term: quantitative real time polymerase chain reaction
definition source: url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction

labeled specimen
type: Class
subclass of: processed specimen
subclass of: molecular-labeled material
editor preferred label: labeled specimen
has curation status: IAO_0000123
definition: A specimen that has been modified in order to be able to detect it in future experiments
editor note: added during call 3/1/2010
definition editor: OBI group

material separation device
type: Class
subclass of: device
editor preferred label: material separation device
example of usage: flow cytometer
definition: A device with a separation function realized in a planed process

service consumer role
type: Class
subclass of: role
editor preferred label: service consumer role
example of usage: A biologist who uses a sequencing services fulfills the role of a service consumer
has curation status: IAO_0000120
definition: a role which inheres in a person who uses a service
definition editor: Person:Helen Parkinson
definition source: OBI

service provider role
type: Class
subclass of: role
editor preferred label: service provider role
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has curation status: IAO_0000123
definition: is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
definition editor: PERSON:Helen Parkinson

accessed material role
type: Class
subclass of: role
editor preferred label: accessed material role
example of usage: the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
has curation status: IAO_0000123
definition: is realized in a planned process where the bearer participates
editor note: AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it

processed specimen
type: Class
subclass of: processed material
subclass of: specimen
editor preferred label: processed specimen
example of usage: 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.
has curation status: IAO_0000122
definition: A specimen that has been intentionally physically modified.
definition editor: Bjoern Peters
definition source: Bjoern Peters
comment: A tissue sample that has been sliced and stained for a histology study.

reagent application function
type: Class
subclass of: function
editor preferred label: reagent application function
example of usage: An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
definition: A function that is realized when a reagent is automatically added to some research material.
definition editor: PERSON: Nicole Vasilevsky, Matthew Brush
definition source: PERSON: Nicole Vasilevsky, Matthew Brush
curator note: 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people?

training objective
type: Class
subclass of: objective specification
editor preferred label: training objective
example of usage: A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package
has curation status: IAO_0000120
definition: An objective specification which is fulfilled by the provision of some training.
definition editor: Helen Parkinson
definition source: OBI

container
type: Class
subclass of: device
editor preferred label: container
definition: A device that can be used to restrict the location of material entities over time
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
definition editor: PERSON: Bjoern Peters

device
type: Class
subclass of: processed material
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 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…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.

sequence data
type: Class
subclass of: measurement datum
editor preferred label: sequence data
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has curation status: IAO_0000120
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
definition editor: Person:Chris Stoeckert
definition source: GROUP: OBI

PCR instrument
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: polymerase chain reaction
editor preferred label: PCR instrument
has curation status: IAO_0000123
definition: A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
editor note: 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent.

service provision objective
type: Class
subclass of: objective specification
editor preferred label: service provision objective
example of usage: A sequencing centre has a service provision objective
has curation status: IAO_0000120
definition: An objective which is fulfilled by the provision of some service e.g. a training service
definition editor: Helen Parkinson
definition source: OBI

device creation objective
type: Class
subclass of: material transformation objective
editor preferred label: device creation objective
has curation status: IAO_0000120
definition: an objective which aims to create a device with a specified function
definition editor: PERSON: Helen Parkinson
definition source: OBI

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
editor preferred label: nucleic acid extract
has curation status: IAO_0000120
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
definition editor: PERSON: Jie Zheng
definition source: UPenn Group

pH meter
type: Class
subclass of: measurement device
editor preferred label: pH meter
definition: A device that is used to measure the pH (acidity or alkalinity) of a liquid.
definition editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/PH_meter

RNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
editor preferred label: RNA extraction/purification instrument
definition: A device that is used to isolate and collect RNA for subsequent molecular analysis.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

DNA extract
type: Class
subclass of: specimen derivative
subclass of: nucleic acid extract
editor preferred label: DNA extract
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
definition editor: Person: Jie Zheng
definition source: Group: UPenn group

automatic staining machine
type: Class
subclass of: device
editor preferred label: automatic staining machine
definition: A device that is used to automatically stain tissue sections on slides or tissue specimens.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

automatic tissue processor
type: Class
subclass of: device
editor preferred label: automatic tissue processor
definition: A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
definition editor: PERSON: Erik Segerdell
definition source: United States Patent 3762362

computer cluster
type: Class
subclass of: computer
editor preferred label: computer cluster
definition: A group of linked computers, working together closely so that in many respects they form a single computer.
definition editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Cluster_(computing)

microcentrifuge
type: Class
subclass of: centrifuge
editor preferred label: microcentrifuge
definition: A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
definition editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge

electronic repeater pipette
type: Class
subclass of: micropipette
editor preferred label: electronic repeater pipette
definition: A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations.
definition editor: PERSON: Erik Segerdell
definition source: http://www.faqs.org/patents/app/20090196797

tissue embedding station
type: Class
subclass of: device
editor preferred label: tissue embedding station
definition: A device that is used to perform paraffin embedding of tissue specimens.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

nucleic acid sequencer
type: Class
subclass of: measurement device
editor preferred label: nucleic acid sequencer
definition: An device that is used to determine the order of nucleotides in nucleic acid sequences.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

real-time PCR machine
type: Class
subclass of: PCR instrument
editor preferred label: real-time PCR machine
has curation status: IAO_0000120
definition: An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
definition editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction

microplate washer
type: Class
subclass of: device
editor preferred label: microplate washer
definition: A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
definition editor: PERSON: Erik Segerdell
definition source: http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037

nucleic acid extraction/purification instrument
type: Class
subclass of: material separation device
editor preferred label: nucleic acid extraction/purification instrument
definition: A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

ELISA microplate washer
type: Class
subclass of: microplate washer
editor preferred label: ELISA microplate washer
definition: A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

DNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
editor preferred label: DNA extraction/purification instrument
definition: A device that is used to isolate and collect DNA for subsequent molecular analysis.
definition editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/DNA_extraction

freeze substitution system
type: Class
subclass of: device
editor preferred label: freeze substitution system
definition: A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins.
definition editor: PERSON: Erik Segerdell
definition source: doi:10.1017/S143192760707866X

micropipette
type: Class
subclass of: measurement device
editor preferred label: micropipette
definition: A microinjection device that is used to measure very small volumes of liquids.
definition editor: PERSON: Erik Segerdell
definition source: http://www.answers.com/topic/micropipette

protein sequencer
type: Class
subclass of: measurement device
editor preferred label: protein sequencer
definition: An device that is used to determine the order of amino acids in protein sequences.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

labeled nucleic acid extract
type: Class
subclass of: labeled specimen
editor preferred label: labeled nucleic acid extract
has curation status: IAO_0000120
definition: a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
definition editor: Person: Jie Zheng
alternative term: labeled extract
definition source: MO_221 labeledExtract
OBI_0001847: labeled extract

genetic transformation objective
type: Class
subclass of: material transformation objective
editor preferred label: genetic transformation objective
has curation status: IAO_0000120
definition: a material transformation objective aims to create genetically modified organism or cell
definition editor: Person: Jie Zheng
definition source: Person: Jie Zheng
curator note: suggested to be added by BP and AR during Oct 25, 2010 dev call

assay validation objective
type: Class
subclass of: objective specification
editor preferred label: assay validation objective
has curation status: IAO_0000120
definition: an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: GROUP: Penn Group

validation by real time PCR design
type: Class
subclass of: validation of known variant protocol
editor preferred label: validation by real time PCR design
has curation status: IAO_0000120
definition: a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_434 real_time_PCR_quality_control

age measurement datum
type: Class
subclass of: time measurement datum
editor preferred label: age measurement datum
definition: A time measurement datum that is the result of measurement of age of an organism
editor note: 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
definition editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
definition source: MO_178 Age
curator note: 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
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.

selective organism creation objective
type: Class
subclass of: objective specification
editor preferred label: selective organism creation objective
has curation status: IAO_0000120
definition: an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29

RNA sequencing assay
type: Class
subclass of: sequencing assay
editor preferred label: RNA sequencing assay
has curation status: IAO_0000120
definition: An assay that determines the sequence of an RNA molecule.
definition editor: Bjoern Peters
definition source: Bjoern Peters

SNP microarray
type: Class
subclass of: DNA microarray
editor preferred label: SNP microarray
definition: a DNA microarray used to detect polymorphisms in DNA samples
definition editor: Person: Helen Parkinson
definition source: EFO_0002703 SNP array

transcription profiling by tiling array assay
type: Class
subclass of: transcription profiling by array assay
editor preferred label: transcription profiling by tiling array assay
has curation status: IAO_0000120
definition: A transcription profiling by array assay that uses a tiling path array.
definition editor: James Malone
definition source: EFO:0002769

RNA-seq assay
type: Class
subclass of: transcription profiling assay
subclass of: sequencing assay
editor preferred label: RNA-seq assay
has curation status: IAO_0000120
definition: An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
definition editor: James Malone
alternative term: transcription profiling by high throughput sequencing
definition source: EFO:0002770

tiling microarray
type: Class
subclass of: DNA microarray
editor preferred label: tiling microarray
definition: a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
definition editor: Person: Helen Parkinson
alternative term: genome tiling array
definition source: EFO_0002704: tiling array

transcription profiling identification objective
type: Class
subclass of: molecular feature identification objective
editor preferred label: transcription profiling identification objective
has curation status: IAO_0000120
definition: A molecular feature identification objective that aims to characterize the abundance of transcripts
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: Penn Group

microRNA profiling by array assay
type: Class
subclass of: microRNA profiling assay
editor preferred label: microRNA profiling by array assay
has curation status: IAO_0000120
definition: An assay that analyses the microRNA component of the transcriptome using a microRNA array.
definition editor: James Malone
definition source: EFO:0000753

transcription profiling by RT-PCR assay
type: Class
subclass of: transcription profiling assay
editor preferred label: transcription profiling by RT-PCR assay
has curation status: IAO_0000120
definition: A transcription profiling assay that uses reverse transcription PCR (RT-PCR).
definition editor: Anna Farne
definition source: EFO:0002943

transcription profiling by array assay
type: Class
subclass of: transcription profiling assay
editor preferred label: transcription profiling by array assay
has curation status: IAO_0000120
definition: A transcription profiling assay that uses array technology.
definition editor: James Malone
alternative term: RNA profiling by array assay
definition source: EFO:0002768
IAO_0000233: https://sourceforge.net/p/obi/obi-terms/757/

specimen with known storage state
type: Class
subclass of: specimen
editor preferred label: specimen with known storage state
definition: A specimen for which it is known whether it has been subjected to storage of a specified type.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_95 BiosourceType

specimen from organism
type: Class
subclass of: specimen
editor preferred label: specimen from organism
definition: A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
alternative term: tissue specimen
definition source: MO_954 organism_part

cell collecting
type: Class
subclass of: material component separation
editor preferred label: cell collecting
has curation status: IAO_0000120
definition: A planned process that collects cells from culture.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_982 harvest

linear amplification
type: Class
subclass of: enzymatic amplification
editor preferred label: linear amplification
example of usage: An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
has curation status: IAO_0000120
definition: An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_997 linear_amplification

sequence assembly algorithm
type: Class
subclass of: algorithm
editor preferred label: sequence assembly algorithm
has curation status: IAO_0000120
definition: 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.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
OBI_0001886: Assembly Algorithm
source: NIAID GSCID-BRC

DNA sequence data
type: Class
subclass of: sequence data
editor preferred label: DNA sequence data
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: IAO_0000120
definition: A sequence data item that is about the primary structure of DNA
definition editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
curator note: 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.

investigation description
type: Class
subclass of: textual entity
editor preferred label: investigation description
has curation status: IAO_0000120
definition: A textual entity that describes an investigation.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001847: study description
OBI_0001886: project description
source: NIAID GSCID-BRC
in subset: NCBI BioProject

specimen identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: identifier
subclass of: Restriction
  on property: denotes
  all values from: specimen
editor preferred label: specimen identifier
has curation status: IAO_0000120
definition: A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: specimen ID
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Specimen ID
source: NIAID GSCID-BRC
has synonym: sample identifier

average depth of sequence coverage
type: Class
subclass of: average value
editor preferred label: average depth of sequence coverage
has curation status: IAO_0000120
definition: An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
OBI_0001886: Depth of Coverage - Average
source: NIAID GSCID-BRC

specimen collection time measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process boundary
    intersection of: Restriction
      on property: starts
      some values from: specimen collection process
editor preferred label: specimen collection time measurement datum
definition: A time measurement datum that is the measure of the time when the specimens are collected.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: collection date
definition source: NIAID GSCID-BRC metadata working group
OBI_0001886: Specimen Collection Date
source: NIAID GSCID-BRC

organism identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: organism identification objective
has curation status: IAO_0000120
definition: A biological feature identification objective to identify the organism species in a specimen.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: Penn Group

sequence annotation algorithm
type: Class
subclass of: algorithm
editor preferred label: sequence annotation algorithm
has curation status: IAO_0000120
definition: An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
OBI_0001886: Annotation Algorithm
source: NIAID GSCID-BRC

Bioinformatics Resource Center
type: Class
subclass of: organization
editor preferred label: Bioinformatics Resource Center
has curation status: IAO_0000120
definition: An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: BRC
definition source: Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
source: NIAID GSCID-BRC

nano-cap analysis of gene expression assay
type: Class
subclass of: transcription profiling assay
editor preferred label: nano-cap analysis of gene expression assay
example of usage: Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846
has curation status: IAO_0000122
definition: A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE).
definition editor: Marcus Chibucos
definition editor: Philippe Rocca-Serra
alternative term: nano-CAGE
definition source: PMID:20543846

cap analysis of gene expression assay
type: Class
subclass of: transcription profiling assay
subclass of: sequencing assay
editor preferred label: cap analysis of gene expression assay
example of usage: 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160
has curation status: IAO_0000122
definition: A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
definition editor: Marcus Chibucos
definition editor: Philippe Rocca-Serra
alternative term: CAGE
definition source: PMID:14663149

molecular function identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: molecular function identification objective
has curation status: IAO_0000122
definition: is an objective specification which aims to discover molecular function realized by a molecular entity
definition editor: PERSON:Philippe Rocca-Serra
definition source: OBI group

cellular structure feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: cellular structure feature identification objective
has curation status: IAO_0000122
definition: is an objective specification which aims to discover cellular structure properties
definition editor: PERSON:Philippe Rocca-Serra
definition source: OBI group

structural analysis by paired-end tag sequencing assay
type: Class
subclass of: DNA sequencing assay
editor preferred label: structural analysis by paired-end tag sequencing assay
example of usage: Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419]
has curation status: IAO_0000120
definition: An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: DNA-PET
alternative term: DNA-PET assay
definition source: PMID:23029419

transcript analysis by paired-end tag sequencing assay
type: Class
subclass of: sequencing assay
editor preferred label: transcript analysis by paired-end tag sequencing assay
example of usage: Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299]
has curation status: IAO_0000120
definition: A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: RNA-PET
alternative term: RNA-PET assay
definition source: PMID:22113299

transcription start site identification objective
type: Class
subclass of: transcription profiling identification objective
editor preferred label: transcription start site identification objective
has curation status: IAO_0000120
definition: A transcription profiling identification objective that aims to characterize the transcription start sites of genes.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: Penn Group

paired-end library preparation
type: Class
equivalent class: Class
  intersection of: library preparation
  intersection of: Restriction
    on property: has_specified_output
    some values from: paired-end library
subclass of: library preparation
editor preferred label: paired-end library preparation
has curation status: IAO_0000120
definition: A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
definition editor: Person: Venkat Malladi, Jie Zheng
definition source: Venkat Malladi, Jie Zheng
source: ENCODE project

DNase I hypersensitive sites sequencing assay
type: Class
subclass of: DNA sequencing assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: DNA sequencer
  intersection of: Restriction
    on property: has_specified_input
    some values from: DNA sequencer
subclass of: Restriction
  on property: has part
  some values from: DNA sequencing assay
subclass of: Restriction
  on property: has part
  some values from: library preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: DNA sequence data
editor preferred label: DNase I hypersensitive sites sequencing assay
example of usage: Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541]
has curation status: IAO_0000120
definition: An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
definition source: url:http://en.wikipedia.org/wiki/DNase-Seq

protein and RNA interaction identification objective
type: Class
subclass of: sequence feature identification objective
editor preferred label: protein and RNA interaction identification objective
has curation status: IAO_0000120
definition: A sequence feature identification objective that aims to characterize the interactions between protein and RNA.
editor note: JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'.
definition editor: Person: Jie Zheng
definition source: Jie Zheng

formaldehyde-assisted isolation of regulatory elements assay
type: Class
subclass of: DNA sequencing assay
subclass of: Restriction
  on property: has part
  some values from: DNA sequencing assay
subclass of: Restriction
  on property: has part
  some values from: library preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: DNA sequence data
editor preferred label: formaldehyde-assisted isolation of regulatory elements assay
example of usage: Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217]
has curation status: IAO_0000120
definition: An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: FAIRE-seq
alternative term: FAIRE-seq assay
definition source: url:http://en.wikipedia.org/wiki/FAIRE-Seq

RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
type: Class
subclass of: transcription profiling assay
subclass of: sequencing assay
editor preferred label: RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
example of usage: Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248]
has curation status: IAO_0000120
definition: An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: RAMPAGE
definition source: PMID:22936248

assay array
type: Class
subclass of: device
editor preferred label: assay array
definition: A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
definition editor: PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
definition source: Penn Group

establishing cell line
type: Class
subclass of: establishing cell culture
editor preferred label: establishing cell line
definition: 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).
editor note: 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.
definition editor: Person: Matthew Brush
definition source: PERSON:Matthew Brush

Illumina BeadChip
type: Class
subclass of: assay array
editor preferred label: Illumina BeadChip
definition: An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides.
definition editor: PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi
definition source: http://www.illumina.com/technology/beadarray_technology.ilmn

Illumina methylation BeadChip
type: Class
subclass of: Illumina BeadChip
editor preferred label: Illumina methylation BeadChip
definition: A BeadChip made for an analyte assay that generates information about DNA methylation.
definition editor: PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
definition source: Penn Group

sequence assembly process
type: Class
subclass of: sequence analysis data transformation
editor preferred label: sequence assembly process
has curation status: IAO_0000122
definition: A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs).
editor note: PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly.
definition editor: Alejandra Gonzalez-Beltran
definition editor: PERSON: Jie Zheng, Chris Stoeckert
definition editor: Philippe Rocca-Serra
definition source: NIAID GSCID-BRC metadata working group
source: NIAID GSCID-BRC

reagent
type: Class
subclass of: processed material
editor preferred label: reagent
has curation status: IAO_0000120
definition: 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.
editor note: 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.
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
comment: (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…

organization of specimen provider principal investigator
type: Class
subclass of: organization
editor preferred label: organization of specimen provider principal investigator
has curation status: IAO_0000120
definition: An organization that is the affiliation of the principal investigator providing the specimens for the investigation
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Sample Provider PI's Institution
source: NIAID GSCID-BRC

organization of Bioinformatics Resource Center contact person
type: Class
subclass of: organization
editor preferred label: organization of Bioinformatics Resource Center contact person
has curation status: IAO_0000120
definition: An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
OBI_0001886: Bioinformatics Resource Center Contact's Institution
source: NIAID GSCID-BRC

specimen repository organization
type: Class
subclass of: organization
editor preferred label: specimen repository organization
has curation status: IAO_0000120
definition: An organization that provides a service to store and distribute specimens
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Specimen Repository
source: NIAID GSCID-BRC

sequencing facility organization
type: Class
subclass of: molecular analysis facility organization
editor preferred label: sequencing facility organization
has curation status: IAO_0000120
definition: An organization that provides sequence determination service
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Sequencing Facility
source: NIAID GSCID-BRC

specification of data to be generated in an investigation
type: Class
subclass of: specimen collection objective
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        union of: assay
        union of: data transformation
editor preferred label: specification of data to be generated in an investigation
example of usage: Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype
has curation status: IAO_0000120
definition: An objective specification which indicates the type of data that will be generated and submitted to a database.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
OBI_0001886: Project Objectives
source: NIAID GSCID-BRC

organization of specimen collector
type: Class
subclass of: organization
editor preferred label: organization of specimen collector
has curation status: IAO_0000120
definition: An organization that is the affiliation of the person collecting the specimen
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Specimen Collector's Institution
source: NIAID GSCID-BRC

organization of sequencing facility contact person
type: Class
subclass of: organization
editor preferred label: organization of sequencing facility contact person
has curation status: IAO_0000120
definition: An organization that is the affiliation of the contact representative at the sequencing facility
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Sequencing Facility Contact's Institution
source: NIAID GSCID-BRC

specimen identifier assigned by specimen repository
type: Class
subclass of: personally identifiable information
subclass of: specimen identifier
editor preferred label: specimen identifier assigned by specimen repository
has curation status: IAO_0000120
definition: A specimen identifier which is assigned by a specimen repository
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Specimen Repository Sample ID
source: NIAID GSCID-BRC

specimen identifier assigned by sequencing facility
type: Class
subclass of: personally identifiable information
subclass of: specimen identifier
editor preferred label: specimen identifier assigned by sequencing facility
has curation status: IAO_0000120
definition: A specimen identifier which is assigned by a sequencing facility
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
OBI_0001886: Sample ID - Sequencing Facility
source: NIAID GSCID-BRC

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion based on data
example of usage: 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".
has curation status: IAO_0000122
definition: An information content entity that is inferred from data.
editor note: 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.
definition editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group

DNA replication identification objective
type: Class
subclass of: molecular feature identification objective
editor preferred label: DNA replication identification objective
has curation status: IAO_0000120
definition: A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time.
definition editor: Chris Stoeckert, Jie Zheng
definition source: Group: Penn Group

chromosome conformation identification objective
type: Class
subclass of: molecular feature identification objective
editor preferred label: chromosome conformation identification objective
has curation status: IAO_0000120
definition: A molecular feature identification objective that aims to determine spatial organization of chromatin.
definition editor: Chris Stoeckert, Jie Zheng
definition source: Group: Penn Group

microRNA profiling by high throughput sequencing assay
type: Class
subclass of: microRNA profiling assay
editor preferred label: microRNA profiling by high throughput sequencing assay
example of usage: Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767
has curation status: IAO_0000120
definition: A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: miRNA-HTS
alternative term: miRNA-seq
alternative term: microRNA-seq
alternative term: microRNA-seq assay
definition source: url:http://www.ebi.ac.uk/efo/EFO_0002896

micrococcal nuclease digestion followed by high throughput sequencing assay
type: Class
subclass of: DNA sequencing assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: DNA sequencer
  intersection of: Restriction
    on property: has_specified_input
    some values from: DNA sequencer
subclass of: Restriction
  on property: has part
  some values from: library preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: DNA sequence data
editor preferred label: micrococcal nuclease digestion followed by high throughput sequencing assay
example of usage: Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607]
has curation status: IAO_0000120
definition: An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: MNase-seq
alternative term: MNase-seq assay
definition source: PMID:17038564

microRNA profiling assay
type: Class
subclass of: transcription profiling assay
editor preferred label: microRNA profiling assay
has curation status: IAO_0000120
definition: A transcription profiling assay that quantifies the microRNA species within a biological sample.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: miRNA expression assay
alternative term: microRNA expression assay
definition source: PMID: 23382819

selection
type: Class
subclass of: planned process
editor preferred label: selection
example of usage: PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
definition: A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
editor note: this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
definition editor: Person: Philippe Rocca-Serra
alternative term: selection process
definition source: OBI

molecular-labeled material
type: Class
subclass of: processed material
editor preferred label: molecular-labeled material
has curation status: IAO_0000125
definition: a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
definition editor: PERSON:Matthew Brush
definition source: OBI developer call, 3-12-12

grant agency
type: Class
subclass of: organization
editor preferred label: grant agency
has curation status: IAO_0000120
definition: An organization that provides funding support for projects such as investigations.
definition editor: PERSON: Jie Zheng, Chris Stoeckert
alternative term: funding organization
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
source: NIAID GSCID-BRC
see also: 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization

software pipeline
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: software
subclass of: Restriction
  on property: has part
  some values from: algorithm
subclass of: Restriction
  on property: has part
  some values from: database
editor preferred label: software pipeline
has curation status: IAO_0000120
definition: A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements.
definition editor: PERSON: Jie Zheng, Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29
source: NIAID GSCID-BRC

sequence annotation
type: Class
subclass of: bioinformatics analysis
subclass of: sequence analysis data transformation
editor preferred label: sequence annotation
has curation status: IAO_0000120
definition: A sequence annotation bioinformatics analysis that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
definition editor: PERSON: Jie Zheng, Chris Stoeckert
definition source: NIAID GSCID-BRC metadata working group
source: NIAID GSCID-BRC

target gene specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: is about
  some values from: DNA sequence data
editor preferred label: target gene specification
example of usage: http://www.ncbi.nlm.nih.gov/pubmed/25367129 "performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene)
has curation status: IAO_0000122
definition: is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey
definition editor: PERSON:Philippe Rocca-Serra
definition source: PRS for OBI
OBI_0001847: target gene

decision-theoretic analysis objective
type: Class
subclass of: objective specification
editor preferred label: decision-theoretic analysis objective
has curation status: IAO_0000120
definition: An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric.
editor note: The best action to take is typically defined as the one that maximizes expected utility.
definition editor: PERSON: Bill Hogan
alternative term: decision analysis objective
definition source: PERSON: Bill Hogan

biodiversity assessment objective
type: Class
subclass of: biological feature identification objective
editor preferred label: biodiversity assessment objective
has curation status: IAO_0000122
definition: biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level
definition editor: PERSON:Philippe Rocca-Serra
definition source: PRS for OBI

Methylation 450K BeadChip
type: Class
subclass of: Illumina methylation BeadChip
editor preferred label: Methylation 450K BeadChip
editor preferred label: surgical cancer treatment
example of usage: Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710
definition: A cancer therapeutic procedure that involves a surgical procedure as a main part.
definition: A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Illumina Infinium Human Methylation 450K BeadChip
definition source: NCI BBRB, OBIB
definition source: http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn
ontology term requester: NCI BBRB
source: ENCODE project
label: surgical cancer treatment

Methylation 27K BeadChip
type: Class
subclass of: Illumina methylation BeadChip
editor preferred label: Methylation 27K BeadChip
editor preferred label: specimen gross appearance of metastatic tumor
example of usage: Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139
definition: A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution.
definition: A specimen gross appearance of a tumor that has spread from its original site by discontinuous (not direct) spread, e.g. by blood or lymphatics.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Illumina Infinium Human Methylation 27K BeadChip
definition source: NCI BBRB, OBIB
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf
ontology term requester: NCI BBRB
source: ENCODE project
label: specimen gross appearance of metastatic tumor

1M-Duo Infinium HD BeadChip
type: Class
subclass of: Illumina BeadChip
editor preferred label: 1M-Duo Infinium HD BeadChip
editor preferred label: specimen gross appearance of tumor center
example of usage: Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850
definition: A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis.
definition: A specimen gross appearance of the most internal topographic location of the tumor.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Illumina Human 1M-Duo Infinium HD BeadChip
definition source: NCI BBRB, OBIB
definition source: http://www.illumina.com/technology/infinium_hd_assay.ilmn
ontology term requester: NCI BBRB
source: ENCODE project
label: specimen gross appearance of tumor center

SOLiD 3 Plus System
type: Class
subclass of: AB SOLiD System
editor preferred label: SOLiD 3 Plus System
editor preferred label: specimen gross appearance of tumor edge
example of usage: Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407
definition: A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
definition: A specimen gross appearance of the border of the tumor with non-tumorous tissue.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Applied Biosystems SOLiD 3 Plus System
definition source: NCI BBRB, OBIB
definition source: http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf
ontology term requester: NCI BBRB
source: ENCODE project
label: specimen gross appearance of tumor edge

Mouse 385K Whole Genome CGH Tiling Array
type: Class
subclass of: tiling microarray
editor preferred label: Mouse 385K Whole Genome CGH Tiling Array
editor preferred label: research authorization for post mortem specimen donation for a specific tissue or fluid
example of usage: Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/
definition: A research authorization documentation for postmortem specimen donation in which the authorization is for a specified tissue or biological fluid.
definition: A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Nimblegen Mouse 385K Whole Genome CGH Tiling Array
definition source: NCI BBRB, OBIB
definition source: http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
ontology term requester: NCI BBRB
source: ENCODE project
label: research authorization for post mortem specimen donation for a specific tissue or fluid

Mouse 3x720K Whole Genome CGH Tiling Array
type: Class
subclass of: tiling microarray
editor preferred label: Mouse 3x720K Whole Genome CGH Tiling Array
example of usage: Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584
definition: A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features.
definition: An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array
definition source: NCI BBRB, OBIB
definition source: http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
ontology term requester: NCI BBRB
source: ENCODE project
label: 0-non autolyis

Human 3x720K Whole Genome CGH Tiling Array
type: Class
subclass of: tiling microarray
editor preferred label: Human 3x720K Whole Genome CGH Tiling Array
example of usage: Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464
definition: A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features.
definition: An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Nimblegen Human 3x720K Whole Genome CGH Tiling Array
definition source: NCI BBRB, OBIB
definition source: http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
ontology term requester: NCI BBRB
source: ENCODE project
label: 1-slight autolysis

Human 2.1M Whole-Genome CGH Tiling Array v2.0
type: Class
subclass of: tiling microarray
editor preferred label: Human 2.1M Whole-Genome CGH Tiling Array v2.0
example of usage: Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274
definition: A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features.
definition: An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0
definition source: NCI BBRB, OBIB
definition source: http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
ontology term requester: NCI BBRB
source: ENCODE project
label: 2-moderate autolysis

PacBio RS II
type: Class
subclass of: DNA sequencer
editor preferred label: PacBio RS II
example of usage: Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882
definition: A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.
definition: An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues.
definition editor: Chris Stoeckert, Helena Ellis
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
alternative term: Pacific Biosciences RS II
definition source: NCI BBRB, OBIB
definition source: http://www.pacificbiosciences.com/products/
ontology term requester: NCI BBRB
source: ENCODE project
label: 3-severe autolysis

transcription profiling by MPSS assay
type: Class
subclass of: transcription profiling assay
subclass of: Restriction
  on property: has part
  some values from: DNA sequencing assay
subclass of: Restriction
  on property: has part
  some values from: library preparation
editor preferred label: transcription profiling by MPSS assay
has curation status: IAO_0000120
definition: A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS).
definition editor: Chris Stoeckert
definition editor: Jie Zheng
alternative term: expression MPSS
definition source: url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing

NextSeq 500
type: Class
subclass of: DNA sequencer
editor preferred label: NextSeq 500
definition: A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: Illumina NextSeq 500
definition source: http://systems.illumina.com/systems/nextseq-sequencer.html
source: ENCODE project

Illumina HiSeq 1000
type: Class
subclass of: DNA sequencer
editor preferred label: Illumina HiSeq 1000
definition: A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: HiSeq 1000
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
source: ENCODE project

Human Genome U133 Plus 2.0 tiling array
type: Class
subclass of: tiling microarray
editor preferred label: Human Genome U133 Plus 2.0 tiling array
definition: A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants.
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: Affymetrix HT Human Genome U133 Plus 2 Array Plate Set
alternative term: HG-U133 Plus 2
alternative term: HG-U133 Plus 2 array
definition source: http://www.affymetrix.com/estore/esearch/search.jsp
source: ENCODE project

SOLiD 4 System
type: Class
subclass of: AB SOLiD System
editor preferred label: SOLiD 4 System
definition: An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: Applied Biosystems SOLiD 4 System
alternative term: SOLiD 4
definition source: http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html
source: ENCODE project

Human Exon 1.0 ST tilling array
type: Class
subclass of: tiling microarray
editor preferred label: Human Exon 1.0 ST tilling array
definition: A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: Affymetrix Human Exon 1.0 St Array
alternative term: Human Exon 1.0
alternative term: Human Exon 1.0 ST Array
definition source: http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1
source: ENCODE project

Human Genome U133 tiling array
type: Class
subclass of: tiling microarray
editor preferred label: Human Genome U133 tiling array
definition: A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants.
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: Affymetrix HT Human Genome U133 Array Plate Set
alternative term: HG-U133
alternative term: HG-U133 array
definition source: http://www.affymetrix.com/estore/esearch/search.jsp
source: ENCODE project

Genome Analyzer IIe
type: Class
subclass of: Illumina Genome Analyzer II
editor preferred label: Genome Analyzer IIe
definition: An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories.
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: Illumina GA IIe
alternative term: Illumina Genome Analyzer IIe
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf
source: ENCODE project

SAGE ditag library preparation
type: Class
subclass of: library preparation
editor preferred label: SAGE ditag library preparation
has curation status: IAO_0000120
definition: A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library.
editor note: Related tracker:https://sourceforge.net/p/obi/obi-terms/720/
definition editor: Person:Chris Stoeckert
definition source: PMID:15905473

serial analysis of gene expression assay
type: Class
subclass of: transcription profiling assay
editor preferred label: serial analysis of gene expression assay
example of usage: PMID:15905473
has curation status: IAO_0000120
definition: A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced.
definition editor: Chris Stoeckert
definition editor: Janos Demeter
definition editor: Jie Zheng
alternative term: SAGE
definition source: PMID:7570003
IAO_0000233: https://sourceforge.net/p/obi/obi-terms/720/

translation-associated transcript leader sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: translation-associated transcript leader sequencing assay
example of usage: pmid:23580730
has curation status: IAO_0000120
definition: An RNA-seq assay that combines TL-seq with polysome fractionation
definition editor: Chris Stoeckert
definition editor: Janos Demeter
alternative term: TATL-seq
definition source: PMID:23580730
IAO_0000233: https://sourceforge.net/p/obi/obi-terms/725/

transcript leader sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: transcript leader sequencing assay
example of usage: pmid:23580730
has curation status: IAO_0000120
definition: An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing.
definition editor: Chris Stoeckert
definition editor: Janos Demeter
alternative term: TL-seq
definition source: PMID:23580730
IAO_0000233: https://sourceforge.net/p/obi/obi-terms/725/

ribosomal profiling by sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: ribosomal profiling by sequencing assay
example of usage: Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528
has curation status: IAO_0000120
definition: A RNA-seq assay that sequences only mRNA protected by the ribosome during translation.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: Ribo-seq
alternative term: Ribo-seq assay
alternative term: ribosomal profiling
definition source: PMID:24468696

self-transcribing active regulatory region sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: self-transcribing active regulatory region sequencing assay
example of usage: Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765.
has curation status: IAO_0000120
definition: An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: STARR-seq
alternative term: STARR-seq assay
alternative term: self-transcribing active regulatory region sequencing
definition source: PMID:23328393

RNA Bind-n-Seq assay
type: Class
subclass of: RNA-seq assay
editor preferred label: RNA Bind-n-Seq assay
has curation status: IAO_0000120
definition: An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs).
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: RBNS
alternative term: RNA Bind-n-Seq
alternative term: RNBS assay
definition source: doi: 10.1016/j.molcel.2014.04.016

poly(A)-site sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: poly(A)-site sequencing assay
example of usage: Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615.
has curation status: IAO_0000120
definition: A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
definition editor: Venkat Malladi
alternative term: PAS-seq
alternative term: PAS-seq assay
alternative term: Poly(A)-site sequencing
definition source: doi: 10.1261/rna.2581711

Illumina HiSeq 3000
type: Class
subclass of: DNA sequencer
editor preferred label: Illumina HiSeq 3000
definition: A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
definition editor: PERSON: Sagar Jain, Richard Scheuermann
alternative term: HiSeq 3000
definition source: http://www.illumina.com/systems/hiseq-3000-4000.html

Illumina HiSeq 4000
type: Class
subclass of: DNA sequencer
editor preferred label: Illumina HiSeq 4000
definition: A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
definition editor: PERSON: Sagar Jain, Richard Scheuermann
alternative term: HiSeq 4000
definition source: http://www.illumina.com/systems/hiseq-3000-4000.html

collection of specimens
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: material entity
editor preferred label: collection of specimens
example of usage: Blood cells collected from multiple donors over the course of a study.
definition: A material entity that has two or more specimens as its parts.
editor note: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: OBIB, OBI
source: Biobank

specimen container
type: Class
subclass of: container
editor preferred label: specimen container
example of usage: COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
definition: A container with the function of containing a specimen.
editor note: For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
definition editor: Chris Stoeckert
definition source: Duke Biobank, OBIB
source: Biobank
comment: Specimen containers are typically constructed or treated in a particular manner in order to perform their containing a specimen function. This will be a defined class so that any container (e.g., cryotube, vacutainer, conical test tube) with the function of containing a specimen will be inferred to be a specimen container.

Human 6x630K CGH Whole Genome Tiling Array
type: Class
subclass of: tiling microarray
editor preferred label: Human 6x630K CGH Whole Genome Tiling Array
definition: A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features.
editor note: Term request: https://sourceforge.net/p/obi/obi-terms/791/
definition editor: Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group
alternative term: NimbleGen Human 6x630K CGH Whole Genome Tiling Array
definition source: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi

small RNA sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: small RNA sequencing assay
has curation status: IAO_0000122
definition: An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits.
definition editor: Chris Stoeckert
definition editor: Jason Hilton
definition editor: Mark A. Miller
alternative term: short RNA-seq
alternative term: small RNA-seq
definition source: url:http://science.sciencemag.org/content/316/5830/1484.full
definition source: url:http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html
IAO_0000233: https://github.com/obi-ontology/obi/issues/859

bromouridine labeling and sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: bromouridine labeling and sequencing assay
has curation status: IAO_0000122
definition: An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs.
definition editor: Chris Stoeckert
definition editor: Jason Hilton
alternative term: Bru-seq
definition source: PMC:4009065

bromouridine pulse-chase and sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: bromouridine pulse-chase and sequencing assay
has curation status: IAO_0000122
definition: An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time.
definition editor: Chris Stoeckert
definition editor: Jason Hilton
alternative term: BruChase-seq
definition source: PMC:4009065

whole genome sequencing assay
type: Class
subclass of: DNA sequencing assay
subclass of: Restriction
  on property: has_specified_output
  some values from: whole genome sequence data
editor preferred label: whole genome sequencing assay
example of usage: WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS.
has curation status: IAO_0000120
definition: A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.
editor note: Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later.
definition editor: ImmPort
alternative term: WGS
definition source: PMID:23095910
definition source: PMID:25827230

exome sequencing assay
type: Class
subclass of: DNA sequencing assay
subclass of: Restriction
  on property: has_specified_output
  some values from: whole exome sequence data
editor preferred label: exome sequencing assay
example of usage: DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified.
has curation status: IAO_0000120
definition: A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons).
definition editor: ImmPort
alternative term: WES
definition source: PMID:25827230

H&E-stained fixed tissue slide specimen
type: Class
subclass of: fixed tissue slide specimen
editor preferred label: H&E-stained fixed tissue slide specimen
definition: A fixed tissue slide specimen that is the output of H&E slide staining.
definition editor: Chris Stoeckert, Ned Haubein
definition source: OBIB, OBI

IHC-stained fixed tissue slide specimen
type: Class
subclass of: fixed tissue slide specimen
editor preferred label: IHC-stained fixed tissue slide specimen
definition: A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
definition editor: Chris Stoeckert, Ned Haubein
alternative term: immunohistochemistry slide specimen
definition source: OBIB, OBI

Illumina Genome Analyzer
type: Class
subclass of: DNA sequencer
editor preferred label: Illumina Genome Analyzer
definition: A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.
definition editor: Person: Chris Stoeckert, Jason Hilton
alternative term: Illumina Genome Analyzer I
definition source: http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html
source: ENCODE project

Illumina HiSeq X Ten
type: Class
subclass of: DNA sequencer
editor preferred label: Illumina HiSeq X Ten
definition: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
definition editor: Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann
alternative term: HiSeq X Ten
definition source: http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html
source: ENCODE project

Illumina Infinium Omni5Exome-4 Kit
type: Class
subclass of: Illumina BeadChip
editor preferred label: Illumina Infinium Omni5Exome-4 Kit
definition: An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation.
definition editor: Person: Chris Stoeckert, Jason Hilton
definition source: http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html
source: ENCODE project

Illumina Infinium MethylationEPIC BeadChip
type: Class
subclass of: Illumina methylation BeadChip
editor preferred label: Illumina Infinium MethylationEPIC BeadChip
definition: An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution.
definition editor: Person: Chris Stoeckert, Jason Hilton
definition source: http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf
source: ENCODE project

Nanostring nCounter miRNA expression assay
type: Class
subclass of: microRNA profiling assay
editor preferred label: Nanostring nCounter miRNA expression assay
has curation status: IAO_0000122
definition: A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification.
definition editor: Chris Stoeckert
definition editor: Jason Hilton
alternative term: microRNA counts
definition source: PMID:26729350
definition source: url:http://www.nanostring.com/applications/technology
IAO_0000233: https://github.com/obi-ontology/obi/issues/806
ontology term requester: ENCODE DCC

bromouride labeling and sequencing after UV exposure
type: Class
subclass of: RNA-seq assay
editor preferred label: bromouride labeling and sequencing after UV exposure
has curation status: IAO_0000122
definition: An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions.
definition editor: Chris Stoeckert
definition editor: Jason Hilton
alternative term: BruUV-seq
definition source: PMC:4675984
IAO_0000233: https://github.com/obi-ontology/obi/issues/827
ontology term requester: ENCODE DCC

extrachromosomal circular DNA sequencing assay
type: Class
subclass of: DNA sequencing assay
editor preferred label: extrachromosomal circular DNA sequencing assay
has curation status: IAO_0000122
definition: An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods.
definition editor: Chris Stoeckert
definition editor: Jason Hilton
alternative term: circulome-seq
alternative term: eccDNA-seq
definition source: url:http://biorxiv.org/content/early/2017/04/19/128686
IAO_0000233: https://github.com/obi-ontology/obi/issues/830
ontology term requester: ENCODE DCC

courier organization
type: Class
subclass of: organization
editor preferred label: courier organization
has curation status: IAO_0000122
definition: An organization that delivers messages, packages, and mail.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: courier
definition source: https://en.wikipedia.org/wiki/Courier
ontology term requester: NCI BBRB

courier tracking number
type: Class
subclass of: centrally registered identifier symbol
editor preferred label: courier tracking number
definition: A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

Leica Peloris rapid tissue processor
type: Class
subclass of: automatic tissue processor
editor preferred label: Leica Peloris rapid tissue processor
definition: An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories.
definition editor: Chris Stoeckert, Helena Ellis
definition source: http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf
ontology term requester: NCI BBRB

molecular analysis facility organization
type: Class
subclass of: organization
editor preferred label: molecular analysis facility organization
example of usage: An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs.
has curation status: IAO_0000122
definition: An organization that provides molecular analysis service.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: MAF
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

clinical history of cancer
type: Class
subclass of: clinical history
editor preferred label: clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

clinical history devoid of cancer
type: Class
subclass of: clinical history
editor preferred label: clinical history devoid of cancer
definition: A clinical history in which there was no diagnosis of cancer.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: clinical history of no cancer
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

unknown clinical history of cancer
type: Class
subclass of: clinical history
editor preferred label: unknown clinical history of cancer
definition: A clinical history in which it is not known whether there was a diagnosis of cancer.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

family clinical history of cancer
type: Class
subclass of: clinical history
editor preferred label: family clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a blood relative.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: family history of cancer
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

aunt clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: aunt clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in the female sibling of a parent.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

brother clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: brother clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a male sibling.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

daughter clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: daughter clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a person's female child.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

father clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: father clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a male parent.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

mother clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: mother clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a female parent.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

sister clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: sister clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a female sibling.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

son clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: son clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a person's male child.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

uncle clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: uncle clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a male sibling of a parent.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

grandmother clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: grandmother clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a female parent of a parent.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

grandfather clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: grandfather clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a male parent of a parent.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

nephew clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: nephew clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a male child of a sibling.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

niece clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred label: niece clinical history of cancer
definition: A clinical history in which there is a diagnosis of cancer in a female child of a sibling.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of repeated HIV assays
type: Class
subclass of: clinical history
editor preferred label: clinical history of repeated HIV assays
definition: A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

exposure to second hand smoke
type: Class
subclass of: clinical history
editor preferred label: exposure to second hand smoke
definition: A clinical history in which there has been second hand exposure to tobacco smoking.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

exposure to second hand smoke in household during childhood
type: Class
subclass of: exposure to second hand smoke
editor preferred label: exposure to second hand smoke in household during childhood
definition: An exposure to second hand smoke that occurred in the (patient's) household when the person was a child.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

exposure to second hand smoke in current household
type: Class
subclass of: exposure to second hand smoke
editor preferred label: exposure to second hand smoke in current household
definition: An exposure to second hand smoke in person's current household.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

pregnancy history
type: Class
subclass of: clinical history
editor preferred label: pregnancy history
definition: A clinical history in which a female has had a pregnancy.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

gynecologic surgery history
type: Class
subclass of: clinical history
editor preferred label: gynecologic surgery history
definition: A clinical history in which a woman has had gynecologic surgery in the past.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

hysterectomy history
type: Class
subclass of: gynecologic surgery history
editor preferred label: hysterectomy history
definition: A gynecologic surgery history in which a woman has had a hysterectomy.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

unilateral oophorectomy history
type: Class
subclass of: gynecologic surgery history
editor preferred label: unilateral oophorectomy history
definition: A gynecologic surgery history in which a woman has had a unilateral oophorectomy.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

neither hysterectomy nor oophorectomy history
type: Class
subclass of: gynecologic surgery history
editor preferred label: neither hysterectomy nor oophorectomy history
definition: A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

hormonal replacement therapy history
type: Class
subclass of: clinical history
editor preferred label: hormonal replacement therapy history
definition: A clinical history in which an individual has had hormonal replacement therapy in the past.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

transcription start site mapping by primer extension assay
type: Class
subclass of: transcription profiling assay
editor preferred label: transcription start site mapping by primer extension assay
has curation status: IAO_0000120
definition: A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached.
definition editor: Rebecca Tauber
definition source: PMID:23378648
definition source: url:https://en.wikipedia.org/wiki/Primer_extension

precision nuclear run-on sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: precision nuclear run-on sequencing assay
has curation status: IAO_0000120
definition: An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends.
definition editor: Rebecca Tauber
alternative term: PRO-Seq
alternative term: precision nuclear run-on and sequencing assay
definition source: PMID:23430654
IAO_0000233: https://github.com/obi-ontology/obi/issues/876

alignment counting algorithm
type: Class
subclass of: algorithm
editor preferred label: alignment counting algorithm
has curation status: IAO_0000123
definition: An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts).
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios

alignment counting application
type: Class
subclass of: software application
editor preferred label: alignment counting application
has curation status: IAO_0000120
definition: A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: doi:10.1093/bioinformatics/btu638

base calling application
type: Class
subclass of: software application
editor preferred label: base calling application
has curation status: IAO_0000123
definition: A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios

bcl2fastq software application
type: Class
subclass of: base calling application
editor preferred label: bcl2fastq software application
has curation status: IAO_0000120
definition: A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html

reference genome-transcriptome alignment algorithm
type: Class
subclass of: algorithm
editor preferred label: reference genome-transcriptome alignment algorithm
has curation status: IAO_0000123
definition: An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios

star algorithm
type: Class
subclass of: reference genome-transcriptome alignment algorithm
editor preferred label: star algorithm
has curation status: IAO_0000123
definition: A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference.
definition source: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23104886

microraft
type: Class
subclass of: material separation device
editor preferred label: microraft
definition: A material separation device also commerically known as Isoraft, that is used to isolate single cells.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://en.wikipedia.org/wiki/Microrafts

amniotic fluid specimen
type: Class
subclass of: specimen from organism
editor preferred label: amniotic fluid specimen
definition: A specimen that is derived from amniotic fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

bile specimen
type: Class
subclass of: specimen from organism
editor preferred label: bile specimen
definition: A specimen that is derived from bile.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

cerebrospinal fluid specimen
type: Class
subclass of: specimen from organism
editor preferred label: cerebrospinal fluid specimen
definition: A specimen that is derived from cerbrospinal fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

feces specimen
type: Class
subclass of: specimen from organism
editor preferred label: feces specimen
definition: A specimen that is derived from feces.
definition editor: Chris Stoeckert
alternative term: stool specimen
definition source: Chris Stoeckert, Penn Medicine Biobank

digestive system fluid or secretion specimen
type: Class
subclass of: specimen from organism
editor preferred label: digestive system fluid or secretion specimen
definition: A specimen that is derived from digestive system fluid or secretion.
definition editor: Chris Stoeckert
alternative term: gastric fluid specimen
definition source: Chris Stoeckert, Penn Medicine Biobank

milk specimen
type: Class
subclass of: specimen from organism
editor preferred label: milk specimen
definition: A specimen that is derived from milk.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

pericardial fluid specimen
type: Class
subclass of: specimen from organism
editor preferred label: pericardial fluid specimen
definition: A specimen that is derived from pericardial fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

saliva specimen
type: Class
subclass of: specimen from organism
editor preferred label: saliva specimen
definition: A specimen that is derived from saliva.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

sputum specimen
type: Class
subclass of: specimen from organism
editor preferred label: sputum specimen
definition: A specimen that is derived from sputum.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

sweat specimen
type: Class
subclass of: specimen from organism
editor preferred label: sweat specimen
definition: A specimen that is derived from sweat.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

synovial fluid specimen
type: Class
subclass of: specimen from organism
editor preferred label: synovial fluid specimen
definition: A specimen that is derived from synovial fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

vitreous humor specimen
type: Class
subclass of: specimen from organism
editor preferred label: vitreous humor specimen
definition: A specimen that is derived from vireous humor.
definition editor: Chris Stoeckert
alternative term: vitreous fluid specimen
definition source: Chris Stoeckert, Penn Medicine Biobank

bone marrow specimen
type: Class
subclass of: specimen from organism
editor preferred label: bone marrow specimen
definition: A specimen that is derived from bone marrow.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

placenta specimen
type: Class
subclass of: specimen from organism
editor preferred label: placenta specimen
definition: A specimen that is derived from placenta.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

peritoneal fluid specimen
type: Class
subclass of: specimen from organism
editor preferred label: peritoneal fluid specimen
definition: A specimen that is derived from peritoneal fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

pleural fluid specimen
type: Class
subclass of: specimen from organism
editor preferred label: pleural fluid specimen
definition: A specimen that is derived from pleural fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank

brain specimen
type: Class
subclass of: specimen from organism
editor preferred label: brain specimen
definition: A specimen that is derived from brain.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

hair specimen
type: Class
subclass of: specimen from organism
editor preferred label: hair specimen
definition: A specimen that is derived from hair.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

prostate gland specimen
type: Class
subclass of: specimen from organism
editor preferred label: prostate gland specimen
definition: A specimen that is derived from prostate gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

skeletal muscle tissue specimen
type: Class
subclass of: specimen from organism
editor preferred label: skeletal muscle tissue specimen
definition: A specimen that is derived from skeletal muscle.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

heart specimen
type: Class
subclass of: specimen from organism
editor preferred label: heart specimen
definition: A specimen that is derived from heart.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

renal medulla specimen
type: Class
subclass of: specimen from organism
editor preferred label: renal medulla specimen
definition: A specimen that is derived from renal medulla.
definition editor: Chris Stoeckert
alternative term: kidney medulla specimen
definition source: Chris Stoeckert, NCI BBRB

adrenal gland specimen
type: Class
subclass of: specimen from organism
editor preferred label: adrenal gland specimen
definition: A specimen that is derived from adrenal gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

breast specimen
type: Class
subclass of: specimen from organism
editor preferred label: breast specimen
definition: A specimen that is derived from breast.
definition editor: Chris Stoeckert
alternative term: mammary tissue specimen
definition source: Chris Stoeckert, NCI BBRB

urinary bladder specimen
type: Class
subclass of: specimen from organism
editor preferred label: urinary bladder specimen
definition: A specimen that is derived from urinary bladder.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

tibial artery specimen
type: Class
subclass of: specimen from organism
editor preferred label: tibial artery specimen
definition: A specimen that is derived from tibial artery.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

skin of body specimen
type: Class
subclass of: specimen from organism
editor preferred label: skin of body specimen
definition: A specimen that is derived from skin.
definition editor: Chris Stoeckert
alternative term: skin specimen
definition source: Chris Stoeckert, NCI BBRB

pancreas specimen
type: Class
subclass of: specimen from organism
editor preferred label: pancreas specimen
definition: A specimen that is derived from pancreas.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

stomach specimen
type: Class
subclass of: specimen from organism
editor preferred label: stomach specimen
definition: A specimen that is derived from stomach.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

pituitary gland specimen
type: Class
subclass of: specimen from organism
editor preferred label: pituitary gland specimen
definition: A specimen that is derived from pituitary gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

adipose tissue specimen
type: Class
subclass of: specimen from organism
editor preferred label: adipose tissue specimen
definition: A specimen that is derived from adipose tissue.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

cortex of kidney specimen
type: Class
subclass of: specimen from organism
editor preferred label: cortex of kidney specimen
definition: A specimen that is derived from cortex of kidney.
definition editor: Chris Stoeckert
alternative term: kidney cortex specimen
definition source: Chris Stoeckert, NCI BBRB

esophagus mucosa specimen
type: Class
subclass of: specimen from organism
editor preferred label: esophagus mucosa specimen
definition: A specimen that is derived from esophagus mucosa.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

colon specimen
type: Class
subclass of: specimen from organism
editor preferred label: colon specimen
definition: A specimen that is derived from colon.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

lung specimen
type: Class
subclass of: specimen from organism
editor preferred label: lung specimen
definition: A specimen that is derived from lung.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

esophagus muscularis mucosa specimen
type: Class
subclass of: specimen from organism
editor preferred label: esophagus muscularis mucosa specimen
definition: A specimen that is derived from esophagus muscularis mucosa.
definition editor: Chris Stoeckert
alternative term: esophagus muscularis specimen
definition source: Chris Stoeckert, NCI BBRB

cerebral cortex specimen
type: Class
subclass of: specimen from organism
editor preferred label: cerebral cortex specimen
definition: A specimen that is derived from cerebral cortex.
definition editor: Chris Stoeckert
alternative term: brain cortex specimen
definition source: Chris Stoeckert, NCI BBRB

thyroid gland specimen
type: Class
subclass of: specimen from organism
editor preferred label: thyroid gland specimen
definition: A specimen that is derived from thyroid gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

cerebellum specimen
type: Class
subclass of: specimen from organism
editor preferred label: cerebellum specimen
definition: A specimen that is derived from cerebellum.
definition editor: Chris Stoeckert
alternative term: brain cerebellum specimen
definition source: Chris Stoeckert, NCI BBRB

tibial nerve specimen
type: Class
subclass of: specimen from organism
editor preferred label: tibial nerve specimen
definition: A specimen that is derived from tibial nerve.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

coronary artery specimen
type: Class
subclass of: specimen from organism
editor preferred label: coronary artery specimen
definition: A specimen that is derived from coronary artery.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

spleen specimen
type: Class
subclass of: specimen from organism
editor preferred label: spleen specimen
definition: A specimen that is derived from spleen.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

aorta specimen
type: Class
subclass of: specimen from organism
editor preferred label: aorta specimen
definition: A specimen that is derived from aorta.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

atrial appendage specimen
type: Class
subclass of: specimen from organism
editor preferred label: atrial appendage specimen
definition: A specimen that is derived from the atrium auricular region.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

esophagogastric junction specimen
type: Class
subclass of: specimen from organism
editor preferred label: esophagogastric junction specimen
definition: A specimen that is derived from the esophagogastric junction.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

ileum specimen
type: Class
subclass of: specimen from organism
editor preferred label: ileum specimen
definition: A specimen that is derived from ileum.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

liver specimen
type: Class
subclass of: specimen from organism
editor preferred label: liver specimen
definition: A specimen that is derived from liver.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

minor salivary gland specimen
type: Class
subclass of: specimen from organism
editor preferred label: minor salivary gland specimen
definition: A specimen that is derived from minor salivary gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

omentum specimen
type: Class
subclass of: specimen from organism
editor preferred label: omentum specimen
definition: A specimen that is derived from omentum.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

ovary specimen
type: Class
subclass of: specimen from organism
editor preferred label: ovary specimen
definition: A specimen that is derived from female gonad.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

sigmoid colon specimen
type: Class
subclass of: specimen from organism
editor preferred label: sigmoid colon specimen
definition: A specimen that is derived from sigmoid colon.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

suprapubic skin specimen
type: Class
subclass of: skin of body specimen
editor preferred label: suprapubic skin specimen
definition: A specimen that is derived from suprapubic skin.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

testis specimen
type: Class
subclass of: specimen from organism
editor preferred label: testis specimen
definition: A specimen that is derived from testis.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

uterus specimen
type: Class
subclass of: specimen from organism
editor preferred label: uterus specimen
definition: A specimen that is derived from uterus.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

vagina specimen
type: Class
subclass of: specimen from organism
editor preferred label: vagina specimen
definition: A specimen that is derived from vagina.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

adapter-sequence trimming
type: Class
subclass of: sequence trimming
editor preferred label: adapter-sequence trimming
has curation status: IAO_0000120
definition: A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed).
definition editor: Dan Berrios
definition source: Dan Berrios

file merge
type: Class
subclass of: data transformation
editor preferred label: file merge
has curation status: IAO_0000120
definition: A data transformation in which data contained in 2 or more files are merged into a single file.
definition editor: Dan Berrios
definition source: Dan Berrios

sequence alignment
type: Class
subclass of: alignment
editor preferred label: sequence alignment
has curation status: IAO_0000120
definition: A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm.
definition editor: Dan Berrios
definition source: Dan Berrios

nCounter Mouse miRNA Expression array
type: Class
subclass of: assay array
editor preferred label: nCounter Mouse miRNA Expression array
example of usage: Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819
definition: A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays.
definition editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013
definition source: https://www.nanostring.com/products/mirna-assays/mirna-panels
date: 2018-05-11T14:04:41Z
source: ENCODE project

polyA-selected RNA sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: polyA-selected RNA sequencing assay
has curation status: IAO_0000120
definition: An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing.
definition editor: Jason Hilton
definition editor: Mark A. Miller
alternative term: mRNA-seq
definition source: url:https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419
ontology term requester: ENCODE

polyA-depleted RNA sequencing assay
type: Class
subclass of: RNA-seq assay
editor preferred label: polyA-depleted RNA sequencing assay
has curation status: IAO_0000120
definition: An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing.
definition editor: Jason Hilton
definition editor: Mark A. Miller
alternative term: polyA-depleted RNA-seq
definition source: url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733
definition source: url:http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676
ontology term requester: ENCODE

RNA extraction with polyA depletion
type: Class
subclass of: RNA extraction
editor preferred label: RNA extraction with polyA depletion
has curation status: IAO_0000120
definition: A RNA extraction process in which only RNAs lacking a polyA tail are retained
definition editor: Mark A. Miller, based on OBI_0000848
definition source: UPenn Group
date: 2018-05-11T15:01:14Z

isoform sequencing
type: Class
subclass of: RNA-seq assay
editor preferred label: isoform sequencing
example of usage: Novel transcript forms were assessed by isoform sequencing.
has curation status: IAO_0000123
definition: A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms.
alternative term: ISO-seq
definition source: url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/

adapter sequence data
type: Class
subclass of: sequence data
editor preferred label: adapter sequence data
has curation status: IAO_0000120
definition: Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run.
definition editor: Dan Berrios
definition source: Dan Berrios

adapter-trimmed sequence data
type: Class
subclass of: sequence data
editor preferred label: adapter-trimmed sequence data
has curation status: IAO_0000120
definition: The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed.
definition editor: Dan Berrios
definition source: Dan Berrios

aligned sequence data
type: Class
subclass of: sequence data
editor preferred label: aligned sequence data
has curation status: IAO_0000120
definition: The results of a sequence alignment.
definition editor: Dan Berrios
definition source: Dan Berrios

merged aligned sequence data
type: Class
subclass of: sequence data
editor preferred label: merged aligned sequence data
has curation status: IAO_0000120
definition: The results of a data transformation of sequence data in which files containing aligned sequence data are merged together
definition editor: Dan Berrios
definition source: Dan Berrios

DNA methylation profiling data
type: Class
subclass of: sequence data
editor preferred label: DNA methylation profiling data
has curation status: IAO_0000123
definition: The results of a DNA methylation profiling assay

sequence trimming
type: Class
subclass of: bioinformatics analysis
editor preferred label: sequence trimming
has curation status: IAO_0000123
definition: A data transformation in which subsequences of a molecular sequence are cut (removed).

whole metagenome sequencing assay
type: Class
subclass of: DNA sequencing assay
editor preferred label: whole metagenome sequencing assay
has curation status: IAO_0000125
definition: A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.
editor note: Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.).
definition editor: Rebecca Jackson
alternative term: WMS
definition source: Bjoern Peters
definition source: Michelle Giglio
IAO_0000233: https://github.com/obi-ontology/obi/issues/1056

detection of pathogenic organisms objective
type: Class
subclass of: organism feature identification objective
editor preferred label: detection of pathogenic organisms objective
has curation status: IAO_0000120
definition: An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms.
definition editor: Jie Zheng
definition source: VEuPathDB
IAO_0000233: https://github.com/obi-ontology/obi/issues/1117
ontology term requester: VEuPathDB

insecticide resistance detection objective
type: Class
subclass of: organism feature identification objective
editor preferred label: insecticide resistance detection objective
has curation status: IAO_0000120
definition: An organism feature identification objective that aims to detect insecticide resistance of an insect.
definition editor: Jie Zheng
definition source: VEuPathDB
IAO_0000233: https://github.com/obi-ontology/obi/issues/1117
ontology term requester: VEuPathDB

whole virome sequencing assay
type: Class
subclass of: whole metagenome sequencing assay
editor preferred label: whole virome sequencing assay
has curation status: IAO_0000120
definition: A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.
definition editor: Michelle Giglio
definition editor: Rebecca Jackson
definition editor: Suvarna Nadendla
definition source: OBI:0002623
ontology term requester: CFDE

blood plasma specimen
type: Class
subclass of: processed specimen
editor preferred label: blood plasma specimen
example of usage: PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
has curation status: IAO_0000120
definition: a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
editor note: 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
definition editor: PERSON: Maura Gasparetto
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
alternative term: plasma
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma

blood serum specimen
type: Class
subclass of: processed specimen
editor preferred label: blood serum specimen
example of usage: PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
has curation status: IAO_0000120
definition: A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
definition editor: PERSON: Maura Gasparetto
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma

organism
type: Class
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: IAO_0000122
definition: 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.
editor note: 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')
editor note: 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.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: ido.owl
imported from: obi.owl
imported from: omrse.owl

specimen
type: Class
subclass of: material entity
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
definition: A material entity that has the specimen role.
editor note: 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.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch

bronchial alveolar lavage
type: Class
subclass of: processed specimen
editor preferred label: bronchial alveolar lavage
example of usage: solution containing lung derived T cells, eosinophils, and TNFa.
definition: Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
definition editor: PERSON: Bjoern Peters
alternative term: BAL
definition source: GROUP: IEDB

data transformation
type: Class
subclass of: planned process
editor preferred label: data transformation
example of usage: 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.
definition: A data transformation is a process which produces output data from input data
definition: A planned process that produces output data from input data.
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Philippe Rocca-Serra
definition editor: Richard Scheuermann
definition editor: Ryan Brinkman
definition editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: obi.owl

feature extraction objective
type: Class
subclass of: data transformation objective
editor preferred label: feature extraction objective
has curation status: IAO_0000125
definition: A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition source: TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction

differential expression analysis objective
type: Class
subclass of: data transformation objective
editor preferred label: differential expression analysis objective
example of usage: Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
has curation status: IAO_0000122
definition: A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
definition editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi

descriptive statistical calculation objective
type: Class
subclass of: data transformation objective
editor preferred label: descriptive statistical calculation objective
has curation status: IAO_0000122
definition: A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Monnie McGee
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Monnie McGee

sequence analysis objective
type: Class
subclass of: data transformation objective
editor preferred label: sequence analysis objective
has curation status: IAO_0000120
definition: A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
definition editor: James Malone
definition source: PERSON: James Malone

survival analysis objective
type: Class
subclass of: data transformation objective
editor preferred label: survival analysis objective
example of usage: Kaplan meier data transformation
has curation status: IAO_0000120
definition: A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
definition editor: PERSON: James Malone
definition editor: PERSON: Tina Boussard
alternative term: survival analysis
definition source: http://en.wikipedia.org/wiki/Survival_analysis

inter-rater reliability objective
type: Class
subclass of: data transformation objective
editor preferred label: inter-rater reliability objective
example of usage: A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation.
has curation status: IAO_0000120
definition: a data transformation objective of determining the concordance or agreement between human judges.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Helen Parkinson
alternative term: inter-rater agreement
definition source: http://en.wikipedia.org/wiki/Inter-rater_reliability

data visualization
type: Class
subclass of: planned process
editor preferred label: data visualization
example of usage: Generation of a heatmap from a microarray dataset
definition: An planned process that creates images, diagrams or animations from the input data.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Tina Boussard
alternative term: data encoding as image
alternative term: visualization
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Tina Boussard
curator note: Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
imported from: obi.owl

data vector reduction objective
type: Class
subclass of: data transformation objective
editor preferred label: data vector reduction objective
has curation status: IAO_0000125
definition: Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k.
definition editor: James Malone
definition editor: Richard H. Scheuermann
definition source: PERSON: Richard H. Scheuermann

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
has curation status: IAO_0000122
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
definition editor: James Malone
definition source: PERSON: James Malone

data normalization objective
type: Class
subclass of: data transformation objective
editor preferred label: data normalization objective
example of usage: Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
has curation status: IAO_0000122
definition: A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: Helen Parkinson
definition source: PERSON: James Malone

correction objective
type: Class
subclass of: data transformation objective
editor preferred label: correction objective
example of usage: Type I error correction
has curation status: IAO_0000123
definition: A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
definition editor: James Malone
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot

partitioning objective
type: Class
subclass of: data transformation objective
editor preferred label: partitioning objective
example of usage: A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
has curation status: IAO_0000122
definition: A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition source: PERSON: Elisabetta Manduchi

background correction objective
type: Class
subclass of: correction objective
editor preferred label: background correction objective
has curation status: IAO_0000125
definition: A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition source: PERSON: Elisabetta Manduchi

curve fitting objective
type: Class
subclass of: data transformation objective
editor preferred label: curve fitting objective
has curation status: IAO_0000125
definition: A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition source: PERSON: Elisabetta Manduchi

center calculation objective
type: Class
subclass of: data transformation objective
editor preferred label: center calculation objective
example of usage: A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
has curation status: IAO_0000122
definition: A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
definition editor: James Malone
definition source: PERSON: James Malone

class discovery objective
type: Class
subclass of: data transformation objective
editor preferred label: class discovery objective
has curation status: IAO_0000122
definition: A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
definition editor: James Malone
alternative term: clustering objective
alternative term: discriminant analysis objective
alternative term: unsupervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

class prediction objective
type: Class
subclass of: data transformation objective
editor preferred label: class prediction objective
has curation status: IAO_0000122
definition: A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
definition editor: James Malone
alternative term: classification objective
alternative term: supervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

spread calculation objective
type: Class
subclass of: data transformation objective
editor preferred label: spread calculation objective
example of usage: Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean
has curation status: IAO_0000123
definition: is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set
editor note: Awaiting English definition from Monnie McGee
definition editor: James Malone
definition editor: Person:Helen Parkinson

scaling objective
type: Class
subclass of: data transformation objective
editor preferred label: scaling objective
example of usage: Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
has curation status: IAO_0000123
definition: is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
editor note: Awaiting English definition from Monnie McGee
definition editor: James Malone
definition editor: Person:Helen Parkinson

error correction objective
type: Class
subclass of: correction objective
editor preferred label: error correction objective
example of usage: Application of a multiple testing correction method
has curation status: IAO_0000125
definition: An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
definition editor: James Malone, Helen Parkinson
definition source: PERSON: James Malone

sequence analysis data transformation
type: Class
subclass of: bioinformatics analysis
editor preferred label: sequence analysis data transformation
has curation status: IAO_0000123
definition: A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns.
definition editor: James Malone
definition source: EDITOR

cross validation objective
type: Class
subclass of: partitioning objective
editor preferred label: cross validation objective
has curation status: IAO_0000125
definition: A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
definition editor: James Malone
alternative term: rotation estimation objective
definition source: WEB: http://en.wikipedia.org/wiki/Cross_validation

merging objective
type: Class
subclass of: data transformation objective
editor preferred label: merging objective
example of usage: merging of columns from two different data sets
has curation status: IAO_0000123
definition: A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
definition editor: James Malone
alternative term: combining objective
definition source: PERSON: Data Transformation Branch

correlation study objective
type: Class
subclass of: data transformation objective
editor preferred label: correlation study objective
has curation status: IAO_0000123
definition: A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables.
definition editor: PERSON: Tina Boussard

spectrum analysis objective
type: Class
subclass of: data transformation objective
editor preferred label: spectrum analysis objective
example of usage: Calculation of characteristic path length in mass spectrometry
has curation status: IAO_0000123
definition: is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process.
definition editor: PERSON: Tina Boussard
definition editor: Person:Helen Parkinson

extraction
type: Class
subclass of: material component separation
editor preferred label: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: IAO_0000123
definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
definition editor: Person:Bjoern Peters
definition editor: Philippe Rocca-Serra

filtration
type: Class
subclass of: material component separation
editor preferred label: filtration
example of usage: PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
definition: filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
definition editor: Philippe Rocca-Serra
definition source: OBI-Branch: adapted from wikipedia and wordnet

centrifugation
type: Class
subclass of: material component separation
editor preferred label: centrifugation
example of usage: PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
has curation status: IAO_0000120
definition: centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
definition editor: Philippe Rocca-Serra
definition source: adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm

washing
type: Class
subclass of: material processing
editor preferred label: washing
example of usage: PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
has curation status: IAO_0000120
definition: washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
definition editor: Philippe Rocca-Serra
definition source: OBI-Branch

nucleic acid hybridization
type: Class
subclass of: material processing
editor preferred label: nucleic acid hybridization
example of usage: PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
has curation status: IAO_0000120
definition: a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
definition editor: Philippe Rocca-Serra
definition source: adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
OBI_0001847: hybridization assay

DNA Subtraction
type: Class
subclass of: material component separation
editor preferred label: DNA Subtraction
example of usage: PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81
has curation status: IAO_0000122
definition: a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library.
definition editor: Philippe Rocca-Serra
definition source: OBI-Branch

document editing
type: Class
subclass of: planned process
editor preferred label: document editing
example of usage: Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
definition: is a planned process with specified input original document and specified output edited document
definition editor: Philippe Rocca-Serra and OBI consortium
definition source: adapted from wikipedia

flow cell
type: Class
subclass of: container
editor preferred label: flow cell
example of usage: Biofilm Flow Cell
definition: Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
definition editor: Person:John Quinn
alternative term: flow_cell
definition source: http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm

fluid pressure regulator
type: Class
subclass of: measurement device
editor preferred label: fluid pressure regulator
example of usage: LSR2 fluid pressure regulator
definition: Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank.
definition editor: Person: John Quinn
definition source: Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253

DNA sequencer
type: Class
subclass of: measurement device
editor preferred label: DNA sequencer
example of usage: ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
definition: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
definition editor: Trish Whetzel
definition source: MO

arrayer
type: Class
subclass of: device
editor preferred label: arrayer
example of usage: BioRobotics Microgrid II TAS, Affymetrix GMS 417
definition: a device which deposits biological material onto a substrate in a defined pattern.
definition editor: Trish Whetzel
definition source: MO_697 arrayer

centrifuge
type: Class
subclass of: measurement device
editor preferred label: centrifuge
definition: A device with a rapidly rotating container that applies centrifugal force to its contents
definition editor: Melanie Courtot
definition editor: Person: Jennifer Fostel
definition editor: Trish Whetzel
definition source: http://en.wikipedia.org/wiki/Centrifuge

computer
type: Class
subclass of: device
editor preferred label: computer
example of usage: Apple PowerBook, Dell OptiPlex
definition: A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
definition editor: Melanie Courtot
definition editor: Trish Whetzel
definition source: http://en.wikipedia.org/wiki/Computer

microarray
type: Class
subclass of: assay array
editor preferred label: microarray
example of usage: An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
definition: A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
definition editor: Daniel Schober
definition source: PERSON: Chris Stoeckert

DNA microarray
type: Class
subclass of: microarray
editor preferred label: DNA microarray
example of usage: Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
definition: A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
definition editor: PERSON: Daniel Schober
definition editor: PERSON: Frank Gibson
alternative term: DNA Chip
alternative term: DNA-array
definition source: Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03

protein microarray
type: Class
subclass of: microarray
editor preferred label: protein microarray
example of usage: The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
definition: A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
definition editor: Daniel Schober
definition source: PERSON: Daniel Schober

microscope slide
type: Class
subclass of: device
editor preferred label: microscope slide
example of usage: PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
definition: a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
definition editor: PERSON: Phillippe Rocca-Serra
definition source: OBI biomaterial branch

human subject enrollment
type: Class
subclass of: selection
subclass of: Restriction
  on property: has part
  some values from: informed consent process
editor preferred label: human subject enrollment
example of usage: enlisting familiy members of HIV patients into a study
definition: A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
editor note: As with group assignment, should the specified output here be an organism which bears a role
definition editor: Bjoern Peters
definition source: IEDB
curator note: criteria come from plan / clinical trial branch

collecting specimen from organism
type: Class
subclass of: specimen collection process
editor preferred label: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
definition editor: PERSON:Bjoern Peters
definition source: IEDB

material component separation
type: Class
subclass of: material processing
editor preferred label: material component separation
example of usage: 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
has curation status: IAO_0000122
definition: a material processing in which components of an input material become segregated in space
definition editor: Bjoern Peters
definition source: IEDB

pooling specimens
type: Class
subclass of: material combination
editor preferred label: pooling specimens
example of usage: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
definition: physical combination of several instances of like material
definition editor: PlanAndPlannedProcess Branch
alternative term: sample pooling
definition source: OBI branch derived
curator note: like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.

material portioning
type: Class
subclass of: material component separation
editor preferred label: material portioning
example of usage: pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
definition: a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
definition editor: PERSON:Bjoern Peters
alternative term: aliquoting
alternative term: apportioning
definition source: OBI branch derived

establishing cell culture
type: Class
subclass of: material processing
editor preferred label: 'establishing cell culture'
definition: 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).
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
comment: 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.

cell culture splitting
type: Class
subclass of: material component separation
editor preferred label: cell culture splitting
example of usage: 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.
has curation status: IAO_0000125
definition: 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
definition editor: PlanAndPlannedProcess Branch
alternative term: cell culture passaging
definition source: OBI branch derived
comment: 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.

addition of molecular label
type: Class
subclass of: material processing
editor preferred label: addition of molecular label
example of usage: The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
definition: a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
definition editor: PERSON:Matthew Brush
alternative term: labeling
definition source: OBI developer call, 3-12-12

lavage
type: Class
subclass of: collecting specimen from organism
subclass of: material component separation
editor preferred label: lavage
example of usage: the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
definition: A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
editor note: This is not washing, in which case the material of interest is not the resulting fluid
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

sequencing assay
type: Class
subclass of: omics data generation assay
subclass of: material processing
editor preferred label: sequencing assay
example of usage: The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has curation status: IAO_0000125
definition: An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
definition: the use of a chemical or biochemical means to infer the sequence of a biomaterial
editor note: has_output should be sequence of input; we don't have sequence well defined yet
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl
OBI_0001886: Sequencing Technology
OBI GSCID BRC field ID: SA4
in subset: NIAID GSCID-BRC

DNA polymerase amplification
type: Class
subclass of: enzymatic amplification
editor preferred label: DNA polymerase amplification
example of usage: The use of taq polymerase to amplify a DNA fragment during a PCR.
has curation status: IAO_0000120
definition: DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input
definition editor: PERSON:Kevin Clancy
definition editor: Philippe Rocca-Serra
definition source: OBI branch derived

dialysis
type: Class
subclass of: material component separation
editor preferred label: dialysis
example of usage: the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
definition: a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
definition editor: PERSON:Kevin Clancy
definition source: OBI branch derived

enzymatic DNA replication
type: Class
subclass of: enzymatic amplification
editor preferred label: enzymatic DNA replication
example of usage: the use of enzymes to duplicate DNA molecules
has curation status: IAO_0000125
definition: the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial
definition editor: PERSON:Kevin Clancy
definition source: OBI branch derived

enzymatic amplification
type: Class
subclass of: material processing
editor preferred label: enzymatic amplification
example of usage: the use of a polymerase chain reaction to amplify a fragment of DNA
has curation status: IAO_0000125
definition: the use of enzymes to increase the number of molecules of a biomaterial
definition editor: PERSON:Kevin Clancy
definition source: OBI branch derived

RNA extraction
type: Class
subclass of: nucleic acid extraction
editor preferred label: RNA extraction
has curation status: IAO_0000125
definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO

nucleic acid extraction
type: Class
subclass of: extraction
editor preferred label: nucleic acid extraction
example of usage: Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
has curation status: IAO_0000125
definition: a material separation to recover the nucleic acid fraction of an input material
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO. Could be defined class

donor
type: Class
subclass of: role
editor preferred label: donor
example of usage: A T cell line from a PPD(+) donor.
has curation status: IAO_0000120
definition: 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.
definition editor: IEDB
alternative term: donor role
definition source: IEDB
curator note: Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.

blood harvesting
type: Class
subclass of: material component separation
editor preferred label: blood harvesting
has curation status: IAO_0000123
definition: A material separation where blood is taken from an organism.
definition editor: IEDB
definition source: IEDB

target of material addition
type: Class
subclass of: material entity
editor preferred label: target of material addition
example of usage: A cell culture into which a mixture of peptides is being added.
definition: A material entity into which another is being added in a material combinatino process
editor note: 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
definition source: IEDB

RNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of RNA molecule
definition: A sequence data that is about the primary structure of RNA.
definition editor: ITPPR
definition source: ITPPR
imported from: webService.owl

clinical history
type: Class
subclass of: history
editor preferred label: clinical history
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
imported from: ogms.owl

phenotype
type: Class
subclass of: quality
editor preferred label: phenotype
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
imported from: ogms.owl

disease
type: Class
subclass of: disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
imported from: ogms.owl

disorder
type: Class
subclass of: material entity
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
imported from: ogms.owl

biobank
type: Class
subclass of: object aggregate
subclass of: Restriction
  on property: has part
  some values from: measurement datum
subclass of: Restriction
  on property: has part
  some values from: specimen
definition: A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data.
definition editor: Mathias Brochhausen
definition source: definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf

biobank proper name
type: Class
subclass of: identifier
definition: An identifier in natural language referring to a biobank.
definition editor: Mathias Brochhausen
alternative term: Name of biobank

ISO 3166-1 alpha-2 code
type: Class
subclass of: identifier
definition: An identifier that consists of two letters, is part of the ISO 3166-1, and designates countries, dependent territories, and special areas of geographical interest.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2
comment: Two-letter country codes defined in ISO 3166-1, part of the ISO 3166 standard published by the International Organization for Standardization (ISO), to designate countries, dependent territories, and special areas of geographical interest.

biobank idenfier with ISO 3166-1 alpha-2 code
type: Class
subclass of: biobank proper name
definition: A biobank identifier that has an ISO 3166-1 alpha-2 code as a part.
definition editor: Mathias Brochhausen
alternative term: Biobank ID
comment: Textual string of letters starting with the country code (according to standard ISO1366 alpha2) followed by the underscore “_” and post-fixed by a biobank ID or name specified by its juristic person (nationally specific).

ISO 3166-1 alpha-2 code for sample collection or study contact
type: Class
subclass of: ISO 3166-1 alpha-2 code
definition: The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address.
definition editor: Mathias Brochhausen
alternative term: Sample Collection/Study contact country

contact role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: inheres in
  all values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: is member of organization
      some values from: organization
definition: A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process.
definition editor: Mathias Brochhausen

name of biobank contact person
type: Class
subclass of: personal name
definition: A personal name that designates the person acting as contact for a sample collection or a study.
definition editor: Mathias Brochhausen
alternative term: Biobank contact person

post-office box
type: Class
subclass of: organization
definition: A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Post-office_box

ISO 3166-1 alpha-2 code for biobank contact person
type: Class
subclass of: ISO 3166-1 alpha-2 code
definition: The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address.
definition editor: Mathias Brochhausen
alternative term: Biobank country code

study proper name
type: Class
subclass of: identifier
definition: A proper name that designates a study.
definition editor: Mathias Brochhausen
alternative term: Study name

name of sample collection responsible or principal investigator
type: Class
subclass of: personal name
definition: A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study.
definition editor: Mathias Brochhausen
alternative term: Sample Collection Responsible / Principal Investigator

name of sample collection or study contact person
type: Class
subclass of: personal name
definition: A personal name that designates the person acting as contact for a sample collection or a study.
definition editor: Mathias Brochhausen
alternative term: Sample Collection/Study contact person

biobank location ISO 3166-1 alpha-2 code
type: Class
subclass of: ISO 3166-1 alpha-2 code
definition: An ISO 3166-1 alpha-2 code that designates the country a biobank is located in.
definition editor: Mathias Brochhausen
alternative term: Biobank country code

CTEP organization identifier
type: Class
subclass of: identifier
definition: An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program.
definition editor: Mathias Brochhausen

biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
type: Class
subclass of: biobank idenfier with ISO 3166-1 alpha-2 code
definition: A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code.
definition editor: Mathias Brochhausen

fixed tissue specimen
type: Class
subclass of: processed specimen
editor preferred label: fixed tissue specimen
definition: A processed specimen that is the output of a fixation process.
definition editor: Alice Nzinga
definition editor: Mathias Brochhausen
imported from: omiabis.owl

fixed tissue block specimen
type: Class
subclass of: fixed tissue specimen
definition: A fixed tissue specimen that is in block form.

fixed tissue slide specimen
type: Class
subclass of: fixed tissue specimen
editor preferred label: fixed tissue slide specimen
definition: A fixed tissue specimen that is placed in a slide.
imported from: omiabis.owl

microdissected specimen
type: Class
subclass of: specimen
definition: A specimen that has been procured from a histology slide under direct microscopic visualization.
definition editor: Alice Nzinga
definition source: http://www.ncbi.nlm.nih.gov/pubmed/11269646

biobank contact role
type: Class
subclass of: contact role
definition: A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.
definition: A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study.

sample collection or study contact role
type: Class
subclass of: contact role

fixation
type: Class
subclass of: material processing
definition: A material processing that uses chemical process by which biological tissues are preserved from decay. Fixation terminates any ongoing biochemical reactions and may increase stability of the treated tissues.
definition source: http://en.wikipedia.org/wiki/Fixation_%28histology%29
definition source: http://sharedresources.fhcrc.org/training/tips-about-fixation-and-formalin
comment: The choice of fixation depends on the type of study.

specimen meeting specification
type: Class
subclass of: specimen
definition editor: Mathias Brochhausen
alternative term: adherance to specification
definition source: All specimens that meet the set parameters to be procured on.

specimen preparation contact
type: Class
subclass of: personal name
definition: A personal name that designates the person who prepared the specimen.
definition editor: Alice Nzinga

time in formalin measurement
type: Class
subclass of: time measurement datum
example of usage: 15min
definition: A time measurement datum that states the duration during which a specimen was submerged in formalin.
definition editor: Alice Nzinga

case ID
type: Class
subclass of: identifier
definition: An identifier that refers to a specimen donor who is participating in specimen collection process for tissue procurement purposes and is usually assigned at the time of donor procurement.
definition editor: Alice Nzinga
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf

normal specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: disorder
subclass of: specimen
definition: A specimen that is normal.

specimen donor
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: bearer of
    some values from: Class
      intersection of: role
      intersection of: Restriction
        on property: realized in
        some values from: specimen collection process
subclass of: Homo sapiens
definition editor: Alice Nzinga
definition editor: Mathias Brochhausen
alternative term: sample donor
comment: A Homo sapiens who contributes specimen.

sample handling
type: Class
subclass of: planned process
definition: A planned process of preparing and submitting specimens to storage.
alternative term: specimen handling
definition source: http://www.exchangenetwork.net/standards/SampleHandling_01_06_2006_Final.pdf

DNA Fragmentation
type: Class
subclass of: material processing
definition: DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously

human health care role
type: Class
subclass of: role in human social processes
definition: A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
definition editor: William R. Hogan
alternative term: health care role
imported from: omrse.owl
comment: Mathias Brochhausen

health care provider role
type: Class
subclass of: human health care role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: organization
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      union of: Homo sapiens
      union of: organization
definition: A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
definition editor: Mathias Brochhausen
imported from: omrse.owl
comment: William R. Hogan

role in human social processes
type: Class
subclass of: role
definition: A role inhering in an entity realized by social interactions in human society.
definition editor: Mathias Brochhausen
imported from: omrse.owl
comment: Previous definition: A role played by an entity in human social processes.

legal person role
type: Class
subclass of: role in human social processes
definition: A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
definition editor: Mathias Brochhausen
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
imported from: omrse.owl
comment: We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.

age
type: Class
subclass of: physical quality
subclass of: quality of a single physical entity
editor preferred label: age
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: pato.owl

biological sex
type: Class
subclass of: quality
subclass of: organismal quality
editor preferred label: biological sex
definition: 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.
definition: 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.
definition: 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.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
imported from: pato.owl
MSH definition citation: MSH:D012723
NCI thesaurus definition citation: NCIt:C28421
PATO definition citation: PATO:0000047
has_obo_namespace: quality
id: PATO:0000047
in subset: attribute slim
label: sex

Axiom
annotated source: biological sex
annotated property: definition
annotated target: 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.
has db xref: MGED:MGED

length
type: Class
subclass of: quality
editor preferred label: length
definition: A 1-D extent quality which is equal to the distance between two points.
imported from: pato.owl

mass
type: Class
subclass of: quality
editor preferred label: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: pato.owl

weight
type: Class
subclass of: physical quality
definition: A physical quality inhering in a bearer that has mass near a gravitational body.
imported from: pato.owl

position
type: Class
subclass of: physical quality
definition: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
imported from: pato.owl

temperature
type: Class
subclass of: physical quality
subclass of: quality of a single physical entity
editor preferred label: temperature
definition: A physical quality of the thermal energy of a system.
imported from: pato.owl
in subset: attribute slim
in subset: scalar slim
comment: Damion's Note: Future use might prefer: CMO_0000015 body temperature.

female
type: Class
subclass of: biological sex
subclass of: phenotypic sex
editor preferred label: female
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
imported from: pato.owl
MSH definition citation: MSH:D005260
NCI thesaurus definition citation: NCIt:C16576
PATO definition citation: PATO:0000383
SNOMEDCT definition citation: SNOMEDCT:248152002
has_obo_namespace: quality
id: PATO:0000383
in subset: mpath slim
in subset: value slim

Axiom
annotated source: female
annotated property: definition
annotated target: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
has db xref: MGED:MGED

male
type: Class
subclass of: biological sex
subclass of: phenotypic sex
editor preferred label: male
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
imported from: pato.owl
MSH definition citation: MSH:D008297
NCI thesaurus definition citation: NCIt:C20197
PATO definition citation: PATO:0000384
SNOMEDCT definition citation: SNOMEDCT:248153007
has_obo_namespace: quality
id: PATO:0000384
in subset: mpath slim
in subset: value slim

Axiom
annotated source: male
annotated property: definition
annotated target: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
has db xref: MGED:MGED

volume
type: Class
subclass of: quality of a single physical entity
editor preferred label: volume
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
imported from: pato.owl

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
imported from: hp.owl
imported from: pato.owl
has alternative id: PATO:0002079
has db xref: Wikipedia:Physical_property
has exact synonym: relational physical quality
in subset: attribute slim

quality of a single physical entity
type: Class
subclass of: quality
editor preferred label: quality of a single physical entity
definition: A physical object quality which inheres in a single-bearer.
imported from: pato.owl

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
imported from: pato.owl
has alternative id: PATO:0001237
has alternative id: PATO:0001238
has db xref: snap:Quality
has exact synonym: monadic quality of a continuant
has exact synonym: multiply inhering quality of a physical entity
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

Axiom
annotated source: physical object quality
annotated property: definition
annotated target: A quality which inheres in a continuant.
has db xref: PATOC:GVG

hermaphrodite
type: Class
subclass of: biological sex
subclass of: phenotypic sex
editor preferred label: hermaphrodite
definition: A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
definition: An organism having both male and female sexual characteristics and organs.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
imported from: pato.owl
DOID definition citation: DOID:3763
NCI thesaurus definition citation: NCIt:C45909
PATO definition citation: PATO:0001340
SNOMEDCT definition citation: SNOMEDCT:237821001
has exact synonym: intersex
has_obo_namespace: quality
id: PATO:0001340
in subset: value slim

Axiom
annotated source: hermaphrodite
annotated property: definition
annotated target: A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
has db xref: MGED:MGED

pseudohermaphrodite
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex.
has_obo_namespace: quality
id: PATO:0001827
in subset: value slim

Axiom
annotated source: pseudohermaphrodite
annotated property: definition
annotated target: A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex.
has db xref: WordNet:WordNet

phenotypic sex
type: Class
subclass of: biological sex
definition: An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
has_obo_namespace: quality
id: PATO:0001894
in subset: attribute slim

frozen
type: Class
subclass of: specimen shipping temperature
subclass of: temperature
editor preferred label: frozen
definition: A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
imported from: pato.owl

organismal quality
type: Class
subclass of: physical object quality
editor preferred label: organismal quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001995

Axiom
annotated source: organismal quality
annotated property: definition
annotated target: A quality that inheres in an entire organism or part of an organism.
has db xref: PATOC:CJM

humidity
type: Class
subclass of: temperature
definition: A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content.
imported from: pato.owl

meristematic cell
type: Class
subclass of: native plant cell
definition: A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.

Axiom
annotated source: meristematic cell
annotated property: definition
annotated target: A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: meristematic cell
annotated property: label
annotated target: meristematic cell
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

sporocyte
type: Class
subclass of: native plant cell
definition: A native plant cell (PO:0025606) which is diploid (2n), and undergoes meiosis (GO:0007126) to produce four haploid (1n) plant spores (PO:0025017).

Axiom
annotated source: sporocyte
annotated property: definition
annotated target: A native plant cell (PO:0025606) which is diploid (2n), and undergoes meiosis (GO:0007126) to produce four haploid (1n) plant spores (PO:0025017).
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: sporocyte
annotated property: label
annotated target: sporocyte
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

plant cell
type: Class
subclass of: cell type
definition: A cell which is a plant structure (PO:0009011).
definition editor: Sirarat Sarntivijai
comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.

microgametophyte vegetative cell
type: Class
subclass of: native plant cell
definition: A native plant cell (PO:0025606) that is the larger cell of a microgametophyte (PO:0025280) in seed plants. It does not divide further and develops into a pollen tube cell (PO:0025195).

Axiom
annotated source: microgametophyte vegetative cell
annotated property: definition
annotated target: A native plant cell (PO:0025606) that is the larger cell of a microgametophyte (PO:0025280) in seed plants. It does not divide further and develops into a pollen tube cell (PO:0025195).
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: microgametophyte vegetative cell
annotated property: label
annotated target: microgametophyte vegetative cell
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

columella root cap cell
type: Class
subclass of: native plant cell
definition: Cell that constitutes the central part of the root cap, arranged in longitudinal files.

Axiom
annotated source: columella root cap cell
annotated property: definition
annotated target: Cell that constitutes the central part of the root cap, arranged in longitudinal files.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: columella root cap cell
annotated property: label
annotated target: columella root cap cell
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

native plant cell
type: Class
subclass of: plant cell
definition: A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
comment: A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).

Axiom
annotated source: native plant cell
annotated property: definition
annotated target: A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: native plant cell
annotated property: comment
annotated target: A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: native plant cell
annotated property: label
annotated target: native plant cell
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

meristematic apical cell
type: Class
subclass of: meristematic cell
definition: A single meristematic cell (PO:0004010) at the tip of a plant structure where apical growth occurs.
comment: Apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex, or protonema in bryophytes and some pteridophytes. Apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. The apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped (lenticular) with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo, or later.

Axiom
annotated source: meristematic apical cell
annotated property: definition
annotated target: A single meristematic cell (PO:0004010) at the tip of a plant structure where apical growth occurs.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: meristematic apical cell
annotated property: comment
annotated target: Apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex, or protonema in bryophytes and some pteridophytes. Apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. The apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped (lenticular) with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo, or later.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: meristematic apical cell
annotated property: label
annotated target: meristematic apical cell
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

gametophyte meristematic apical cell
type: Class
subclass of: meristematic apical cell
definition: An apical cell that is part of a whole plant in the gametophytic phase.
comment: Occurs bryophytes and pteridophytes.

Axiom
annotated source: gametophyte meristematic apical cell
annotated property: definition
annotated target: An apical cell that is part of a whole plant in the gametophytic phase.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: gametophyte meristematic apical cell
annotated property: comment
annotated target: Occurs bryophytes and pteridophytes.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: gametophyte meristematic apical cell
annotated property: label
annotated target: gametophyte meristematic apical cell
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

sporophyte meristematic apical cell
type: Class
subclass of: meristematic apical cell
definition: A meristematic apical cell that is part of a whole plant in the sporophytic phase.
comment: Occurs in pteridophytes and the sporophyte of bryophytes.

Axiom
annotated source: sporophyte meristematic apical cell
annotated property: definition
annotated target: A meristematic apical cell that is part of a whole plant in the sporophytic phase.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: sporophyte meristematic apical cell
annotated property: comment
annotated target: Occurs in pteridophytes and the sporophyte of bryophytes.
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

Axiom
annotated source: sporophyte meristematic apical cell
annotated property: label
annotated target: sporophyte meristematic apical cell
created by: http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern

molecular label role
type: Class
subclass of: role
editor preferred label: molecular label role
definition: a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
editor note: MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
alternative term: molecular tracer role
definition source: OBI developer call, 3-12-12
imported from: reo.owl

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: 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.
alternative term: primary structure of sequence macromolecule
alternative term: sequence
imported from: so.owl

polypeptide
type: Class
subclass of: region
editor preferred label: polypeptide
definition: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
alternative term: polypeptide sequence
imported from: so.owl

supercontig
type: Class
subclass of: sequence_assembly
editor preferred label: supercontig
definition: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
imported from: so.owl

contig
type: Class
subclass of: sequence_assembly
editor preferred label: contig
definition: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
imported from: so.owl

miRNA
type: Class
subclass of: region
editor preferred label: miRNA
definition: Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
imported from: so.owl

sequence_assembly
type: Class
subclass of: assembly
editor preferred label: sequence_assembly
definition: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
imported from: so.owl

assembly
type: Class
subclass of: region
editor preferred label: assembly
definition: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
imported from: so.owl

endocrine pancreas
type: Class
subclass of: secretory cell
definition: A pancreatic cell that produces and secretes hormones such as insulin and glucagon.
definition: An Islet cell is a pancreatic cell that produces and secretes hormones such as insulin and glucagon.
definition: The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO].
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C32885
SNOMEDCT definition citation: SNOMEDCT:360555004
SNOMEDCT definition citation: SNOMEDCT:361339003
TAO definition citation: TAO:0001260
ZFA definition citation: ZFA:0001260
has_obo_namespace: uberon
id: UBERON:0000016
in subset: efo slim
in subset: organ slim
in subset: uberon slim
in subset: vertebrate core
comment: Editor notes - endocrine and exocrine pancrease are not co-associated in hagfishes or lampreys [PMID:20959416] - create a separate class for these?

Axiom
annotated source: endocrine pancreas
annotated property: definition
annotated target: The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO].
has db xref: GOC:GO
has db xref: Wikipedia:Islets_of_Langerhans

peripheral blood mononuclear cell isolation
type: Class
subclass of: cell collecting
definition: A cell collecting process used to isolate PBMCs, including T cells, from whole blood using density gradient centrifugation (e.g., Ficoll-Paque).
has synonym: PBMC Separation

object quality
type: Class
subclass of: quality

language entity
type: Class
subclass of: information content entity
subset: nlp+

visual language entity
type: Class
subclass of: language entity

identifier
type: Class
subclass of: symbol
subclass of: label

name
type: Class
subclass of: label

brand name
type: Class
subclass of: name

scientific name
type: Class
subclass of: name

description
type: Class
subclass of: language entity

label
type: Class
subclass of: textual entity

first name
type: Class
subclass of: name

last name
type: Class
subclass of: name

personal name
type: Class
subclass of: name

legal name
type: Class
subclass of: personal name

textual entity
type: Class
subclass of: visual language entity

version label
type: Class
subclass of: identifier

unique identifier
type: Class
subclass of: identifier

answer
type: Class
subclass of: description

URL
type: Class
subclass of: centrally registered identifier symbol
definition: A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource.
imported from: sio.owl

numeric label
type: Class
subclass of: label

study design
type: Class
subclass of: document

annotation
type: Class
subclass of: description

history
type: Class
subclass of: description

gene symbol
type: Class
subclass of: scientific name
description: a gene symbol is a short name assigned to a gene.

evolutionary lineage
type: Class
subclass of: history

family history
type: Class
subclass of: history

medical history
type: Class
subclass of: history

Kaposi's sarcoma cell
type: Class
subclass of: disease cell type
definition: A malignant neoplasm characterized by a vascular proliferation which usually contains blunt endothelial cells. Erythrocyte extravasation and hemosiderin deposition are frequently present. The most frequent site of involvement is the skin; however it may also occur internally. It generally develops in people with compromised immune systems including those with acquired immune deficiency syndrome (AIDS).
definition: A multicentric, malignant neoplastic vascular proliferation characterized by bluish-red cutaneous nodules, usually on the legs, toes, or feet, that slowly increase in size and number and spread to more proximal sites. The tumors have endothelium-lined channels and vascular spaces mixed with aggregates of spindle-shaped cells; they may remain confined to skin and subcutaneous tissue, but widespread visceral involvement may occur.
definition editor: James Malone
definition editor: Tomasz Adamusiak
OMIM definition citation: OMIM:148000

cell type
type: Class
subclass of: material entity
example of usage: epithelial, glial.
definition: A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak

lymphoblast
type: Class
subclass of: cell type
definition: An immature lymphocyte that has enlarged in response to antigenic stimulation.
definition: Often referred to as a blast cell. Unlike other usages of the suffix -blast a lymphoblast is a further differentiation of a lymphocyte, T- or B-, occasioned by an antigenic stimulus. The lymphoblast usually develops by enlargement of a lymphocyte, active re-entry to the S phase of the cell cycle, mitogenesis and production of much m-RNA and ribosomes.
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C13013
SNOMEDCT definition citation: SNOMEDCT:15433008

mesenchymal stem cell
type: Class
subclass of: stem cell
definition editor: James Malone
NCI thesaurus definition citation: NCIt:C43423
SNOMEDCT definition citation: SNOMEDCT:418124002

integumental cell
type: Class
subclass of: cell type
definition: Cell coming from the intergument, organ that constitutes the external surface of the body. The intergument consists of the epidermis, dermis, and skin appendages.
definition editor: James Malone

cumulus-oocyte complex
type: Class
subclass of: cell type
definition editor: Tomasz Adamusiak
definition citation: http://en.wikipedia.org/wiki/Ovulation

mesophyll cell
type: Class
subclass of: cell type
definition editor: Tomasz Adamusiak
PO definition citation: PO:0004006

HUVEC cell
type: Class
subclass of: endothelial cell
definition: A convenient source of human endothelial cells are those that line the large vein in the umbilical cord which is usually discarded together with the placenta after childbirth. The cells can be removed as a fairly pure suspension by mild enzymatic treatment of the vein followed by some mechanical distraction and will grow relatively easily in culture, retaining their differentiated characteristics for several passages.
definition editor: Tomasz Adamusiak

fetal blood cell
type: Class
subclass of: blood cell
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
MSH definition citation: MSH:D005312

nestin positive islet-derived progenitor cell
type: Class
subclass of: cell type
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
PMID definition citation: PMID: 11246871

large adipocyte
type: Class
subclass of: fat cell
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak

small adipocyte
type: Class
subclass of: fat cell
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak

dendritic cell-derived intermediate cell
type: Class
subclass of: cell type
subclass of: Restriction
  on property: derives from
  some values from: dendritic cell

dendritic cell-derived osteoclast
type: Class
subclass of: cell type
subclass of: Restriction
  on property: derives from
  some values from: dendritic cell

monocyte-derived intermediate cell
type: Class
subclass of: cell type

monocyte-derived osteoclast
type: Class
subclass of: cell type

reproductive system cell
type: Class
subclass of: cell type

musculo-skeletal system cell
type: Class
subclass of: cell type

experimental cell
type: Class
subclass of: cell type
definition: experimental cell is a cell which is experimentally derived such as a cell line cell, or a cell differentiated in culture. Experimentally derived cells may have diffrent properties from the cell from which they originally derived, such as through gene expression changes.
definition editor: Helen Parkinson

animal reproductive system cell
type: Class
subclass of: cell type

nervous system cell
type: Class
subclass of: cell type

pancreatic cell
type: Class
subclass of: cell type

embryonic stem cell derived neuronal stem cell
type: Class
subclass of: stem cell
definition: neural stem cells experimentally derived from ES cells

clear cell
type: Class
subclass of: cell type
definition: A cell with empty-appearing cytoplasm when viewed with a light microscope.
definition editor: Tomasz Adamusiak
NCI thesaurus definition citation: NCIt:C12478

thyrocyte
type: Class
subclass of: epithelial cell
definition: An epithelial cell lining the thyroid follicle.
definition editor: Tomasz Adamusiak

risk factor
type: Class
subclass of: disposition
definition: An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.
definition: Any aspect of an individual's life, behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a disease, condition or injury.
alternative term: Factor, Risk
alternative term: Factors, Risk
alternative term: Risk Factors
imported from: efo.owl

mouse erythroleukemia cell
type: Class
subclass of: cell type

mouse embryonic stem cell
type: Class
subclass of: cell type
definition: mouse embryonic stem cell
definition citation: Mikkelsen et al. (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560

mouse neural progenitor cell
type: Class
subclass of: cell type

mouse embryonic fibroblast cell
type: Class
subclass of: fibroblast
definition: Mouse embryonic fibroblast cell
definition editor: James Malone

induced pluripotent stem cell
type: Class
subclass of: pluripotent stem cell
subclass of: experimental cell
definition: Induced pluripotent stem cells (iPS cells or iPSCs) are a type of pluripotent stem cell artificially derived from a non-pluripotent cell. Various methods exist to revert cells to pluripotency such as reprogramming mediated through a mature metaphase II oocyte as in somatic cell nuclear transfer.
definition editor: James Malone
definition editor: Sirarat Sarntivijai
comment: Submitted by Nancy Mah

date of birth
type: Class
subclass of: time measurement datum
definition: The point in time at which an individual was born.
imported from: efo.owl

date of diagnosis
type: Class
subclass of: time measurement datum
definition: The point at which a clinical diagnosis is made.
imported from: efo.owl

embryonal carcinoma cell
type: Class
subclass of: cell type
definition: A cell which bears embryonal carcinoma.
definition editor: James Malone

adipose tissue derived mesenchymal stem cell
type: Class
subclass of: mesenchymal stem cell
definition: A adult mesenchymal stem cell derived from adipose tisssue
definition editor: Helen Parkinson

placental pericyte
type: Class
subclass of: pericyte
definition: A pericyte derived from the placenta.
definition editor: Helen Parkinson

mural granulosa cell
type: Class
subclass of: granulosa cell
definition: The mural granulosa cells form during antral folliculogenesis, process in which a single antral cavity is formed, separating two functionally distinct granulosa cell populations. The mural granulosa cells line the wall of the follicle and are critical for steroidogenesis and ovulation.
definition editor: Drashtti Vasant

B-lymphoblast
type: Class
subclass of: lymphoblast

NSM
type: Class
subclass of: neuroendocrine cell
definition: Neuron class of two pharyngeal neurosecretory-motor neurons.
definition editor: Dani Welter

pharyngeal muscle cell
type: Class
subclass of: muscle cell
definition: type of cells that make up muscle layers in the pharynx in worms such as C. elegans
definition editor: Dani Welter

disease cell type
type: Class
subclass of: cell type

MSiPS
type: Class
subclass of: induced pluripotent stem cell
subclass of: Restriction
  on property: has quality
  some values from: male
definition: Induced pluripotent stem cell line from a Caucasian male with type 2 diabetes, same donor as of MSLCL cell line.
PMID definition citation: PMID:24136358

CWRU1
type: Class
subclass of: induced pluripotent stem cell
subclass of: Restriction
  on property: has quality
  some values from: male
definition: Induced pluripotent stem cells derived from MSC658 fibroblasts.
has db xref: http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab

lympoid tissue
type: Class
subclass of: cell type

utering smooth muscle cell
type: Class
subclass of: cell type

glial brain cell
type: Class
subclass of: cell type

mantle cell
type: Class
subclass of: cell type

merkel cell
type: Class
subclass of: cell type

address
type: Class
subclass of: textual entity
imported from: isf-dev.owl