Neural Electronic Interface Ontology
type: Ontology
version IRI: neio.owl
contributor: Daniel Rathbun
contributor: Alexander D. Diehl
contributor: John Beverley
contributor: Patrick Ray
contributor: Gopikrishnan M. Chandrasekharan
contributor: Jisoo Seo
contributor: Sam Smith
created: 2023-09-17
creator: Bill Duncan
description: The Neural Electronic Interface Ontology represents the types of devices used to interface with the central nervous system to enhance (or augment) stimuli from a subject's external environment, the conditions under which these devices should be employed, the assessment of a subject's sensory ability, and the metrics for evaluating the performance.
version info: 2024-06-25

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only

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
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term 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 of usage
has curation status: ready for release
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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

in branch
type: AnnotationProperty
editor preferred label: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

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

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

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: ready for release
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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred label: term editor
has curation status: ready for release
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 https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred label: alternative label
editor preferred label: alternative term
has curation status: pending final vetting
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: alternative term

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: ready for release
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
term 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
editor preferred label: ontology term requester
has curation status: pending final vetting
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term 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.

is denotator type
type: AnnotationProperty
editor preferred label: is denotator type
definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term 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.org/obo/owl/GO#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
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred label: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred label: first order logic expression
term editor: PERSON:Alan Ruttenberg

antisymmetric property
type: AnnotationProperty
editor preferred label: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg
sub property of: logical characteristic of object property

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: pending final vetting
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 .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has ID digit count
type: AnnotationProperty
editor preferred label: has ID digit count
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
editor preferred label: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
editor preferred label: has ID policy for
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
editor preferred label: has ID prefix
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

elucidation
type: AnnotationProperty
editor preferred label: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred label: is allocated id range
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

has ontology root term
type: AnnotationProperty
editor preferred label: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred label: may be identical to
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
editor preferred label: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred label: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

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

logical characteristic of object property
type: AnnotationProperty
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call
created by: http://orcid.org/0000-0001-5208-3432

defined by construct
type: AnnotationProperty
example of usage: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8688-6599

abbreviation
type: AnnotationProperty
example of usage: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
definition: A synonym type for describing abbreviations or initalisms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

ambiguous synonym
type: AnnotationProperty
definition: A synonym type for describing ambiguous synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

dubious synonym
type: AnnotationProperty
definition: A synonym type for describing dubious synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

layperson synonym
type: AnnotationProperty
example of usage: EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
definition: A synonym type for describing layperson or colloquial synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

plural form
type: AnnotationProperty
example of usage: CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
definition: A synonym type for describing pluralization synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

UK spelling synonym
type: AnnotationProperty
example of usage: CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
definition: A synonym type for describing UK spelling variants
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

misspelling
type: AnnotationProperty
definition: A synonym type for common misspellings
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/132
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

misnomer
type: AnnotationProperty
definition: A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/133
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymType

previous name
type: AnnotationProperty
example of usage: MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
definition: A synonym type for names that have been used as primary labels in the past.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/139
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-07-25
sub property of: SynonymType

legal name
type: AnnotationProperty
example of usage: The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
definition: A synonym type for the legal entity name
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/141
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-07-27
sub property of: SynonymType

International Nonproprietary Name
type: AnnotationProperty
example of usage: CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
definition: The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/149
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-09-30
sub property of: SynonymType

latin term
type: AnnotationProperty
example of usage: nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
definition: A synonym type for describing Latin term synonyms.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/146
contributor: https://orcid.org/0000-0002-1773-2692
created: 2023-10-12
sub property of: SynonymType

has broad synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
sub property of: alternative label

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
sub property of: alternative label

has narrow synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
sub property of: alternative label

has related synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
sub property of: alternative label

label
type: AnnotationProperty
editor preferred label: label

implant location
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T00:59:42Z

implant processor location
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:00:24Z

electrode layout
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:00:54Z

electrode pitch
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:01:12Z

electrode diameter
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:01:33Z

clinical trial
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:02:09Z

first patient year
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:02:55Z

FDA approval year
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:03:11Z

end of product year
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:03:36Z

ce mark year
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:03:45Z

implant type
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T01:06:27Z

electrode number
type: AnnotationProperty
contributor: Bill Duncan
created: 2024-06-25T03:05:36Z

part of
type: ObjectProperty
sub property of: overlaps
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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 label: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable entity
RO_0040042: BFO_0000019
RO_0040042: specifically dependent continuant
RO_0040042: generically dependent continuant
has db xref: BFO:0000050
has OBO namespace: quality
has OBO namespace: spatial
has OBO namespace: uberon
id: part_of
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam
shorthand: part_of
label: part_of

has part
type: ObjectProperty
sub property of: overlaps
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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 label: has_part
RO_0001900: RO_0001901
has db xref: BFO:0000051
has OBO namespace: quality
has OBO namespace: spatial
has OBO namespace: uberon
id: has_part
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_part
label: has_part

is_manufactured_by
type: ObjectProperty
sub property of: topObjectProperty
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)
has curation status: metadata incomplete
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.
term editor: Alan Ruttenberg
term editor: Liju Fan
alternative label: has_make
alternative label: has_manufacturer

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: bearer_of
type: FunctionalProperty
editor preferred label: inheres in
example of usage: this fragility is a characteristic of this vase
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
alternative label: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

bearer_of
type: ObjectProperty
type: InverseFunctionalProperty
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: Inverse of characteristic_of
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 label: bearer_of
alternative label: is bearer of
RO_0001900: RO_0001901
label: has characteristic

has function
type: ObjectProperty
sub property of: bearer_of
domain: independent continuant
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 label: has_function

has quality
type: ObjectProperty
sub property of: bearer_of
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 label: has_quality

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 label: has_role

has disposition
type: ObjectProperty
sub property of: bearer_of
domain: independent continuant
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
definition: x overlaps y iff they have some part in common.
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
has db xref: RO:0002131
has OBO namespace: spatial
has OBO namespace: uberon
id: overlaps
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco
shorthand: overlaps
comment: "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []

Axiom
annotated source: overlaps
annotated property: definition
annotated target: x overlaps y iff they have some part in common.
has db xref: BSPO:cjm

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
has db xref: RO:0002215
has OBO namespace: uberon
id: capable_of
in subset: ro-eco
shorthand: capable_of

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function in
has db xref: RO:0002216
has OBO namespace: uberon
id: capable_of_part_of
shorthand: capable_of_part_of

characteristic of part of
type: ObjectProperty
sub property of: depends on
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901
has db xref: RO:0002323
shorthand: mereotopologically_related_to

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
term editor: https://orcid.org/0000-0002-6601-2165
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function
has db xref: RO:0002328
has OBO namespace: uberon
id: functionally_related_to
shorthand: functionally_related_to

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
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 yie…
term editor: https://orcid.org/0000-0002-6601-2165
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 db xref: RO:0002410
shorthand: causally_related_to

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
has db xref: https://en.wikipedia.org/wiki/Causality

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations
has db xref: RO:0002500
shorthand: causal_agent_in_process

depends on
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165

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.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
has db xref: RO:0002595
shorthand: causal_relation_between_material_entity_and_a_process

device commercialized by
type: ObjectProperty
example of usage: The commerical partner conducts clinic trials of the device.
example of usage: The commerical partner sets up the manufacturing workflow.
definition: A relation between a device and an organization in which the organization assists in the process of commercializing the device.
contributor: Bill Duncan
created: 2024-02-20T16:42:25Z

device origin organization
type: ObjectProperty
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:21:54Z

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
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
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

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

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
editor preferred label: continuant
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: pato.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
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: elucidation
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

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
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
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.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
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: elucidation
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

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
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
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])
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]
comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

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

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
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]
comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

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
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
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.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
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: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/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
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
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.
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
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: elucidation
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/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

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
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 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.
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: 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

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

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
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.
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/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

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
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: 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 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
BFO OWL specification label: function
BFO CLIF specification label: Function
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.
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/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

material entity
type: Class
subclass of: independent continuant
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
editor preferred label: material 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: cl.owl
imported from: ido.owl
imported from: uberon.owl
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
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: elucidation
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

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

cell
type: Class
subclass of: anatomical structure
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has db xref: CALOHA:TS-2035
has db xref: FBbt:00007002
has db xref: FMA:68646
has db xref: GO:0005623
has db xref: KUPO:0000002
has db xref: MESH:D002477
has db xref: VHOG:0001533
has db xref: WBbt:0004017
has db xref: XAO:0003012
in subset: upper level
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

Axiom
annotated source: cell
annotated property: definition
annotated target: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has db xref: CARO:mah

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

Axiom
annotated source: electrically active cell
annotated property: definition
annotated target: A cell whose function is determined by the generation or the reception of an electric signal.
has db xref: FB:ma

electrically responsive cell
type: Class
subclass of: electrically active cell
definition: A cell whose function is determined by its response to an electric signal.

Axiom
annotated source: electrically responsive cell
annotated property: definition
annotated target: A cell whose function is determined by its response to an electric signal.
has db xref: FB:ma

electrically signaling cell
type: Class
subclass of: electrically active cell
definition: A cell that initiates an electrical signal and passes that signal to another cell.

Axiom
annotated source: electrically signaling cell
annotated property: definition
annotated target: A cell that initiates an electrical signal and passes that signal to another cell.
has db xref: FB:ma

neuron
type: Class
subclass of: electrically responsive cell
subclass of: electrically signaling cell
subclass of: neural cell
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.
RO_0002175: Homo sapiens
has db xref: BTO:0000938
has db xref: CALOHA:TS-0683
has db xref: FBbt:00005106
has db xref: FMA:54527
has db xref: VHOG:0001483
has db xref: WBbt:0003679
has exact synonym: nerve cell
in subset: general cell types upper slim
in subset: human reference atlas
comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.

Axiom
annotated source: neuron
annotated property: definition
annotated target: 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.
has db xref: MESH:D009474
has db xref: http://en.wikipedia.org/wiki/Neuron

neural cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: nervous system
subclass of: cell
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: A cell that is part of the nervous system.
contributor: https://orcid.org/0000-0003-1980-3228
creation date: 2010-09-15T01:34:57Z
has db xref: CALOHA:TS-2040
has db xref: FMA:70333

Axiom
annotated source: neural cell
annotated property: definition
annotated target: A cell that is part of the nervous system.
has db xref: GOC:tfm
has db xref: ISBN:0618947256

visual system neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of part of
    some values from: visual perception
subclass of: neuron
subclass of: Restriction
  on property: capable of part of
  some values from: visual perception
contributor: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-09T19:12:36Z

compound eye retinal cell
type: Class
subclass of: retinal cell
definition: Any cell in the compound eye, a light sensing organ composed of ommatidia.
has db xref: GOC:pr
has db xref: PMID:12021768

retinal cell
type: Class
equivalent class: Class
  intersection of: neural cell
  intersection of: Restriction
    on property: part of
    some values from: photoreceptor array
subclass of: neural cell
subclass of: Restriction
  on property: part of
  some values from: photoreceptor array
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.
has db xref: PMID:10702418
in subset: general cell types upper slim

Axiom
annotated source: retinal cell
annotated property: definition
annotated target: 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.
has db xref: GOC:pr

system process
type: Class
subclass of: multicellular organismal process
definition: A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
has exact synonym: organ system process
has OBO namespace: biological_process
id: GO:0003008

Axiom
annotated source: system process
annotated property: definition
annotated target: A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
has db xref: GOC:mtg_cardio

sensory perception
type: Class
subclass of: nervous system process
definition: The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
has db xref: Wikipedia:Perception
has OBO namespace: biological_process
id: GO:0007600
in subset: goslim drosophila

Axiom
annotated source: sensory perception
annotated property: definition
annotated target: The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
has db xref: GOC:ai
has db xref: GOC:dph

visual perception
type: Class
subclass of: sensory perception of light stimulus
definition: The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
has db xref: Wikipedia:Visual_perception
has exact synonym: sense of sight
has exact synonym: sensory visual perception
has exact synonym: vision
has OBO namespace: biological_process
id: GO:0007601

Axiom
annotated source: visual perception
annotated property: definition
annotated target: The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
has db xref: GOC:ai

biological_process
type: Class
subclass of: process
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
term tracker item: https://github.com/geneontology/go-ontology/issues/24968
created by: jl
creation date: 2012-09-19T15:05:24Z
has alternative id: GO:0000004
has alternative id: GO:0007582
has alternative id: GO:0044699
has db xref: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has OBO namespace: biological_process
has related synonym: single organism process
has related synonym: single-organism process
id: GO:0008150
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim pombe
in subset: goslim yeast
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
has db xref: GOC:pdt

response to radiation
type: Class
subclass of: response to abiotic stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
has exact synonym: response to electromagnetic radiation stimulus
has exact synonym: response to radiation stimulus
has OBO namespace: biological_process
id: GO:0009314
comment: Note that 'radiation' refers to electromagnetic radiation of any wavelength.

Axiom
annotated source: response to radiation
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
has db xref: GOC:jl
has db xref: Wikipedia:Electromagnetic_radiation

response to light stimulus
type: Class
subclass of: response to radiation
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
has OBO namespace: biological_process
id: GO:0009416
in subset: goslim plant

Axiom
annotated source: response to light stimulus
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
has db xref: GOC:go_curators
has db xref: ISBN:0582227089

detection of external stimulus
type: Class
subclass of: response to external stimulus
subclass of: detection of stimulus
definition: The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
has OBO namespace: biological_process
has related synonym: perception of external stimulus
id: GO:0009581

Axiom
annotated source: detection of external stimulus
annotated property: definition
annotated target: The series of events in which an external stimulus is received by a cell and converted into a molecular signal.
has db xref: GOC:hb

detection of abiotic stimulus
type: Class
subclass of: response to abiotic stimulus
subclass of: detection of stimulus
definition: The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
has OBO namespace: biological_process
has related synonym: perception of abiotic stimulus
id: GO:0009582

Axiom
annotated source: detection of abiotic stimulus
annotated property: definition
annotated target: The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal.
has db xref: GOC:hb

detection of light stimulus
type: Class
subclass of: response to light stimulus
subclass of: detection of external stimulus
subclass of: detection of abiotic stimulus
definition: The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal.
has exact synonym: detection of light
has OBO namespace: biological_process
has related synonym: perception of light
id: GO:0009583

Axiom
annotated source: detection of light stimulus
annotated property: definition
annotated target: The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal.
has db xref: GOC:go_curators

detection of visible light
type: Class
subclass of: detection of light stimulus
definition: The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
has OBO namespace: biological_process
has related synonym: perception of visible light
id: GO:0009584

Axiom
annotated source: detection of visible light
annotated property: definition
annotated target: The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
has db xref: GOC:go_curators
has db xref: ISBN:0198506732

response to external stimulus
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
has exact synonym: response to environmental stimulus
has OBO namespace: biological_process
id: GO:0009605
in subset: gocheck do not manually annotate
in subset: goslim drosophila
in subset: goslim plant
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: response to external stimulus
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
has db xref: GOC:hb

response to abiotic stimulus
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
term tracker item: https://github.com/geneontology/go-ontology/issues/16572
has narrow synonym: response to abiotic stress
has OBO namespace: biological_process
id: GO:0009628
in subset: gocheck do not manually annotate
in subset: goslim metagenomics
in subset: goslim plant
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: response to abiotic stimulus
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
has db xref: GOC:hb

multicellular organismal process
type: Class
subclass of: biological_process
definition: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
RO_0002161: NCBITaxon 2
RO_0002161: NCBITaxon 2157
RO_0002161: NCBITaxon 4896
RO_0002161: NCBITaxon 4932
created by: jl
creation date: 2012-09-19T16:07:47Z
has alternative id: GO:0044707
has alternative id: GO:0050874
has exact synonym: organismal physiological process
has OBO namespace: biological_process
has related synonym: single-multicellular organism process
id: GO:0032501
in subset: gocheck do not annotate
in subset: goslim pir

Axiom
annotated source: multicellular organismal process
annotated property: definition
annotated target: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
has db xref: GOC:curators
has db xref: GOC:dph
has db xref: GOC:isa_complete
has db xref: GOC:tb

nervous system process
type: Class
subclass of: system process
definition: A organ system process carried out by any of the organs or tissues of neurological system.
term tracker item: https://github.com/geneontology/go-ontology/issues/13824
has exact synonym: neurological system process
has exact synonym: neurophysiological process
has OBO namespace: biological_process
has related synonym: pan-neural process
id: GO:0050877
in subset: goslim agr
in subset: goslim chembl
in subset: goslim flybase ribbon
in subset: goslim generic
in subset: goslim pir

Axiom
annotated source: nervous system process
annotated property: definition
annotated target: A organ system process carried out by any of the organs or tissues of neurological system.
has db xref: GOC:ai
has db xref: GOC:mtg_cardio

response to stimulus
type: Class
subclass of: biological_process
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
has alternative id: GO:0051869
has exact synonym: physiological response to stimulus
has OBO namespace: biological_process
id: GO:0050896
in subset: gocheck do not manually annotate
in subset: goslim agr
in subset: goslim flybase ribbon
in subset: goslim mouse
in subset: goslim pir
in subset: prokaryote subset
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: response to stimulus
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
has db xref: GOC:ai
has db xref: GOC:bf

sensory perception of light stimulus
type: Class
subclass of: sensory perception
definition: The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
has OBO namespace: biological_process
id: GO:0050953

Axiom
annotated source: sensory perception of light stimulus
annotated property: definition
annotated target: The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
has db xref: GOC:ai

detection of stimulus
type: Class
subclass of: response to stimulus
definition: The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
has exact synonym: stimulus detection
has OBO namespace: biological_process
has related synonym: perception of stimulus
has related synonym: stimulus sensing
id: GO:0051606
in subset: goslim pir

Axiom
annotated source: detection of stimulus
annotated property: definition
annotated target: The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
has db xref: GOC:add
has db xref: GOC:ai
has db xref: GOC:dph
has db xref: GOC:mah

data item
type: Class
subclass of: information content entity
editor preferred label: data item
definition: 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.
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred label: information content entity
definition: A generically dependent continuant that is about some thing.
imported from: iao.owl

infectious disorder
type: Class
subclass of: disorder
definition: An infection that is clinically abnormal.
imported from: ido.owl

infection
type: Class
subclass of: material entity
definition: A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
imported from: ido.owl

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

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
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

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: ready for release
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.
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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

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.
has curation status: ready for release
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…
term editor: PERSON: Helen Parkinson
alternative label: instrument
definition source: OBI development call 2012-12-17.

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: organizational term
has curation status: ready for release
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.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism

clinical finding
type: Class
subclass of: clinical data item
definition: A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:02Z

clinical history
type: Class
subclass of: clinical data item
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:59Z

clinical picture
type: Class
subclass of: clinical data item
definition: A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:20:20Z

image finding
type: Class
subclass of: clinical finding
definition: A representation of an image that supports an inference to an assertion about some quality of a patient.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T10:21:10Z

laboratory finding
type: Class
subclass of: clinical finding
definition: A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T10:21:58Z

predisposition to disease of type X
type: Class
subclass of: disposition
definition: A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:20:25Z

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.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:21:20Z

homeostasis
type: Class
subclass of: disposition
term editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:22:01Z

genetic predisposition to disease of type X
type: Class
subclass of: predisposition to disease of type X
definition: A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:23:07Z

acquired genetic disease
type: Class
subclass of: disease
definition: A disease whose physical basis is an acquired genetic disorder.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:24:05Z

constitutional genetic disease
type: Class
subclass of: disease
definition: A disease whose physical basis is a constitutional genetic disorder.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:24:59Z

abnormal homeostasis
type: Class
subclass of: homeostasis
definition: Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:26:44Z

normal homeostasis
type: Class
subclass of: homeostasis
definition: Homeostasis of a type that is not clinically abnormal.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:27:28Z

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.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:39:44Z

epigenetic disorder
type: Class
subclass of: disorder
definition: A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:40:27Z

genetic disorder
type: Class
subclass of: disorder
definition: A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:41:14Z

acquired genetic disorder
type: Class
subclass of: genetic disorder
definition: A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:43:09Z

constitutional genetic disorder
type: Class
subclass of: genetic disorder
definition: A genetic disorder inherited during conception that is part of all cells in the organism.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:43:44Z

diagnosis
type: Class
subclass of: clinical data item
definition: The representation of a conclusion of a diagnostic process.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T12:42:23Z

pathological anatomical structure
type: Class
subclass of: material entity
definition: An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
curator note: creation date: 2009-07-13T02:14:05Z

physical examination finding
type: Class
subclass of: clinical finding
definition: TODO: Define.
term editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2009-11-24T04:51:11Z

congenital disorder
type: Class
subclass of: material entity
definition: A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism.
term editor: Albert Goldfain
alternative label: congenital malformation
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z

injury
type: Class
subclass of: disorder
definition: A disorder that involves some structural damage that is immediately caused by a catastrophic external force.
editor note: At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.
term editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit
curator note: creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015

clinical data item
type: Class
subclass of: data item
definition: A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
curator note: creation date: 2018-11-27

tissue disorder
type: Class
subclass of: disorder
definition: A disorder of some macroscopic part of a tissue

gender role
type: Class
subclass of: organism role
definition: A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Gender_role

male gender role
type: Class
subclass of: gender role
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
  intersection of: Restriction
    on property: characteristic of
    all values from: organism
definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
term editor: Mathias Brochhausen
alternative label: male gender

female gender role
type: Class
subclass of: gender role
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
  intersection of: Restriction
    on property: characteristic of
    all values from: organism
definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
term editor: Mathias Brochhausen
alternative label: female gender

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.
term editor: Mathias Brochhausen
term editor: William R. Hogan
alternative label: health care role

patient role
type: Class
subclass of: human health care role
subclass of: organism role
definition: A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
term editor: Amanda Hicks
term editor: Mathias Brochhausen
alternative label: patient
definition source: CAFE domain expert working group.
comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.

human patient role
type: Class
equivalent class: Class
  intersection of: patient role
  intersection of: Restriction
    on property: characteristic of
    some values from: Homo sapiens
subclass of: patient role
subclass of: Homo sapiens role
definition: A patient role that inheres in a human being.

material entity role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: material entity
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: characteristic of
  all values from: material entity

organism role
type: Class
equivalent class: Class
  intersection of: material entity role
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: organism
subclass of: Restriction
  on property: characteristic of
  all values from: organism

Homo sapiens role
type: Class
equivalent class: Class
  intersection of: organism role
  intersection of: Restriction
    on property: characteristic of
    some values from: Homo sapiens
subclass of: organism role
subclass of: Restriction
  on property: characteristic of
  some values from: Homo sapiens
subclass of: Restriction
  on property: characteristic of
  all values from: Homo sapiens

role in human social processes
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  all values from: material entity
definition: A role that inheres in some entity that is realized in a social act.
term editor: Matthew Diller
contributor: Mathias Brochhausen
comment: Previous definition: A role played by an entity in human social processes.

sense organ
type: Class
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: sensory system
definition: An organ that is capable of transducing sensory stimulus to the nervous system.
contributor: cmungall
has db xref: AEO:0000094
has db xref: BSA:0000121
has db xref: BTO:0000202
has db xref: CALOHA:TS-2043
has db xref: EHDAA2:0001824
has db xref: EHDAA:500
has db xref: EMAPA:35955
has db xref: FBbt:00005155
has db xref: GAID:63
has db xref: HAO:0000930
has db xref: MA:0000017
has db xref: MESH:D012679
has db xref: NCIT:C33224
has db xref: SCTID:244485009
has db xref: UMLS:C0935626
has db xref: VHOG:0001407
has db xref: WBbt:0006929
has exact synonym: organ of sense organ system
has exact synonym: organ of sensory organ system
has exact synonym: organ of sensory system
has exact synonym: sense organ system organ
has exact synonym: sensory organ
has exact synonym: sensory organ system organ
has exact synonym: sensory system organ
has narrow synonym: sensillum
has OBO namespace: uberon
has related synonym: Sinnesorgan
has related synonym: sensor
id: UBERON:0000020
in subset: uberon slim

Axiom
annotated source: sense organ
annotated property: definition
annotated target: An organ that is capable of transducing sensory stimulus to the nervous system.
has db xref: https://github.com/obophenotype/uberon/issues/549
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: sense organ
annotated property: hasDbXref
annotated target: UMLS:C0935626
source: ncithesaurus:Organ_of_the_Special_Sense

Axiom
annotated source: sense organ
annotated property: has exact synonym
annotated target: organ of sense organ system
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: has exact synonym
annotated target: organ of sensory organ system
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: has exact synonym
annotated target: organ of sensory system
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: has exact synonym
annotated target: sense organ system organ
has db xref: OBOL:automatic

Axiom
annotated source: sense organ
annotated property: has exact synonym
annotated target: sensory organ system organ
has db xref: OBOL:automatic

Axiom
annotated source: sense organ
annotated property: has exact synonym
annotated target: sensory system organ
has db xref: OBOL:accepted

Axiom
annotated source: sense organ
annotated property: has narrow synonym
annotated target: sensillum
has db xref: WBbt:0006929

Axiom
annotated source: sense organ
annotated property: has related synonym
annotated target: Sinnesorgan
has db xref: BTO:0000202

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010825
has db xref: AEO:0000003
has db xref: BILA:0000003
has db xref: CARO:0000003
has db xref: EHDAA2:0003003
has db xref: EMAPA:0
has db xref: FBbt:00007001
has db xref: FMA:305751
has db xref: FMA:67135
has db xref: GAID:781
has db xref: HAO:0000003
has db xref: MA:0003000
has db xref: MESH:D000825
has db xref: SCTID:362889002
has db xref: TAO:0000037
has db xref: TGMA:0001823
has db xref: VHOG:0001759
has db xref: XAO:0003000
has db xref: ZFA:0000037
has db xref: http://dbpedia.org/ontology/AnatomicalStructure
has exact synonym: biological structure
has exact synonym: connected biological structure
has OBO namespace: uberon
id: UBERON:0000061
in subset: common anatomy
in subset: upper level

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
has db xref: CARO:0000003

Axiom
annotated source: anatomical structure
annotated property: has exact synonym
annotated target: connected biological structure
has db xref: CARO:0000003

organ
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: anatomical system
subclass of: Restriction
  on property: capable of
  some values from: biological_process
definition: Anatomical structure that performs a specific function or group of functions [WP].
RO_0002161: NCBITaxon_110815
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
UBPROP_0000001: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
UBPROP_0000012: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
has db xref: BIRNLEX:4
has db xref: CARO:0020004
has db xref: EFO:0000634
has db xref: EMAPA:35949
has db xref: ENVO:01000162
has db xref: FMA:67498
has db xref: MA:0003001
has db xref: NCIT:C13018
has db xref: SCTID:272625005
has db xref: UMLS:C0178784
has db xref: WBbt:0003760
has db xref: Wikipedia:Organ_(anatomy)
has OBO namespace: uberon
has related synonym: anatomical unit
has related synonym: body organ
has related synonym: element
id: UBERON:0000062
in subset: common anatomy
in subset: upper level

Axiom
annotated source: organ
annotated property: definition
annotated target: Anatomical structure that performs a specific function or group of functions [WP].
has db xref: Wikipedia:Organ_(anatomy)

Axiom
annotated source: organ
annotated property: RO_0002161
annotated target: NCBITaxon_110815
source: Wikipedia

Axiom
annotated source: organ
annotated property: UBPROP_0000001
annotated target: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
source: GO:0048513

Axiom
annotated source: organ
annotated property: hasDbXref
annotated target: UMLS:C0178784
source: ncithesaurus:Organ

Axiom
annotated source: organ
annotated property: has related synonym
annotated target: element
has db xref: http://orcid.org/0000-0002-6601-2165

organ part
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: organ
definition: A multicellular structure that is a part of an organ.
curator note: currently defined in a very broad sense, may be replaced by more specific classes in the future
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0011124
has db xref: BIRNLEX:16
has db xref: EFO:0000635
has db xref: FMA:82472
has db xref: SCTID:113343008
has db xref: SCTID:91717005
has exact synonym: cardinal organ part
has OBO namespace: uberon
has related synonym: regional part of organ
id: UBERON:0000064
in subset: common anatomy
in subset: efo slim
in subset: non informative
in subset: upper level

Axiom
annotated source: organ part
annotated property: definition
annotated target: A multicellular structure that is a part of an organ.
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: organ part
annotated property: has exact synonym
annotated target: cardinal organ part
has db xref: FMA:82472

Axiom
annotated source: organ part
annotated property: has related synonym
annotated target: regional part of organ
has db xref: BIRNLEX:16

neuron projection bundle
type: Class
subclass of: multi cell part structure
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
has alternative id: UBERON:0005163
has db xref: CARO:0001001
has db xref: FBbt:00005099
has db xref: NLX:147821
has exact synonym: funiculus
has exact synonym: nerve fiber bundle
has exact synonym: neural fiber bundle
has OBO namespace: uberon
id: UBERON:0000122

Axiom
annotated source: neuron projection bundle
annotated property: definition
annotated target: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
has db xref: CARO:0001001
has db xref: FBC:DOS
has db xref: FBbt:00005099

Axiom
annotated source: neuron projection bundle
annotated property: has exact synonym
annotated target: nerve fiber bundle
has db xref: FBbt:00005099

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
definition: Anatomical entity that has mass.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010264
has db xref: AEO:0000006
has db xref: BILA:0000006
has db xref: CARO:0000006
has db xref: EHDAA2:0003006
has db xref: FBbt:00007016
has db xref: FMA:67165
has db xref: HAO:0000006
has db xref: TAO:0001836
has db xref: TGMA:0001826
has db xref: VHOG:0001721
has OBO namespace: uberon
id: UBERON:0000465
in subset: common anatomy
in subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: Anatomical entity that has mass.
has db xref: http://orcid.org/0000-0001-9114-8737

anatomical system
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: has part
  some values from: organ
definition: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has broad synonym: system
has db xref: AAO:0000007
has db xref: AEO:0000011
has db xref: BILA:0000011
has db xref: BIRNLEX:14
has db xref: BSA:0000049
has db xref: CALOHA:TS-2088
has db xref: CARO:0000011
has db xref: EHDAA2:0003011
has db xref: EHDAA:392
has db xref: EMAPA:16103
has db xref: EV:0100000
has db xref: FBbt:00004856
has db xref: FMA:7149
has db xref: HAO:0000011
has db xref: IDOMAL:0002460
has db xref: MA:0000003
has db xref: NCIT:C12919
has db xref: SCTID:278195005
has db xref: TAO:0001439
has db xref: TGMA:0001831
has db xref: UMLS:C0460002
has db xref: VHOG:0001725
has db xref: WBbt:0005746
has db xref: WBbt:0005763
has db xref: Wikipedia:Organ_system
has db xref: XAO:0003002
has db xref: ZFA:0001439
has db xref: galen:AnatomicalSystem
has exact synonym: body system
has exact synonym: connected anatomical system
has exact synonym: organ system
has OBO namespace: uberon
has related synonym: anatomical systems
id: UBERON:0000467
in subset: common anatomy
in subset: pheno slim
in subset: uberon slim
in subset: upper level

Axiom
annotated source: anatomical system
annotated property: definition
annotated target: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
has db xref: CARO:0000011

Axiom
annotated source: anatomical system
annotated property: has broad synonym
annotated target: system
has db xref: GO:0048731

Axiom
annotated source: anatomical system
annotated property: hasDbXref
annotated target: IDOMAL:0002460
contributor: https://orcid.org/0000-0003-4423-4370

Axiom
annotated source: anatomical system
annotated property: hasDbXref
annotated target: UMLS:C0460002
source: ncithesaurus:Organ_System

Axiom
annotated source: anatomical system
annotated property: has exact synonym
annotated target: body system
has db xref: BIRNLEX:14

Axiom
annotated source: anatomical system
annotated property: has exact synonym
annotated target: connected anatomical system
has db xref: CARO:0000011

Axiom
annotated source: anatomical system
annotated property: has related synonym
annotated target: anatomical systems
has db xref: ZFA:0001439
has synonym type: plural form

cranial nerve II
type: Class
subclass of: central nervous system cell part cluster
subclass of: cranial neuron projection bundle
subclass of: Restriction
  on property: part of
  some values from: visual system
definition: Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].
editor note: Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]
UBPROP_0000001: A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]
UBPROP_0000001: Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]
UBPROP_0000003: (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]
UBPROP_0000012: (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon
has broad synonym: 2n
has broad synonym: optic nerve
has db xref: AAO:0010345
has db xref: BAMS:2n
has db xref: BAMS:IIn
has db xref: BAMS:nII
has db xref: BIRNLEX:1640
has db xref: CALOHA:TS-0713
has db xref: DHBA:15544
has db xref: EFO:0004258
has db xref: EHDAA2:0001313
has db xref: EHDAA:6788
has db xref: EMAPA:17575
has db xref: FMA:50863
has db xref: GAID:831
has db xref: HBA:9307
has db xref: MA:0001097
has db xref: MBA:848
has db xref: MESH:D009900
has db xref: NCIT:C12761
has db xref: SCTID:180938001
has db xref: TAO:0000435
has db xref: UMLS:C0029130
has db xref: VHOG:0000543
has db xref: Wikipedia:Optic_nerve
has db xref: XAO:0000188
has db xref: ZFA:0000435
has db xref: neuronames:289
has exact synonym: 02 optic nerve
has exact synonym: cranial II
has exact synonym: nervus opticus
has exact synonym: nervus opticus [II]
has exact synonym: optic II
has exact synonym: optic II nerve
has exact synonym: optic nerve [II]
has exact synonym: second cranial nerve
has OBO namespace: uberon
has related synonym: CN-II
has related synonym: nerve II
has related synonym: optic
id: UBERON:0000941
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: cranial nerve II
annotated property: definition
annotated target: Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].
has db xref: ISBN:0471209627
has db xref: ISBN:0471888893

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000001
annotated target: A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000435
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000001
annotated target: Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010345
ontology: AAO
source: AAO:EJS

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000003
annotated target: (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000543
ontology: VHOG
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk
source: http://bgee.unil.ch/

Axiom
annotated source: cranial nerve II
annotated property: UBPROP_0000012
annotated target: (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon
external ontology: MA

Axiom
annotated source: cranial nerve II
annotated property: has broad synonym
annotated target: 2n
has db xref: BIRNLEX:1640
has db xref: NIFSTD:NeuroNames_abbrevSource
has synonym type: abbreviation

Axiom
annotated source: cranial nerve II
annotated property: has broad synonym
annotated target: optic nerve
has db xref: FMA:50863
has db xref: ZFA:0000435
has synonym type: SENSU

Axiom
annotated source: cranial nerve II
annotated property: hasDbXref
annotated target: UMLS:C0029130
source: BIRNLEX:1640
source: ncithesaurus:Optic_Nerve

Axiom
annotated source: cranial nerve II
annotated property: hasDbXref
annotated target: neuronames:289
source: BIRNLEX:1640

Axiom
annotated source: cranial nerve II
annotated property: has exact synonym
annotated target: 02 optic nerve
has db xref: AAO:0010345

Axiom
annotated source: cranial nerve II
annotated property: has exact synonym
annotated target: nervus opticus
has synonym type: LATIN

Axiom
annotated source: cranial nerve II
annotated property: has exact synonym
annotated target: nervus opticus [II]
has db xref: FMA:50863
has db xref: FMA:TA
has synonym type: LATIN

Axiom
annotated source: cranial nerve II
annotated property: has exact synonym
annotated target: optic II
has db xref: EHDAA2:0001313

Axiom
annotated source: cranial nerve II
annotated property: has exact synonym
annotated target: optic II nerve
has db xref: EHDAA2:0001313

Axiom
annotated source: cranial nerve II
annotated property: has related synonym
annotated target: CN-II
has db xref: ZFA:0000435

Axiom
annotated source: cranial nerve II
annotated property: has related synonym
annotated target: nerve II
has db xref: NeuroNames:289

Axiom
annotated source: cranial nerve II
annotated property: has related synonym
annotated target: optic
has db xref: TAO:0000435

retina
type: Class
subclass of: ectoderm-derived structure
subclass of: photoreceptor array
definition: The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
RO_0002161: NCBITaxon 6656
RO_0002175: Homo sapiens
UBPROP_0000001: The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
UBPROP_0000003: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
UBPROP_0000007: retinal
has db xref: AAO:0010352
has db xref: BAMS:R
has db xref: BIRNLEX:1153
has db xref: BTO:0001175
has db xref: CALOHA:TS-0865
has db xref: EFO:0000832
has db xref: EHDAA2:0001627
has db xref: EHDAA:4757
has db xref: EMAPA:17168
has db xref: EV:0100348
has db xref: FMA:58301
has db xref: GAID:755
has db xref: MA:0000276
has db xref: MAT:0000142
has db xref: MBA:304325711
has db xref: MESH:D012160
has db xref: MIAA:0000142
has db xref: NCIT:C12343
has db xref: NIFSTD_RETIRED:birnlex_1156
has db xref: SCTID:181171005
has db xref: TAO:0000152
has db xref: UMLS:C0035298
has db xref: UMLS:C1278894
has db xref: VHOG:0000229
has db xref: Wikipedia:Retina
has db xref: XAO:0000009
has db xref: ZFA:0000152
has db xref: neuronames:1862
has exact synonym: inner layer of eyeball
has exact synonym: retina of camera-type eye
has exact synonym: tunica interna of eyeball
has OBO namespace: uberon
has related synonym: Netzhaut
has related synonym: retinas
id: UBERON:0000966
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
comment: Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods

Axiom
annotated source: retina
annotated property: definition
annotated target: The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
has db xref: Wikipedia:Retina
has db xref: ZFIN:curator

Axiom
annotated source: retina
annotated property: UBPROP_0000001
annotated target: The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
date retrieved: 2012-08-14
external class: TAO:0000152
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: retina
annotated property: UBPROP_0000003
annotated target: The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000229
ontology: VHOG
source: DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
source: http://bgee.unil.ch/

Axiom
annotated source: retina
annotated property: hasDbXref
annotated target: UMLS:C0035298
source: BIRNLEX:1153
source: ncithesaurus:Retina

Axiom
annotated source: retina
annotated property: hasDbXref
annotated target: UMLS:C1278894
source: BIRNLEX:1153

Axiom
annotated source: retina
annotated property: has exact synonym
annotated target: retina of camera-type eye
has db xref: GO:0060041

Axiom
annotated source: retina
annotated property: has related synonym
annotated target: Netzhaut
has db xref: BTO:0001175

Axiom
annotated source: retina
annotated property: has related synonym
annotated target: retinas
has db xref: ZFA:0000152
has synonym type: plural form

eye
type: Class
subclass of: sense organ
subclass of: Restriction
  on property: part of
  some values from: visual system
subclass of: Restriction
  on property: capable of
  some values from: detection of visible light
definition: An organ that detects light.
curator note: This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
RO_0002175: Homo sapiens
UBPROP_0000007: ocular
UBPROP_0000007: optic
UBPROP_0000010: Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
has db xref: BILA:0000017
has db xref: BTO:0000439
has db xref: CALOHA:TS-0309
has db xref: EFO:0000827
has db xref: EV:0100336
has db xref: FBbt:00005162
has db xref: GAID:69
has db xref: MAT:0000140
has db xref: MESH:D005123
has db xref: MIAA:0000140
has db xref: Wikipedia:Eye
has OBO namespace: uberon
has related synonym: light-detecting organ
has related synonym: visual apparatus
id: UBERON:0000970
in subset: efo slim
in subset: functional classification
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: uberon slim

Axiom
annotated source: eye
annotated property: definition
annotated target: An organ that detects light.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: eye
annotated property: has related synonym
annotated target: visual apparatus
has db xref: EV:0100336

nervous system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: neuron
subclass of: Restriction
  on property: capable of
  some values from: nervous system process
definition: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
RO_0002161: NCBITaxon 6040
UBPROP_0000001: A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
UBPROP_0000001: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
UBPROP_0000003: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
UBPROP_0000007: nervous
UBPROP_0000007: neural
has db xref: AAO:0000324
has db xref: BILA:0000079
has db xref: BIRNLEX:844
has db xref: BTO:0001484
has db xref: CALOHA:TS-1313
has db xref: EFO:0000802
has db xref: EHDAA2:0001246
has db xref: EHDAA:826
has db xref: EMAPA:16469
has db xref: EV:0100162
has db xref: FBbt:00005093
has db xref: FMA:7157
has db xref: GAID:466
has db xref: MA:0000016
has db xref: MAT:0000026
has db xref: MESH:D009420
has db xref: MIAA:0000026
has db xref: NCIT:C12755
has db xref: SCTID:278196006
has db xref: TAO:0000396
has db xref: UMLS:C0027763
has db xref: VHOG:0000402
has db xref: WBbt:0005735
has db xref: Wikipedia:Nervous_system
has db xref: XAO:0000177
has db xref: ZFA:0000396
has db xref: neuronames:3236
has exact synonym: neurological system
has narrow synonym: nerve net
has OBO namespace: uberon
has related synonym: systema nervosum
id: UBERON:0001016
in subset: cumbo
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: nervous system
annotated property: definition
annotated target: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
has db xref: BIRNLEX:844
has db xref: ISBN:0-14-051288-8
has db xref: ISBN:3110148986
has db xref: NLM:nervous+system
has db xref: WB:rynl
has db xref: Wikipedia:Nervous_system
has db xref: ZFIN:curator

Axiom
annotated source: nervous system
annotated property: UBPROP_0000001
annotated target: A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
date retrieved: 2012-08-14
external class: TAO:0000396
ontology: TAO
source: ZFIN:curator

Axiom
annotated source: nervous system
annotated property: UBPROP_0000001
annotated target: Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000324
ontology: AAO
source: AAO:BJB

Axiom
annotated source: nervous system
annotated property: UBPROP_0000003
annotated target: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000402
ontology: VHOG
source: ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
source: http://bgee.unil.ch/

Axiom
annotated source: nervous system
annotated property: hasDbXref
annotated target: UMLS:C0027763
source: ncithesaurus:Nervous_System

Axiom
annotated source: nervous system
annotated property: has exact synonym
annotated target: neurological system
has db xref: GO:0050877

Axiom
annotated source: nervous system
annotated property: has narrow synonym
annotated target: nerve net
has db xref: Wikipedia:Nerve_net

Axiom
annotated source: nervous system
annotated property: has related synonym
annotated target: systema nervosum
has db xref: Wikipedia:Nervous_system
has synonym type: LATIN

sensory system
type: Class
subclass of: non-connected functional system
subclass of: Restriction
  on property: overlaps
  some values from: nervous system
subclass of: Restriction
  on property: capable of part of
  some values from: sensory perception
definition: Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
UBPROP_0000003: An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
UBPROP_0000012: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
has db xref: AAO:0000555
has db xref: BAMS:SEN
has db xref: BILA:0000099
has db xref: EFO:0000805
has db xref: EHDAA2:0003094
has db xref: EMAPA:16192
has db xref: FBbt:00007692
has db xref: FMA:75259
has db xref: MA:0002442
has db xref: MAT:0000031
has db xref: MIAA:0000031
has db xref: NLXANAT:090816
has db xref: TAO:0000282
has db xref: VHOG:0001674
has db xref: Wikipedia:Sensory_system
has db xref: XAO:0003194
has db xref: ZFA:0000282
has exact synonym: organa sensuum
has exact synonym: sense organ subsystem
has exact synonym: sense organs
has exact synonym: sense organs set
has exact synonym: sensory subsystem
has exact synonym: sensory systems
has OBO namespace: uberon
has related synonym: organa sensuum
has related synonym: sensory organ system
has related synonym: set of sense organs
id: UBERON:0001032
in subset: efo slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: sensory system
annotated property: definition
annotated target: Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
has db xref: Wikipedia:Sensory_system

Axiom
annotated source: sensory system
annotated property: UBPROP_0000003
annotated target: An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001674
ontology: VHOG
source: DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
source: http://bgee.unil.ch/

Axiom
annotated source: sensory system
annotated property: has exact synonym
annotated target: organa sensuum
has db xref: FMA:75259
has db xref: FMA:TA
has synonym type: LATIN

Axiom
annotated source: sensory system
annotated property: has exact synonym
annotated target: sense organs
has db xref: FMA:75259

Axiom
annotated source: sensory system
annotated property: has exact synonym
annotated target: sense organs set
has db xref: FMA:75259

Axiom
annotated source: sensory system
annotated property: has exact synonym
annotated target: sensory systems
has db xref: TAO:0000282
has synonym type: plural form

Axiom
annotated source: sensory system
annotated property: has related synonym
annotated target: organa sensuum
has db xref: Wikipedia:Sensory_system
has synonym type: LATIN

Axiom
annotated source: sensory system
annotated property: has related synonym
annotated target: set of sense organs
has db xref: FMA:75259

anatomical entity
type: Class
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010841
has db xref: AEO:0000000
has db xref: BILA:0000000
has db xref: BIRNLEX:6
has db xref: CARO:0000000
has db xref: EHDAA2:0002229
has db xref: FBbt:10000000
has db xref: FMA:62955
has db xref: HAO:0000000
has db xref: MA:0000001
has db xref: NCIT:C12219
has db xref: TAO:0100000
has db xref: TGMA:0001822
has db xref: UMLS:C1515976
has db xref: WBbt:0000100
has db xref: XAO:0000000
has db xref: ZFA:0100000
has OBO namespace: uberon
id: UBERON:0001062
in subset: common anatomy
in subset: upper level

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
has db xref: FMA:62955
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical entity
annotated property: hasDbXref
annotated target: UMLS:C1515976
source: ncithesaurus:Anatomic_Structure_System_or_Substance

visual system
type: Class
subclass of: sensory system
subclass of: Restriction
  on property: capable of part of
  some values from: visual perception
definition: The sensory system subserving the sense of vision.
UBPROP_0000001: The sensory system used for sight.[AAO]
has alternative id: UBERON:0007036
has db xref: AAO:0000632
has db xref: BILA:0000140
has db xref: EMAPA:36003
has db xref: FMA:7191
has db xref: MA:0002444
has db xref: NCIT:C12888
has db xref: SCTID:281831001
has db xref: TAO:0001127
has db xref: UMLS:C0587900
has db xref: Wikipedia:Visual_system
has db xref: XAO:0003198
has db xref: ZFA:0001127
has db xref: http://uri.neuinfo.org/nif/nifstd/FMAID_7191
has exact synonym: photosensory system
has exact synonym: visual organ system
has OBO namespace: uberon
id: UBERON:0002104
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

Axiom
annotated source: visual system
annotated property: definition
annotated target: The sensory system subserving the sense of vision.
has db xref: NIFSTD:FMAID_7191

Axiom
annotated source: visual system
annotated property: UBPROP_0000001
annotated target: The sensory system used for sight.[AAO]
date retrieved: 2012-06-20
external class: AAO:0000632
ontology: AAO
source: AAO:EJS

Axiom
annotated source: visual system
annotated property: hasDbXref
annotated target: UMLS:C0587900
source: ncithesaurus:Visual_System

Axiom
annotated source: visual system
annotated property: has exact synonym
annotated target: photosensory system
has db xref: BILA:0000140

ectoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the ectoderm.
curator note: Grouping term for query purposes
has exact synonym: ectodermal deriviative
has OBO namespace: uberon
id: UBERON:0004121
in subset: grouping class

Axiom
annotated source: ectoderm-derived structure
annotated property: definition
annotated target: An anatomical structure that develops (entirely or partially) from the ectoderm.
has db xref: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: ectoderm-derived structure
annotated property: has exact synonym
annotated target: ectodermal deriviative
has db xref: FBbt:00025990

anatomical projection
type: Class
subclass of: morphological feature
subclass of: Restriction
  on property: part of
  some values from: organ
definition: A projection or outgrowth of tissue from a larger body or organ.
editor note: should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
UBPROP_0000001: Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]
UBPROP_0000001: Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]
UBPROP_0000001: Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]
contributor: cmungall
contributor: wdahdul
has broad synonym: anatomical process
has broad synonym: process
has db xref: AAO:0010278
has db xref: FMA:67601
has db xref: HAO:0000822
has db xref: NCIT:C61549
has db xref: TAO:0001834
has db xref: VSAO:0000180
has db xref: Wikipedia:Process_(anatomy)
has db xref: XAO:0004020
has db xref: galen:Ridge
has exact synonym: processus
has exact synonym: projection
has narrow synonym: flange
has narrow synonym: flanges
has narrow synonym: lamella
has narrow synonym: lamellae
has narrow synonym: lamina
has narrow synonym: laminae
has narrow synonym: organ process
has narrow synonym: papilla
has narrow synonym: process of organ
has narrow synonym: processes
has narrow synonym: projection
has narrow synonym: projections
has narrow synonym: ridge
has narrow synonym: ridges
has narrow synonym: shelf
has narrow synonym: shelves
has OBO namespace: uberon
has related synonym: anatomical protrusion
has related synonym: protrusion
has related synonym: spine
id: UBERON:0004529
in subset: common anatomy
in subset: upper level

Axiom
annotated source: anatomical projection
annotated property: definition
annotated target: A projection or outgrowth of tissue from a larger body or organ.
has db xref: Wikipedia:Process_(anatomy)
has db xref: https://github.com/obophenotype/uberon/issues/39

Axiom
annotated source: anatomical projection
annotated property: UBPROP_0000001
annotated target: Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]
date retrieved: 2012-06-20
external class: AAO:0010278
ontology: AAO
source: AAO:BJB

Axiom
annotated source: anatomical projection
annotated property: UBPROP_0000001
annotated target: Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]
date retrieved: 2012-08-14
external class: TAO:0001834
ontology: TAO
source: TAO:wd

Axiom
annotated source: anatomical projection
annotated property: UBPROP_0000001
annotated target: Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]
date retrieved: 2012-08-14
external class: VSAO:0000180
ontology: VSAO
source: TAO:curator

Axiom
annotated source: anatomical projection
annotated property: has broad synonym
annotated target: process
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has exact synonym
annotated target: processus
has db xref: FMA:67601
has db xref: FMA:TA
has synonym type: LATIN

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: flange
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: flanges
has db xref: VSAO:0000180
has synonym type: plural form

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: lamella
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: lamellae
has db xref: VSAO:0000180
has synonym type: plural form

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: lamina
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: laminae
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: processes
has db xref: VSAO:0000180
has synonym type: plural form

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: projection
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: projections
has db xref: VSAO:0000180
has synonym type: plural form

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: ridge
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: ridges
has db xref: VSAO:0000180
has synonym type: plural form

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: shelf
has db xref: VSAO:0000180

Axiom
annotated source: anatomical projection
annotated property: has narrow synonym
annotated target: shelves
has db xref: VSAO:0000180
has synonym type: plural form

organ component layer
type: Class
subclass of: organ part
definition: A part of a wall of an organ that forms a layer.
has db xref: FMA:82485
has OBO namespace: uberon
id: UBERON:0004923
in subset: upper level

Axiom
annotated source: organ component layer
annotated property: definition
annotated target: A part of a wall of an organ that forms a layer.
has db xref: http://orcid.org/0000-0002-6601-2165

multi cell part structure
type: Class
subclass of: anatomical structure
definition: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
UBPROP_0000012: we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
has db xref: AAO:0011000
has db xref: CARO:0001000
has db xref: FBbt:00007060
has db xref: FMA:83115
has exact synonym: multi-cell-component structure
has exact synonym: multi-cell-part structure
has OBO namespace: uberon
has related synonym: cell part cluster
id: UBERON:0005162
in subset: upper level

Axiom
annotated source: multi cell part structure
annotated property: definition
annotated target: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
has db xref: CARO:0001000

Axiom
annotated source: multi cell part structure
annotated property: UBPROP_0000012
annotated target: we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
external ontology: CARO
external ontology: FMA

Axiom
annotated source: multi cell part structure
annotated property: has exact synonym
annotated target: multi-cell-component structure
has db xref: CARO:0001000

Axiom
annotated source: multi cell part structure
annotated property: has exact synonym
annotated target: multi-cell-part structure
has db xref: CARO:0001000

Axiom
annotated source: multi cell part structure
annotated property: has related synonym
annotated target: cell part cluster
has db xref: FMA:83115

photoreceptor array
type: Class
subclass of: organ component layer
subclass of: Restriction
  on property: part of
  some values from: eye
subclass of: Restriction
  on property: part of
  some values from: nervous system
definition: An array of photoreceptors and any supporting cells found in an eye.
has db xref: FBbt:00004200
has exact synonym: light-sensitive tissue
has OBO namespace: uberon
id: UBERON:0005388

Axiom
annotated source: photoreceptor array
annotated property: definition
annotated target: An array of photoreceptors and any supporting cells found in an eye.
has db xref: https://orcid.org/0000-0002-6601-2165

multicellular anatomical structure
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: has part
  some values from: cell
definition: An anatomical structure that has more than one cell as a part.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: CARO:0010000
has db xref: FBbt:00100313
has exact synonym: multicellular structure
has OBO namespace: uberon
id: UBERON:0010000
in subset: common anatomy
in subset: upper level

Axiom
annotated source: multicellular anatomical structure
annotated property: definition
annotated target: An anatomical structure that has more than one cell as a part.
has db xref: CARO:0010000

Axiom
annotated source: multicellular anatomical structure
annotated property: has exact synonym
annotated target: multicellular structure
has db xref: FBbt:00100313

central nervous system cell part cluster
type: Class
subclass of: ectoderm-derived structure
subclass of: multi cell part structure
definition: A multi cell part structure that is part of a central nervous system.
has db xref: FMA:83143
has exact synonym: cell part cluster of neuraxis
has exact synonym: neuraxis layer
has OBO namespace: uberon
id: UBERON:0011215
in subset: upper level

Axiom
annotated source: central nervous system cell part cluster
annotated property: definition
annotated target: A multi cell part structure that is part of a central nervous system.
has db xref: OBOL:automatic

Axiom
annotated source: central nervous system cell part cluster
annotated property: has exact synonym
annotated target: cell part cluster of neuraxis
has db xref: FMA:83143

Axiom
annotated source: central nervous system cell part cluster
annotated property: has exact synonym
annotated target: neuraxis layer
has db xref: FMA:83143

non-connected functional system
type: Class
subclass of: disconnected anatomical group
definition: An anatomical group whose component structures share a common function.
has db xref: AEO:0000093
has db xref: FBbt:00007278
has OBO namespace: uberon
id: UBERON:0015203

Axiom
annotated source: non-connected functional system
annotated property: definition
annotated target: An anatomical group whose component structures share a common function.
has db xref: AEO:0000093
has db xref: AEO:JB
has db xref: FBC:DOS
has db xref: FBbt:00007278

lateral structure
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: material anatomical entity
definition: Any structure that is placed on one side of the left-right axis of a bilaterian.
curator note: This class is primarily to implement taxon constraints. It may be removed in the future.
has OBO namespace: uberon
id: UBERON:0015212
in subset: grouping class
in subset: non informative

Axiom
annotated source: lateral structure
annotated property: definition
annotated target: Any structure that is placed on one side of the left-right axis of a bilaterian.
has db xref: http://orcid.org/0000-0002-6601-2165

ridge of tooth
type: Class
subclass of: ectoderm-derived structure
subclass of: skeletal element projection
definition: A linear flat evelation on a tooth.
has db xref: SCTID:245699009
has exact synonym: crista of tooth
has exact synonym: tooth ridge
has OBO namespace: uberon
id: UBERON:0016930

Axiom
annotated source: ridge of tooth
annotated property: definition
annotated target: A linear flat evelation on a tooth.
has db xref: Wikipedia:Dental_anatomy#Ridges

cingulum of tooth
type: Class
subclass of: ridge of tooth
definition: The portion of the teeth, occurring on the lingual or palatal aspects, that forms a convex protuberance at the cervical third of the anatomic crown. It represents the lingual or palatal developmental lobe of these teeth.
UBPROP_0000012: FMA has no definition but places this generically with upper, lower, canine, incisor subclasses. Wiktionary states cingulum is lower jaw molar only, and cingulid is upper molar only
has db xref: FMA:56731
has db xref: SCTID:245650005
has db xref: Wikipedia:Cingulum_(tooth)
has exact synonym: cingulum (dentis)
has exact synonym: cingulum dentis
has exact synonym: tooth cingulum
has OBO namespace: uberon
id: UBERON:0017295

Axiom
annotated source: cingulum of tooth
annotated property: definition
annotated target: The portion of the teeth, occurring on the lingual or palatal aspects, that forms a convex protuberance at the cervical third of the anatomic crown. It represents the lingual or palatal developmental lobe of these teeth.
has db xref: Wikipedia:Cingulum_(tooth)

Axiom
annotated source: cingulum of tooth
annotated property: has exact synonym
annotated target: cingulum (dentis)
has db xref: FMA:56731

Axiom
annotated source: cingulum of tooth
annotated property: has exact synonym
annotated target: cingulum dentis
has db xref: FMA:56731
has db xref: FMA:TA
has synonym type: LATIN

Axiom
annotated source: cingulum of tooth
annotated property: has exact synonym
annotated target: tooth cingulum
has db xref: FMA:56731

cingulum of canine tooth
type: Class
subclass of: cingulum of tooth
has db xref: FMA:56734
has exact synonym: canine tooth cingulum
has OBO namespace: uberon
id: UBERON:0017297

Axiom
annotated source: cingulum of canine tooth
annotated property: has exact synonym
annotated target: canine tooth cingulum
has db xref: FMA:56734

cranial neuron projection bundle
type: Class
subclass of: neuron projection bundle
subclass of: lateral structure
definition: Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.
RO_0002175: Homo sapiens
has OBO namespace: uberon
has related synonym: cranial nerve fiber bundle
has related synonym: cranial nerve fiber tract
has related synonym: cranial nerve or tract
has related synonym: neuron projection bundle from brain
id: UBERON:0034713
in subset: human reference atlas

Axiom
annotated source: cranial neuron projection bundle
annotated property: definition
annotated target: Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.
has db xref: ISBN:0471888893
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cranial neuron projection bundle
annotated property: has related synonym
annotated target: cranial nerve fiber bundle
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cranial neuron projection bundle
annotated property: has related synonym
annotated target: cranial nerve fiber tract
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cranial neuron projection bundle
annotated property: has related synonym
annotated target: cranial nerve or tract
has db xref: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: cranial neuron projection bundle
annotated property: has related synonym
annotated target: neuron projection bundle from brain
has db xref: http://orcid.org/0000-0002-6601-2165

morphological feature
type: Class
subclass of: anatomical structure
definition: A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has OBO namespace: uberon
id: UBERON:0034768
in subset: common anatomy

Axiom
annotated source: morphological feature
annotated property: definition
annotated target: A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
has db xref: http://orcid.org/0000-0002-6601-2165

disconnected anatomical group
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
has db xref: CARO:0020000
has db xref: FBbt:00007276
has OBO namespace: uberon
id: UBERON:0034923
in subset: common anatomy

Axiom
annotated source: disconnected anatomical group
annotated property: definition
annotated target: Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
has db xref: CARO:0020000

skeletal element projection
type: Class
subclass of: anatomical projection
definition: Anatomical projection that is composed of bone or cartilage tissue.
has OBO namespace: uberon
id: UBERON:4100000

Axiom
annotated source: skeletal element projection
annotated property: definition
annotated target: Anatomical projection that is composed of bone or cartilage tissue.
has db xref: PHENOSCAPE

electrode array
type: Class
subclass of: device
subclass of: Restriction
  on property: has part
  some values from: electrode
contributor: Bill Duncan
created: 2024-05-14T20:29:46Z

electrode
type: Class
subclass of: device
contributor: Bill Duncan
created: 2024-05-14T20:30:09Z

neural electronic interface device
type: Class
subclass of: device
contributor: Bill Duncan
created: 2024-05-14T20:39:16Z

bionic vision device
type: Class
subclass of: neural electronic interface device
contributor: Bill Duncan
created: 2024-05-14T20:39:31Z

bionic hearing device
type: Class
subclass of: neural electronic interface device
contributor: Bill Duncan
created: 2024-05-14T20:41:47Z

brain computer interface
type: Class
subclass of: neural electronic interface device
contributor: Bill Duncan
created: 2024-05-14T20:43:31Z

brain machine interface
type: Class
subclass of: neural electronic interface device
contributor: Bill Duncan
created: 2024-05-14T20:43:46Z

cortical bionic vision device
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
created: 2024-05-14T20:59:44Z

retinal bionic vision device
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
created: 2024-05-14T21:00:00Z

Alpha AMS
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Retina Implant AG
subclass of: Restriction
  on property: device origin organization
  has value: Universität Tübingen
contributor: Bill Duncan
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-06-25T18:00:00Z
description: The Alpha AMS is an advanced subretinal implant developed by Retina Implant AG, designed to assist individuals with retinitis pigmentosa, a condition marked by the progressive loss of vision. This implant is an evolution of its predecessor, the [Alpha IMS](/devices/alpha-ims), featuring enhanced functionality with 1,600 light-sensitive photodiodes that more effectively mimic the natural processing of visual signals. Implanted under the retina, the Alpha AMS converts light into electrical signals that are sent to the brain, enabling patients to detect light and dark, and recognize large objects and outlines.
implant location: subretinal
electrode layout: rectilinear
electrode pitch: 70
ce mark year: 2016
implant type: electronic
electrode number: 1600

Alpha IMS
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Retina Implant AG
subclass of: Restriction
  on property: device origin organization
  has value: Universität Tübingen
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3027
created: 2024-06-25T18:00:00Z
description: The Alpha IMS is a subretinal implant developed by Retina Implant AG, aimed at restoring functional vision for individuals with retinitis pigmentosa, a group of genetic disorders characterized by progressive vision loss. Implanted beneath the retina, the device features a microchip equipped with 1,500 light-sensitive photodiodes, amplifiers, and electrodes. It functions by mimicking the role of photoreceptor cells: capturing light signals and converting them into electrical impulses transmitted to the brain via the optic nerve. Alpha IMS enables patients to perceive light patterns, assisting in navigation and object recognition. Clinical trials have shown that the implant can enhance visual perception, marking a significant advancement in vision restoration technologies.
implant location: subretinal
electrode layout: rectilinear
electrode pitch: 70
ce mark year: 2013
implant type: electronic

AmazingVision
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: A-Neuron Electronic Corp.
subclass of: Restriction
  on property: device origin organization
  has value: National Chiao Tung University
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3028
created: 2024-06-25T18:00:00Z
description: This technology is an improved version of what the National Chiao Tung University’s Biomedical Electronics Translational Research Center (BETRC) has been developing. The BETRC created an artificial retina that uses two threads to transmit power from the eyewear worn by the user to a chip implanted in the eyeball. Amazing Vision has added a tiny solar panel to the chip that generates power by absorbing infrared light. This improvement reduces inflammation to the eye, reduces infection risk, and gives clearer and wider vision to the patient it was implanted in. Animal tests have already been conducted and have proven useful. Human testing was delayed due to the pandemic, but is soon to be conducted.
implant location: subretinal
implant type: electronic

Argus I
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Second Sight Medical Products
subclass of: Restriction
  on property: device origin organization
  has value: University of Southern California
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3029
created: 2024-06-25T18:00:00Z
description: Argus I was the first-generation prototype of an epiretinal implant manufactured by Second Sight Medical Products.
implant location: epiretinal
electrode layout: 4x4
electrode pitch: 800
electrode diameter: 250/500
implant type: electronic
electrode number: 16

Argus II
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Second Sight Medical Products
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3030
created: 2024-06-25T18:00:00Z
description: The Argus II is a retinal prosthesis device developed by Second Sight Medical Products, designed for individuals with retinitis pigmentosa, a condition characterized by severe vision impairment. As an epiretinal implant, it is placed directly on the retina's surface and consists of a small camera on eyeglasses that captures visual data. This data is processed by a portable unit and transmitted wirelessly to an electrode array in the eye, stimulating the retina's remaining cells to send visual information to the brain. Approved by the FDA in 2013 and previously granted the CE Mark in 2011 in Europe, the Argus II was the first retinal implant to receive these certifications, allowing users to perform basic visual tasks. However, in 2019, Second Sight discontinued the Argus II due to financial challenges, shifting their focus to the development of the [Orion Visual Cortical Prosthesis System](/devices/orion), intended to stimulate the brain's visual cortex directly.
implant location: epiretinal
electrode layout: 6x10
electrode pitch: 575
electrode diameter: 225
ce mark year: 2011
implant type: electronic
electrode number: 60

ASR Artificial Silicon Retina
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Optobionics
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3031
created: 2024-06-25T18:00:00Z
description: Optobionics’ Artificial Silicon Retina microchip (ASR) was invented by Dr. Alan Chow and his brother Vincent Chow. Dr. Chow is an ophthalmic surgeon and assistant professor and his brother Vincent is an electrical engineer. The ASR was designed to stimulate damaged retinal cells from within the retina to allow the cells to recreate visual signals that are processed and sent to the brain. The ASR microchip is a silicon chip 2 mm in diameter, 25 microns in thickness and is less than the thickness of a human hair. It fabricated using technology similar to that used in the fabrication of computer chips and contains approximately 5,000 microscopic solar cells called “microphotodiodes,” each with its own stimulating electrode.
implant location: subretinal
electrode diameter: 25
implant type: electronic
electrode number: 5000 microphotodiodes

AV-DONE
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Nidek Co., Ltd.
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3032
created: 2024-06-25T18:00:00Z
description: AV-DONE is a direct optic nerve electrode that produces artificial vision in blind patients with retinitis pigmentosa.
implant location: optic nerve
electrode diameter: 50
implant type: electronic
electrode number: 7-Mar

Bar-Ilan Hybrid Retinal Prosthesis
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3033
created: 2024-06-25T18:00:00Z
description: The Hybrid Retinal Prosthesis is a novel device that combines an implantable high density electrode array integrated with neurons. The electrode-neuron coupling allows for an increase in phosphene density while preserving retinal circuitry.
implant location: subretinal
implant type: electronic

Biohybrid
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Nidek Co., Ltd.
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3034
created: 2024-06-25T18:00:00Z
implant location: optic nerve
implant type: electronic

Boston Retinal Implant
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Bionic Eye Technologies
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3035
created: 2024-06-25T18:00:00Z
description: The Boston Retinal Implant Project has developed a subretinal, hermetically-enclosed, chronically-implantable vision prosthesis to restore some useful vision to people with degenerative retinal diseases, especially retinitis pigmentosa and age-related macular degeneration. The prosthesis offers advantages over the competing epiretinal devices by providing a lower risk of eye infection, reduced erosion through the delicate tissues that cover the front of the eye (i.e. the conjunctiva), and the ability to place stimulating electrodes closer to retinal nerve cells.
implant location: subretinal
implant type: electronic

Brindley Cortical Implant
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device origin organization
  has value: University of London
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3035
created: 2024-06-25T18:00:00Z
implant location: cortical
implant type: electronic
electrode number: 78

BS01
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Bionic Sight, LLC
subclass of: Restriction
  on property: device origin organization
  has value: Cornell University
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3036
created: 2024-06-25T18:00:00Z
description: BS01 is an optogenetic prosthesis.
implant location: epiretinal
implant type: optogenetic

C-Sight
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device origin organization
  has value: Shanghai Jiao Tong University
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3037
created: 2024-06-25T18:00:00Z
description: The C-Sight group proposed an implantable visual prosthesis based on optic nerve stimulation with an electrode array. (Chai et al. 2013)
implant location: optic nerve
electrode layout: hexagonal
implant type: electronic
electrode number: 13

CORTIVIS
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Biomedical Technologies
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3038
created: 2024-06-25T18:00:00Z
description: CORTIVIS is a cortical visual neuroprosthesis that is based on the Utah Electrode Array. It will be used to improve the quality of life of profoundly blind people.
implant location: cortical
electrode layout: 10x10
electrode diameter: 25
implant type: electronic
electrode number: 100

Diamond Eye Implant
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: iBionics
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3039
created: 2024-06-25T18:00:00Z
description: iBionics has developed the Diamond Eye implant with a high density of hermatically-enclosed electrodes, allowing for higher spatial resolution.
implant location: epiretinal
implant type: electronic
electrode number: 256

Dobelle Eye
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device origin organization
  has value: Dobelle Institute
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3035
created: 2024-06-25T18:00:00Z
implant location: cortical
implant type: electronic

Electronic Visual Cortical Stimulator
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Cortivision
subclass of: Restriction
  on property: device origin organization
  has value: Polytechnique Montréal
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3040
created: 2024-06-25T18:00:00Z
description: The Cortivision team from Polystim neurotechnologies developed a visual cortical stimulator which consists of image sensing, image processing, and brain cortex stimulation to help blind patients acquire a sense of visual perception (Ghannoum 2010). They hope to elaborate a model of the layer 4 of the visual cortex V1 using a large-scale network of biologically realistic neurons.
implant location: cortical
implant type: electronic

ELVIS
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Sensor-Tech
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3041
created: 2024-06-25T18:00:00Z
description: ELVIS, or 'Electronic Vision,' is a cortical implant that utilizes small currents to stimulate the visual cortex to produce vision. A microcomputer attached to the belt processes the outdoor scene and uses an AI algoirthm to help simplify objects for the user. Sensor Tech expects human trials to begin in 2023 and implants to be made available to the public in 2027.
implant location: cortical
implant type: electronic
electrode number: 100

EPIRET1
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Epi-Ret GmBH
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3042
created: 2024-06-25T18:00:00Z
implant location: epiretinal
electrode layout: hexagonal
implant type: electronic

EPIRET2
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Epi-Ret GmBH
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3043
created: 2024-06-25T18:00:00Z
implant location: epiretinal
electrode layout: hexagonal
implant type: electronic

EPIRET3
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Epi-Ret GmBH
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3044
created: 2024-06-25T18:00:00Z
description: The EPIRET3 implant is a remotely controlled, fully intraocular wireless device consisting of a receiver and a stimulator module. The stimulator is placed on the retinal surface. Data and energy are transmitted via an inductive link from outside the eye to the implant. Surgery included removal of the lens, vitrectomy, and implantation of the EPIRET3 device through a corneal incision.
implant location: epiretinal
electrode layout: hexagonal
electrode pitch: 500
electrode diameter: 100
implant type: electronic
electrode number: 25

Gennaris
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Grey Innovations
subclass of: Restriction
  on property: device origin organization
  has value: Monash University
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3045
created: 2024-06-25T18:00:00Z
description: Gennaris is a cortical visual prosthesis. It has been designed to bypass damage to the eye and optic nerve, to restore functional vision to people who have lost their sight through traumatic injury and conditions such as glaucoma and acquired retinal disease. Gennaris is currently preparing to undergo human clinical trials in Australia.
implant location: cortical
electrode layout: hexagonal
implant type: electronic
electrode number: 473

HARP High-Acuity Retinal Prosthesis
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Iridium Medical Technology Co. Ltd.
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3046
created: 2024-06-25T18:00:00Z
description: HARP is a proprietary contact lens-shaped, 4000 pixel retinal prostheses currently in development by Iridium Medical Technologies. HARP is made for patients with Retinitis Pigmentosa and Age-Related Macular Degeneration.
implant location: subretinal
implant type: electronic

IMI Retinal Implant System
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: IMI Intelligent Medical Implants GmbH
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3047
created: 2024-06-25T18:00:00Z
implant location: epiretinal
implant type: electronic
electrode number: 49

IMIE 256 Channel Intelligent Micro Implant Eye
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: IntelliMicro Medical Co., Ltd.
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3048
created: 2024-06-25T18:00:00Z
description: The 256 Channel Intelligent Micro Eye Implant is an epiretinal implant developed by IntelliMicro Micro Co and Golden Eye Bionic. The implant features advanced technology for a micro implant with an extended electrode array.
implant location: epiretinal
electrode diameter: 210
implant type: electronic
electrode number: 256

Intracortical Visual Prosthesis
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: MicroProbes for Life Science
subclass of: Restriction
  on property: device origin organization
  has value: Illinois Institute of Technology
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3049
created: 2024-06-25T18:00:00Z
description: The Intracortical Visual Prosthesis is currently being developed at the Illinois Institute of Technology and is being prepared for clinical testing.
implant location: cortical
implant type: electronic
electrode number: 16

IRIS I
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Pixium Vision
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3050
created: 2024-06-25T18:00:00Z
description: Pixium's first device, IRIS1 (Intelligent Retinal Implantable System), used an epi-retinal implant (on the retinal surface) and made it to clinical trials with the goal of obtaining CE Mark.
implant location: epiretinal
electrode pitch: 120
electrode diameter: 250
implant type: electronic
electrode number: 49

IRIS II
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Pixium Vision
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3051
created: 2024-06-25T18:00:00Z
description: The IRIS II is a second generation epiretinal implant developed by Pixium vision to deliver light and shape perception, and to localize objects giving the patient the ability to negotiate unfamiliar environments. It consists of a 150 electrode array which allows for a better perceieved visual resolution by the user. The IRIS implant also uses asynchronous time-based image sensor technology resulting in faster, real-time image processing.
implant location: epiretinal
ce mark year: 2016
implant type: electronic
electrode number: 150

Leuven Optic Nerve Visual Prosthesis
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3052
created: 2024-06-25T18:00:00Z
description: The optic nerve visual prosthesis (ONVP) uses a self-sizing spiral cuff electrode to electrically stimulate the optic nerve and thus create the perception of phosphenes.
implant location: optic nerve
implant type: electronic
electrode number: 1

Link N1
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Neuralink
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3053
created: 2024-06-25T18:00:00Z
description: The N1 implant consists of 1024 electrodes distributed across 64 threads, composed mostly of polyimide with a thin gold or platinum conductor, which are inserted into the brain through an automated process performed by a surgical robot (R1). Each thread consists of an area of wires that contains electrodes capable of locating electrical signals in the brain, and a sensory area where the wire interacts with an electronic system that allows amplification and acquisition of the brain signal. Neuralink received FDA approval for human clinical trials with the N1 in May 2023. On January 29, 2024, [Musk said](https://twitter.com/elonmusk/status/1752098683024220632) that Neuralink had successfully implanted a Neuralink device in a human on the day prior, and that the patient was recovering:"Initial results show promising neuron spike detection".
implant location: cortical
implant type: electronic
electrode number: 1024

Newcastle Visual Prosthesis
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3054
created: 2024-06-25T18:00:00Z
description: The Optogenetic Retinal Prostheses uses an optoelectronic headset to capture the visual scene, have an LED array display the image onto photosensitized retinal cells and stimulate them with light. A key advantage of this approach is that it is possible to target ON and OFF bipolar cells.
implant location: cortical
implant type: optogenetic

NR600
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Nano Retina
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3055
created: 2024-06-25T18:00:00Z
description: The miniature Nano Retina device, the NR600 Implant, replaces the functionality of the damaged photoreceptor cells and creates the electrical stimulation required to activate the remaining healthy retinal cells. NR600 consists of two components; a miniature implantable chip and a set of eyeglasses worn by the patient.
implant location: subretinal
electrode layout: 26x26
implant type: electronic

OpticSELINE
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3056
created: 2024-06-25T18:00:00Z
description: OpticSELENE is a device with intraneural electrodes that stimulates the optic nerve with light sensation to promote activation of the visual cortex-in to try to restore the sight of the blind.
implant location: optic nerve
implant type: electronic

Optoelectronic Nanowire Retinal Prosthesis
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Nanovision Biosciences
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3057
created: 2024-06-25T18:00:00Z
implant location: subretinal
implant type: optogenetic

OPTOEPIRET
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Epi-Ret GmBH
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3058
created: 2024-06-25T18:00:00Z
description: OPTOEPIRET extends the EPIRET implant with an integrated epiretinal recording of the image produced by the eye lens onto the retina.
implant location: epiretinal
implant type: electronic

Orion Cortical Visual Prosthesis System
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Vivani Medical
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3059
created: 2024-06-25T18:00:00Z
description: The Orion Visual Cortical Prosthesis System is an implanted cortical stimulation device intended to provide useful artificial vision to individuals who are blind due to a wide range of causes, including glaucoma, diabetic retinopathy, optic nerve injury or disease, and eye injury. (Eyewire, 2019).
implant location: cortical
implant type: electronic

OUReP
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Minori Industry Co., Ltd.
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3060
created: 2024-06-25T18:00:00Z
description: Okayama University-type retinal prosthesis (OUReP) is a photoelectric dye-coupled polyethylene film which generates electric potential in response to light and stimulates nearby neurons.
implant location: subretinal
implant type: electronic

Phoenix 99
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Bionic Vision Technologies
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3061
created: 2024-06-25T18:00:00Z
description: The new Phoenix99 bionic eye being developed by engineers at the University of Sydney uses a camera linked to a retinal implant to help people with a debilitating problem with their vision to see again.
implant location: suprachoroidal
implant type: electronic
electrode number: 98

POLYRETINA
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3062
created: 2024-06-25T18:00:00Z
description: POLYRETINA is a foldable, wide-field, epiretinal prosthesis that can wirelessly stimulate retinal ganglion cells. The current prototype, POLYRETINA β, features 10,498 Titanium-Nitride electrodes (80μm diameter, 120μm pitch) distributed in a tiled fashion over a 13mm-diameter active area. Future prototypes are planned to miniaturize the electrode design and increase the number of electrodes (POLYRETINA γ: 18,693 electrodes, 60μm diameter, 90μm pitch; POLYRETINA δ: 42,235 electrodes, 60μm diameter, 90μm pitch). So far, device safety and efficacy has been assessed <emph>ex vivo</emph> and <emph>in vitro</emph>.
implant location: epiretinal
electrode layout: hexagonal
electrode pitch: 120
electrode diameter: 80
implant type: electronic
electrode number: 10,498

PolySTIM
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Cortivision
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3063
created: 2024-06-25T18:00:00Z
description: PolySTIM is an implantable wireless intracortical interface designed to aid the visually impaired. It uses a multi-chip intracortical microstimulation system for wireless data and power transmission.
implant location: cortical
implant type: electronic

PRIMA
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Pixium Vision
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3064
created: 2024-06-25T18:00:00Z
description: The Prima System is intended to partially replace the normal physiological function of the eyes photoreceptor cells by electrically stimulating the nerve cells of the inner retina, which then transmit the visual information to the brain via the optic nerve.
implant location: subretinal
implant type: electronic
electrode number: 378

QuantumRetina
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3065
created: 2024-06-25T18:00:00Z
implant location: epiretinal
implant type: electronic

Science Eye
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Science
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3066
created: 2024-06-25T18:00:00Z
description: The Science Eye is a visual prosthesis targeted at retinitis pigmentosa (RP) and dry age-related macular degeneration (AMD), two forms of serious blindness presently without good options for patients. The Science Eye is a combination device that uses an optogenetic gene therapy targeted at the cells of the optic nerve (the retinal ganglion cells) in conjunction with an implanted flexible thin-film, ultradense microLED display panel inserted directly over the retina.
implant location: epiretinal
implant type: optogenetic

Seoul Artificial Retina
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3067
created: 2024-06-25T18:00:00Z
description: Seoul Artificial Retina Project started since the year 2000 at National University Seoul in Korea, aiming to develop a safe retinal prothesis implant for sight restoration.
implant location: suprachoroidal
electrode layout: 4x4
electrode pitch: 100
implant type: electronic
electrode number: 16

SiBionics Prosthesis
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: SiBionics
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3068
created: 2024-06-25T18:00:00Z
description: The SIBionics prostheses features 60 electrodes, high system complexity, and an integrated circuit.
implant location: epiretinal
implant type: electronic
electrode number: 80

Stanford Artificial Retina Project
type: Class
subclass of: bionic vision device
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3069
created: 2024-06-25T18:00:00Z
description: The goal of the Stanford Artificial Retina Project is to develop an advanced artificial retina that will reproduce the precise retinal code at a cellular resolution with cell-type specificity, resulting in high-fidelity artificial vision.
implant location: epiretinal
implant type: electronic

STS Retinal Prosthesis
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Nidek Co., Ltd.
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3070
created: 2024-06-25T18:00:00Z
description: The semichronic suprachoroid transscleral (STS) prosthesis is developed by Fujikado et al. in Japan. In 2011 and 2016, this retinal prosthesis was reported to be able to elicit phosphenes in all five patients with advanced RP without major complications.
implant location: suprachoroidal
electrode layout: 7x7
electrode pitch: 700
electrode diameter: 500
implant type: electronic
electrode number: 49

Suprachoroidal Prosthesis (24-channel)
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Bionic Vision Technologies
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3071
created: 2024-06-25T18:00:00Z
description: The BVT Bionic Eye System is a suprachoroidal implant manufactured by Bionic Vision Technologies. The Gen1 Bionic Eye System was previously known as BVA 24 and was manufactured by the Bionic Vision Australia consortium in 2012. The commercialization rights and research rights of BVA were then taken over by Bionic Vision Technologies (BVT) in 2017. The Gen1 Bionic Eye System used a non-implantable percutaneous connector whereas the Gen2 Bionic Eye System is fully implantable. BVT is now developing the Gen3 Bionic Eye System.
implant location: suprachoroidal
implant type: electronic

Suprachoroidal Prosthesis (44-channel)
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Bionic Vision Technologies
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3072
created: 2024-06-25T18:00:00Z
description: The 44 Channel Suprachoroidal Retinal Prosthesis is a second generation device boasting a higher electrode array and larger field of view than the first generation device launched by Bionic Vision Technologies. Since launching a 4-patient clinical trial in 2018, the results have indicated that the device offers functional benefits to patients while providing a safe and reproducible surgical procedure.
implant location: suprachoroidal
implant type: electronic
electrode number: 44

Thalamic Visual Prosthesis
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Bionic Eye Technologies
subclass of: Restriction
  on property: device origin organization
  has value: Massachusetts General Hospital
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3073
created: 2024-06-25T18:00:00Z
description: The goal of the MGH Thalamic Visual Prosthesis project is to build a machine-brain interface that can convey information from an external visual source directly to the visual parts of the brain for image processing.
implant location: thalamic
implant type: electronic

Utah Intracortical Electrode Array
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Blackrock Microsystems LLC
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3074
created: 2024-06-25T18:00:00Z
description: Utah intracortical Electrode Array (UIEA) is a fixed geometry penetrating intracortical microelectrode array developed by a team at the University of Utah in the 1990s, aiming to provide a solid foundation for creating a cortically based visual prosthesis.
implant location: cortical
electrode layout: 10x10
implant type: electronic
electrode number: 100

VISNE
type: Class
subclass of: bionic vision device
subclass of: Restriction
  on property: device commercialized by
  has value: Nerve Biomed S.L.
contributor: Bill Duncan
contributor: https://orcid.org/0009-0006-7251-3075
created: 2024-06-25T18:00:00Z
implant location: thalamic
electrode layout: 4x6
implant type: electronic
electrode number: 24

example to be eventually removed
type: NamedIndividual
editor preferred label: example to be eventually removed

failed exploratory term
type: NamedIndividual
editor preferred label: failed exploratory term
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
term editor: Person:Alan Ruttenberg

metadata complete
type: NamedIndividual
editor preferred label: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
editor preferred label: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
editor preferred label: ready for release
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
editor preferred label: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
editor preferred label: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
editor preferred label: pending final vetting
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

placeholder removed
type: NamedIndividual
editor preferred label: placeholder removed

terms merged
type: NamedIndividual
editor preferred label: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
editor preferred label: term imported
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
editor preferred label: term split
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

universal
type: NamedIndividual
editor preferred label: universal
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
term editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
editor preferred label: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
term editor: Alan Ruttenberg

named class expression
type: NamedIndividual
editor preferred label: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
term editor: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
editor preferred label: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
editor preferred label: requires discussion
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
term editor: Alan Ruttenberg
definition source: group:OBI

out of scope
type: NamedIndividual
definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/77
ontology term requester: https://orcid.org/0000-0001-5208-3432

domain entity does not exist
type: NamedIndividual
definition: The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
editor note: This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
term editor: http://orcid.org/0000-0002-4142-7153
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/136
ontology term requester: https://orcid.org/0000-0002-4142-7153

Michael Beyeler
type: NamedIndividual

Daniel Rathbun
type: NamedIndividual

Bill Duncan
type: NamedIndividual

Alexander D. Diehl
type: NamedIndividual

John Beverley
type: NamedIndividual

Patrick Ray
type: NamedIndividual

Gopikrishnan M. Chandrasekharan
type: NamedIndividual
contributor: Bill Duncan
created: 2024-06-25T03:46:56Z
label: Gopikrishnan M Chandrasekharan

Jisoo Seo
type: NamedIndividual

Sam Smith
type: NamedIndividual

A-Neuron Electronic Corp.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

ATLAS Neuroengineering
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Avery Laboratories
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Biomedical Technologies
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Bionic Eye Technologies
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Bionic Sight, LLC
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Bionic Vision Technologies
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Blackrock Microsystems Europe GmbH
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Blackrock Microsystems LLC
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Cortigent, Inc.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Cortivision
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Epi-Ret GmBH
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Golden Eye Bionics, LLC
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Grey Innovations
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

iBionics
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

IMI Intelligent Medical Implants GmbH
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

IntelliMicro Medical Co., Ltd.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Iridium Medical Technology Co. Ltd.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

MicroProbes for Life Science
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Nano Retina
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Nanovision Biosciences
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Nerve Biomed S.L.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Neuralink
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Nidek Co., Ltd.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Nurotron Biotechnology Co., Ltd.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Optobionics
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Phosphoenix
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Pixium Vision
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Polystim Neurotechnologies
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Retina Implant AG
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

ReVision Implant
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

SCHOTT MiniFab
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Science
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Second Sight Medical Products
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Sensor-Tech
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

SiBionics
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Sigenics
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Visus Technology, Inc.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Vivani Medical
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Minori Industry Co., Ltd.
type: NamedIndividual
type: organization
contributor: Bill Duncan
created: 2024-02-20T18:00:00Z

Universität Tübingen
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

National Chiao Tung University
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

University of Southern California
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

University of London
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

Cornell University
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

Shanghai Jiao Tong University
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

Dobelle Institute
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

Polytechnique Montréal
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

Monash University
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

Illinois Institute of Technology
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z

Massachusetts General Hospital
type: NamedIndividual
type: organization
contributor: Gopikrishnan M. Chandrasekharan
created: 2024-04-26T18:00:00Z