Vibrational Spectroscopy Ontology
type: Ontology
version IRI: vibso.owl
contributor: Rainer Stosch
contributor: Philip Strömert
contributor: Giacomo Lanza
contributor: Johannes Hunold
creator: NFDI4Chem
creator: VIBSO Workgroup
description: _WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays.
license: https://creativecommons.org/licenses/by/4.0/
version info: 2024-09-23

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
sub property of: label

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
sub property of: label

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
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>

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

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: ready for release
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>

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

antisymmetric property
type: AnnotationProperty
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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: SynonymTypeProperty

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
has exact synonym: INN
sub property of: SynonymTypeProperty

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: SynonymTypeProperty

acronym
type: AnnotationProperty
example of usage: NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
definition: A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/135
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-11-01
sub property of: SynonymTypeProperty

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

contributor
type: AnnotationProperty

creator
type: AnnotationProperty

description
type: AnnotationProperty

license
type: AnnotationProperty

title
type: AnnotationProperty

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

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred term: 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: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative label: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable entity
RO_0040042: quality
RO_0040042: specifically dependent continuant
RO_0040042: generically dependent continuant
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
editor preferred term: 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: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative label: has_part
RO_0001900: RO_0001901
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

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

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
definition: A (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: entity
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition: A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
term editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

is quality measurement of
type: ObjectProperty
sub property of: is about
inverse of: is quality measured as
domain: measurement datum
range: quality
definition: m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
term editor: Alan Ruttenberg

denoted by
type: ObjectProperty
domain: entity
range: information content entity
definition: inverse of the relation 'denotes'
term editor: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/206

is quality measured as
type: ObjectProperty
has curation status: metadata complete
definition: inverse of the relation of is quality measurement of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
term editor: Person:Alan Ruttenberg

is_supported_by_data
type: ObjectProperty
range: data item
editor preferred term: is_supported_by_data
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
has curation status: ready for release
definition: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
term editor: OBI
definition source: OBI
definition source: Philly 2011 workshop

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
definition: The inverse property of is_specified_input_of
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: is_specified_input_of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
editor preferred term: has_specified_output
has curation status: ready for release
definition: The inverse property of is_specified_output_of
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: is_specified_output_of
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred term: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: metadata complete
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred term: objective_achieved_by
has curation status: ready for release
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
term editor: OBI
definition source: OBI

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

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization
editor preferred term: has organization member
has curation status: metadata incomplete
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
term editor: Person: Jie Zheng

specifies value of
type: ObjectProperty
sub property of: is about
domain: value specification
editor preferred term: specifies value of
has curation status: metadata incomplete
definition: A relation between a value specification and an entity which the specification is about.

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

has performer
type: ObjectProperty
sub property of: has participant
domain: planned process
range: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
    union of: device
  intersection of: Restriction
    on property: has role
    some values from: investigation agent role
editor preferred term: has performer
has curation status: requires discussion
definition: A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process.
term editor: OBI
definition source: OBI
comment: The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system).

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: bearer of
type: FunctionalProperty
editor preferred term: inheres in
example of usage: this fragility inheres in this vase
example of usage: this fragility is a characteristic of this vase
example of usage: this red color inheres in this apple
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.
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative 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.
label: inheres in

bearer of
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred term: 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
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative label: bearer_of
alternative label: is bearer of
RO_0001900: RO_0001901
label: has characteristic

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

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative label: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative label: function_of
alternative label: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative label: is quality of
alternative label: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative label: is role of
alternative label: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative label: has_function

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

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in subset: RO_0002259
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

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
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
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

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

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

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative label: is member of
alternative label: member part of
definition source: SIO
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
RO_0001900: RO_0001901

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

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

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

has numerator
type: ObjectProperty
type: AsymmetricProperty
definition: the relationship between a fraction and the number above the line
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

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

has denominator
type: ObjectProperty
definition: the relationship between a fraction and the number below the line (or divisor)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

has measurement value
type: DatatypeProperty
domain: scalar measurement datum
range: double

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: value specification
range: real
editor preferred term: has specified numeric value
has curation status: metadata complete
definition: A relation between a value specification and a number that quantifies it.
editor note: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
term editor: PERSON: James A. Overton
definition source: OBI

has specified value
type: DatatypeProperty
domain: value specification
editor preferred term: has specified value
has curation status: metadata incomplete
definition: A relation between a value specification and a literal.
editor note: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
definition source: OBI

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
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 term: 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
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
disjoint with: specifically dependent continuant
disjoint with: generically 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]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

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

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

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

spatial region
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

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

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

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

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

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

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

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

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

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

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

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

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

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

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

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

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

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

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

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

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

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

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

process
type: Class
subclass of: occurrent
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: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
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
disjoint with: quality
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

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

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

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
editor preferred term: quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: pato.owl
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

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

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
editor preferred term: specifically dependent continuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: pato.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

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

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

Axiom
annotated source: fiat object part
annotated property: elucidation
annotated target: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

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

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

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

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

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

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

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

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

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

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

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

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: elucidation
annotated target: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

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

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
annotated source: object
annotated property: elucidation
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

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: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
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

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: definition
annotated target: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

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

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

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

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

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

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
editor preferred term: 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

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

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

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

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

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

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

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

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

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

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

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

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: a marriage bond, an instance of requited love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]

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

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

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

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

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

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

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

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

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative label: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

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

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
annotated source: history
annotated property: elucidation
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

chemical entity
type: Class
subclass of: material entity
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
has exact synonym: chemical entity
has OBO namespace: chebi_ontology
id: CHEBI:24431
in subset: 3 STAR

Axiom
annotated source: chemical entity
annotated property: has exact synonym
annotated target: chemical entity
has db xref: UniProt

chemical substance
type: Class
subclass of: chemical entity
definition: A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
has OBO namespace: chebi_ontology
has related synonym: Chemische Substanz
id: CHEBI:59999
in subset: 3 STAR

Axiom
annotated source: chemical substance
annotated property: has related synonym
annotated target: Chemische Substanz
has db xref: ChEBI

mixture
type: Class
subclass of: chemical substance
definition: A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
has OBO namespace: chebi_ontology
has related synonym: Mischung
id: CHEBI:60004
in subset: 3 STAR

Axiom
annotated source: mixture
annotated property: has related synonym
annotated target: Mischung
has db xref: ChEBI

chemical imaging
type: Class
subclass of: imaging assay
definition: The simultaneous measurement of spectra and images. A radiation source illuminates the sample and a series of spatially resolved spectra are collected.
has exact synonym: CIS
has exact synonym: chemical imaging spectrometry
has exact synonym: chemical imaging spectroscopy
has exact synonym: hyperspectral imaging
has exact synonym: imaging spectrometry
has exact synonym: imaging spectroscopy
has exact synonym: multispectral imaging
has exact synonym: spectral imaging
has exact synonym: spectroscopic imaging
id: CHMO:0000049

Axiom
annotated source: chemical imaging
annotated property: definition
annotated target: The simultaneous measurement of spectra and images. A radiation source illuminates the sample and a series of spatially resolved spectra are collected.
has db xref: https://orcid.org/0000-0002-0640-0422

Raman microscopy
type: Class
equivalent class: Class
subclass of: Raman spectroscopy
subclass of: vibrational microscopy
definition: The collection of spatially resolved Raman spectra of a sample during optical microscopy.
has alternative id: CHMO:0000673
has alternative id: FIX:0000697
has exact synonym: LRMA
has exact synonym: MRS
has exact synonym: RCIS
has exact synonym: Raman chemical imaging spectrometry
has exact synonym: Raman chemical imaging spectroscopy
has exact synonym: Raman imaging
has exact synonym: Raman mapping
has exact synonym: Raman micro spectrometry
has exact synonym: Raman micro spectroscopy
has exact synonym: Raman microprobe spectroscopy
has exact synonym: Raman microspectrometry
has exact synonym: Raman microspectroscopy
has exact synonym: Raman spectral imaging
has exact synonym: laser Raman microanalysis
has exact synonym: micro Raman spectrometry
has exact synonym: micro Raman spectroscopy
has exact synonym: micro-Raman spectrometry
has exact synonym: micro-Raman spectroscopy
id: CHMO:0000056

Axiom
annotated source: Raman microscopy
annotated property: equivalentClass
annotated target: Class
comment: Equivalence asserted manually in VIBSO based on the textual definition of this class.

Axiom
annotated source: Raman microscopy
annotated property: definition
annotated target: The collection of spatially resolved Raman spectra of a sample during optical microscopy.
has db xref: https://doi.org/10.1039/b815117b

microscopy
type: Class
equivalent class: microscopy assay
subclass of: imaging assay
subclass of: Restriction
  on property: BFO_0000057
  some values from: microscope
definition: Any technique where a microscope is used to view a small object (or specimen) by producing a magnified image.
has alternative id: FIX:0000005
id: CHMO:0000067

Axiom
annotated source: microscopy
annotated property: equivalentClass
annotated target: microscopy assay
comment: Equivalence asserted manually in VIBSO based on the definitions of both classes.

Axiom
annotated source: microscopy
annotated property: definition
annotated target: Any technique where a microscope is used to view a small object (or specimen) by producing a magnified image.
has db xref: https://orcid.org/0000-0002-0640-0422

light microscopy assay
type: Class
subclass of: microscopy
subclass of: microscopy assay
definition: Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
alternative label: OM
alternative label: light microscopy
alternative label: optical microscopy
definition source: CHMO
has alternative id: FIX:0000113
has exact synonym: OM
has exact synonym: light microscopy
id: CHMO:0000102
label: optical microscopy

Axiom
annotated source: light microscopy assay
annotated property: definition
annotated target: Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
has db xref: https://orcid.org/0000-0002-0640-0422

confocal microscopy
type: Class
subclass of: light microscopy assay
definition: Microscopy where visible light coming from the specimen is collected and guided through a pinhole before it is detected. The pinhole allows only light from the focal point to pass to the detector, reducing background interference.
id: CHMO:0000103

Axiom
annotated source: confocal microscopy
annotated property: definition
annotated target: Microscopy where visible light coming from the specimen is collected and guided through a pinhole before it is detected. The pinhole allows only light from the focal point to pass to the detector, reducing background interference.
has db xref: ISBN:978-3-540-74597-6

spectroscopy
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: spectrum
definition: The study of the interaction of a sample with radiation or particles for measurement or detection.
has exact synonym: spectrometry
id: CHMO:0000228

Axiom
annotated source: spectroscopy
annotated property: definition
annotated target: The study of the interaction of a sample with radiation or particles for measurement or detection.
has db xref: https://doi.org/10.1351/goldbook.S05848

microspectroscopy
type: Class
equivalent class: Class
subclass of: chemical imaging
subclass of: light microscopy assay
subclass of: spectroscopy
definition: Any type of chemical imaging spectroscopy where an optical microscope is used to image the sample and locate a small area for spectral analysis.
has exact synonym: microspectrometry
id: CHMO:0000581

Axiom
annotated source: microspectroscopy
annotated property: equivalentClass
annotated target: Class
comment: Equivalence asserted manually in VIBSO based on the textual definition of this class.

Axiom
annotated source: microspectroscopy
annotated property: definition
annotated target: Any type of chemical imaging spectroscopy where an optical microscope is used to image the sample and locate a small area for spectral analysis.
has db xref: https://orcid.org/0000-0002-0640-0422

vibrational spectroscopy
type: Class
subclass of: spectroscopy
definition: Spectroscopy which probes the vibrational degrees of freedom of a molecule.
has exact synonym: vibrational spectroscopic analysis
id: CHMO:0000628

Axiom
annotated source: vibrational spectroscopy
annotated property: definition
annotated target: Spectroscopy which probes the vibrational degrees of freedom of a molecule.
has db xref: https://orcid.org/0000-0002-0640-0422

inelastic electron tunnelling spectroscopy
type: Class
subclass of: vibrational spectroscopy
definition: Spectroscopy where a metal-molecule-metal sandwich is formed and electrons tunnel from metal to metal through the molecules. Any additional molecules adsorbed onto the inner layer of the sandwhich can affect the tunneling via the excitation of vibrational states.
has exact synonym: IETS
has exact synonym: inelastic electron tunnelling spectrometry
id: CHMO:0000629

Axiom
annotated source: inelastic electron tunnelling spectroscopy
annotated property: definition
annotated target: Spectroscopy where a metal-molecule-metal sandwich is formed and electrons tunnel from metal to metal through the molecules. Any additional molecules adsorbed onto the inner layer of the sandwhich can affect the tunneling via the excitation of vibrational states.
has db xref: https://orcid.org/0000-0002-0640-0422

infrared absorption spectroscopy
type: Class
subclass of: vibrational spectroscopy
definition: Spectroscopy where the sample absorbs radiation from the infrared region (0.78 to 1000 micrometres).
has alternative id: FIX:0000015
has alternative id: FIX:0000658
has exact synonym: IR absorption spectrometry
has exact synonym: IR absorption spectroscopy
has exact synonym: IR spectrometry
has exact synonym: IR spectrophotometry
has exact synonym: IR spectroscopy
has exact synonym: infra-red absorption spectrometry
has exact synonym: infra-red absorption spectroscopy
has exact synonym: infra-red spectrometry
has exact synonym: infra-red spectrophotometry
has exact synonym: infrared (IR) spectroscopy
has exact synonym: infrared absorption spectrometry
has exact synonym: infrared spectrometry
has exact synonym: infrared spectrophotometry
has exact synonym: infrared spectroscopy
has related synonym: IR
id: CHMO:0000630

Axiom
annotated source: infrared absorption spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from the infrared region (0.78 to 1000 micrometres).
has db xref: FIX:0000015
has db xref: FIX:0000658
has db xref: ISBN:978-3-540-74597-6

Axiom
annotated source: infrared absorption spectroscopy
annotated property: has related synonym
annotated target: IR
has synonym type: non-mining synonym

infrared evanescent wave spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy using radiation in the infrared region (0.78–1000 μm) where an evanescent wave is generated using an optical fibre.
has exact synonym: IR-EWS
has exact synonym: infra-red evanescent wave spectrometry
has exact synonym: infrared evanescent wave spectrometry
has exact synonym: infrared evanescent wave spectroscopy
id: CHMO:0000631

Axiom
annotated source: infrared evanescent wave spectroscopy
annotated property: definition
annotated target: Spectroscopy using radiation in the infrared region (0.78–1000 μm) where an evanescent wave is generated using an optical fibre.
has db xref: https://doi.org/10.1088/0022-3727/34/9/306

infrared multiphoton dissociation spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm) with sufficient energy to cause photodissociation by the absorption of two or more photons.
has exact synonym: IRMPD spectrometry
has exact synonym: IRMPD spectroscopy
has exact synonym: infra-red multiphoton dissociation spectrometry
has exact synonym: infrared multiphoton dissociation spectrometry
has exact synonym: infrared multiphoton dissociation spectroscopy
id: CHMO:0000633

Axiom
annotated source: infrared multiphoton dissociation spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm) with sufficient energy to cause photodissociation by the absorption of two or more photons.
has db xref: https://orcid.org/0000-0002-0640-0422

resonant infrared multiphoton dissociation spectroscopy
type: Class
subclass of: infrared multiphoton dissociation spectroscopy
definition: Spectroscopy where the sample absorbs resonant radiation from the infrared region (0.78–1000 μm) with sufficient energy to cause photodissociation by the absorption of two or more photons.
has exact synonym: IR REMPD
has exact synonym: IR REMPD spectrometry
has exact synonym: IR REMPD spectroscopy
has exact synonym: IR-REMPD
has exact synonym: resonance-enhanced infrared multiphoton dissociation spectrometry
has exact synonym: resonance-enhanced infrared multiphoton dissociation spectroscopy
has exact synonym: resonant infra-red multiphoton dissociation spectrometry
has exact synonym: resonant infra-red multiphoton dissociation spectroscopy
has exact synonym: resonant infrared multiphoton dissociation spectrometry
id: CHMO:0000634

Axiom
annotated source: resonant infrared multiphoton dissociation spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs resonant radiation from the infrared region (0.78–1000 μm) with sufficient energy to cause photodissociation by the absorption of two or more photons.
has db xref: https://orcid.org/0000-0002-0640-0422

mid-infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation in the mid infrared region (3–8 μm).
has exact synonym: mid infrared spectroscopy
has exact synonym: mid-IR
has exact synonym: mid-IR spectroscopy
has exact synonym: mid-infra-red spectrometry
has exact synonym: mid-infrared spectrometry
id: CHMO:0000635

Axiom
annotated source: mid-infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation in the mid infrared region (3–8 μm).
has db xref: FIX:0000642
has db xref: ISBN:0-534-98144-5

Fourier transform infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a Fourier transform.
has alternative id: FIX:0000110
has exact synonym: FT-IR
has exact synonym: FT-IR spectroscopy
has exact synonym: FTIR
has exact synonym: FTIR spectrometry
has exact synonym: FTIR spectroscopy
has exact synonym: Fourier transform infra-red absorption spectroscopy
has exact synonym: Fourier transform infra-red spectrometry
has exact synonym: Fourier transform infrared (FT-IR)
has exact synonym: Fourier transform infrared (FT-IR) spectroscopy
has exact synonym: Fourier transform infrared spectrometry
has exact synonym: Fourier transform infrared spectroscopy
has exact synonym: Fourier-transform infra-red absorption spectrometry
has exact synonym: Fourier-transform infrared (FTIR) absorption spectroscopy
id: CHMO:0000636

Axiom
annotated source: Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

micro infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation from a finely focused beam (<10 μm diameter) of infrared light (0.78–1000 μm).
has exact synonym: infrared microanalysis
has exact synonym: micro infra-red spectrometry
has exact synonym: micro-infrared spectrometry
has exact synonym: micro-infrared spectroscopy
id: CHMO:0000637

Axiom
annotated source: micro infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from a finely focused beam (<10 μm diameter) of infrared light (0.78–1000 μm).
has db xref: https://orcid.org/0000-0002-0640-0422

near-infrared absorption spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation from the near infrared region (0.8–2 μm).
has exact synonym: NIR absorbance spectrometry
has exact synonym: NIR absorbance spectroscopy
has exact synonym: near infra-red absorbance spectrometry
has exact synonym: near infra-red absorbance spectroscopy
has exact synonym: near infra-red absorption spectrometry
has exact synonym: near infra-red spectrometry
has exact synonym: near infrared absorbance spectrometry
has exact synonym: near infrared absorbance spectroscopy
has exact synonym: near infrared absorption spectrometry
has exact synonym: near infrared absorption spectroscopy
has exact synonym: near infrared spectrometry
has exact synonym: near infrared spectroscopy
has exact synonym: near-infra-red absorption spectrometry
has related synonym: NIRS
id: CHMO:0000638

Axiom
annotated source: near-infrared absorption spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from the near infrared region (0.8–2 μm).
has db xref: FIX:0000321
has db xref: ISBN:978-3-540-74597-6

Axiom
annotated source: near-infrared absorption spectroscopy
annotated property: has related synonym
annotated target: NIRS
has synonym type: non-mining synonym

Fourier transform near infrared absorbance spectroscopy
type: Class
subclass of: near-infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs a single pulse of radiation from the near infrared region (0.8–2 μm) and the spectrum obtained is subject to a Fourier transform.
has exact synonym: FT NIRS
has exact synonym: FT-NIRS
has exact synonym: FTNIRS
has exact synonym: Fourier transform near infra-red absorbance spectrometry
has exact synonym: Fourier transform near infra-red absorption spectrometry
has exact synonym: Fourier transform near infra-red spectrometry
has exact synonym: Fourier transform near infra-red spectroscopy
has exact synonym: Fourier transform near infrared absorbance spectrometry
has exact synonym: Fourier transform near infrared absorbance spectroscopy
has exact synonym: Fourier transform near infrared absorption spectrometry
has exact synonym: Fourier transform near infrared absorption spectroscopy
id: CHMO:0000639

Axiom
annotated source: Fourier transform near infrared absorbance spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs a single pulse of radiation from the near infrared region (0.8–2 μm) and the spectrum obtained is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

non-dispersive infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the difference in infrared radiation (0.78–1000 μm) bsorption of a sample cell against a reference cell is measured.
has exact synonym: NDIR
has exact synonym: NDIR spectrometry
has exact synonym: NDIR spectroscopy
has exact synonym: non-dispersive infra-red spectrometry
has exact synonym: non-dispersive infra-red spectroscopy
has exact synonym: non-dispersive infrared spectrometry
id: CHMO:0000640

Axiom
annotated source: non-dispersive infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the difference in infrared radiation (0.78–1000 μm) bsorption of a sample cell against a reference cell is measured.
has db xref: ISBN:0824753593

surface enhanced infrared absorption spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the rough metal surface of a sample absorbs radiation in the infrared region (0.78–1000 μm).
has exact synonym: SEIRA
has exact synonym: SEIRA spectrometry
has exact synonym: SEIRA spectroscopy
has exact synonym: surface enhanced infra-red absorption spectrometry
has exact synonym: surface enhanced infra-red absorption spectroscopy
has exact synonym: surface enhanced infrared absorption spectrometry
id: CHMO:0000641

Axiom
annotated source: surface enhanced infrared absorption spectroscopy
annotated property: definition
annotated target: Spectroscopy where the rough metal surface of a sample absorbs radiation in the infrared region (0.78–1000 μm).
has db xref: https://doi.org/10.1039/b805223a

transient infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where transient species such as radicals, ions or reactive intermediates are studied using pulses from an infrared laser. The infrared absorbance of the sample before and after an excitation laser pulse is measured.
has alternative id: FIX:0001068
has exact synonym: IR laser transient absorption spectroscopy
has exact synonym: IR transient absorption spectroscopy
has exact synonym: TIRS
has exact synonym: infrared laser transient absorption spectroscopy
has exact synonym: infrared transient absorption spectroscopy
has exact synonym: transient infrared spectrometry
has exact synonym: transient infrared spectroscopy
id: CHMO:0000642

Axiom
annotated source: transient infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where transient species such as radicals, ions or reactive intermediates are studied using pulses from an infrared laser. The infrared absorbance of the sample before and after an excitation laser pulse is measured.
has db xref: ISBN:9810217498

infrared reflectance spectroscopy
type: Class
subclass of: vibrational spectroscopy
definition: Spectroscopy where the reflection or scattering of infrared radiation (0.78–1000 μm) by a sample is detected.
has alternative id: FIX:0000652
has exact synonym: IR reflectance spectrometry
has exact synonym: IR reflectance spectroscopy
has exact synonym: IR reflection spectroscopy
has exact synonym: infra-red reflectance spectrometry
has exact synonym: infrared reflectance spectrometry
has exact synonym: infrared reflectance spectroscopy
has exact synonym: infrared reflection spectroscopy
id: CHMO:0000643

Axiom
annotated source: infrared reflectance spectroscopy
annotated property: definition
annotated target: Spectroscopy where the reflection or scattering of infrared radiation (0.78–1000 μm) by a sample is detected.
has db xref: https://orcid.org/0000-0002-0640-0422

diffuse reflectance infrared spectroscopy
type: Class
subclass of: infrared reflectance spectroscopy
definition: Spectroscopy where the diffuse reflection of infrared radiation by a sample is measured.
has alternative id: FIX:0000656
has exact synonym: diffuse reflectance IR spectroscopy
id: CHMO:0000644

Axiom
annotated source: diffuse reflectance infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the diffuse reflection of infrared radiation by a sample is measured.
has db xref: https://orcid.org/0000-0002-0640-0422

diffuse reflectance infrared Fourier transform spectroscopy
type: Class
subclass of: diffuse reflectance infrared spectroscopy
definition: Spectroscopy where the diffuse reflection of a single pulse of infrared radiation by a sample is measured, and the spectrum obtained is subject to a Fourier transform.
has exact synonym: DRIFT
has exact synonym: DRIFTS
has exact synonym: diffuse reflectance infra-red Fourier transform spectrometry
has exact synonym: diffuse reflectance infrared Fourier transform spectrometry
has exact synonym: diffuse reflectance infrared Fourier transform spectroscopy
has exact synonym: diffuse reflectance infrared spectroscopy by Fourier transform
id: CHMO:0000645

Axiom
annotated source: diffuse reflectance infrared Fourier transform spectroscopy
annotated property: definition
annotated target: Spectroscopy where the diffuse reflection of a single pulse of infrared radiation by a sample is measured, and the spectrum obtained is subject to a Fourier transform.
has db xref: FIX:0000657
has db xref: https://orcid.org/0000-0002-0640-0422

near-infrared reflectance spectroscopy
type: Class
subclass of: infrared reflectance spectroscopy
definition: Spectroscopy where the reflection or scattering of near infrared radiation (0.8-2 micrometres) by a sample is detected.
has exact synonym: NIR reflectance spectrometry
has exact synonym: NIR reflectance spectroscopy
has exact synonym: NIRS
has exact synonym: near infra-red reflectance spectrometry
has exact synonym: near infrared reflectance spectroscopy
id: CHMO:0000646

Axiom
annotated source: near-infrared reflectance spectroscopy
annotated property: definition
annotated target: Spectroscopy where the reflection or scattering of near infrared radiation (0.8-2 micrometres) by a sample is detected.
has db xref: https://orcid.org/0000-0002-0640-0422

reflection–absorption infrared spectroscopy
type: Class
subclass of: vibrational spectroscopy
definition: Spectroscopy where the absorption and reflection of low incident angle infrared light by the surface molecules of a highly reflective or polished sample is measured.
has exact synonym: IRAS
has exact synonym: IRRAS
has exact synonym: RA-IR
has exact synonym: RAIRS
has exact synonym: infrared reflection absorption spectrometry
has exact synonym: infrared reflection absorption spectroscopy
has exact synonym: reflection absorption (RA) IR
has exact synonym: reflection absorption infra-red spectrometry
has exact synonym: reflection absorption infrared spectrometry
has exact synonym: reflection absorption infrared spectroscopy
has exact synonym: reflection-absorption infrared spectroscopy
id: CHMO:0000647

Axiom
annotated source: reflection–absorption infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the absorption and reflection of low incident angle infrared light by the surface molecules of a highly reflective or polished sample is measured.
has db xref: FIX:0000659
has db xref: ISBN:0-471-96523-5

attenuated total reflectance infrared spectroscopy
type: Class
subclass of: infrared reflectance spectroscopy
definition: Spectroscopy where infrared light is introduced into a prism at an angle exceeding the critical angle for internal reflection. This produces an evanescent wave at the reflecting surface (a surface which is transparent to infrared such as thallium bromide) on which the sample is supported, and the distortion of the evanescent wave by the sample is measured.
has db xref: FIX:0000653
has exact synonym: ATR spectrometry
has exact synonym: ATR spectroscopy
has exact synonym: ATR-IR
has exact synonym: ATR-IR spectrometry
has exact synonym: ATR-IR spectroscopy
has exact synonym: ATR/IR
has exact synonym: ATR/IRS
has exact synonym: MIRS
has exact synonym: attenuated total reflectance infra-red spectroscopy
has exact synonym: attenuated total reflectance spectrometry
has exact synonym: internal reflection spectrometry
has exact synonym: internal reflection spectroscopy
has exact synonym: multiple internal reflection spectrometry
has exact synonym: multiple internal reflection spectroscopy
has related synonym: IRS
id: CHMO:0000648

Axiom
annotated source: attenuated total reflectance infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where infrared light is introduced into a prism at an angle exceeding the critical angle for internal reflection. This produces an evanescent wave at the reflecting surface (a surface which is transparent to infrared such as thallium bromide) on which the sample is supported, and the distortion of the evanescent wave by the sample is measured.
has db xref: ISBN:0-471-96523-5

infrared emission spectroscopy
type: Class
subclass of: vibrational spectroscopy
definition: Spectroscopy where the sample is heated and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has exact synonym: IES
has exact synonym: infra-red emission spectrometry
has exact synonym: infrared emission spectrometry
has exact synonym: infrared emission spectroscopy
id: CHMO:0000649

Axiom
annotated source: infrared emission spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is heated and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has db xref: FIX:0000651
has db xref: https://orcid.org/0000-0002-0640-0422

flame infrared emission spectroscopy
type: Class
subclass of: infrared emission spectroscopy
definition: Spectroscopy where the sample is heated in a flame and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has exact synonym: FIRE
has exact synonym: flame infra-red emission spectrometry
has exact synonym: flame infrared emission spectroscopy
id: CHMO:0000650

Axiom
annotated source: flame infrared emission spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is heated in a flame and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has db xref: https://orcid.org/0000-0002-0640-0422

Fourier transform flame infrared emission spectroscopy
type: Class
subclass of: flame infrared emission spectroscopy
definition: Spectroscopy where the sample is heated in a flame and the infrared radiation (0.78–1000 μm) emitted during cooling is detected. The spectrum obtained is subject to a Fourier transform.
has exact synonym: FT-FIRE
has exact synonym: Fourier transform FIRE
has exact synonym: Fourier transform flame infra-red emission spectrometry
has exact synonym: Fourier transform flame infrared emission spectroscopy
id: CHMO:0000651

Axiom
annotated source: Fourier transform flame infrared emission spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is heated in a flame and the infrared radiation (0.78–1000 μm) emitted during cooling is detected. The spectrum obtained is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

Fourier transform infrared emission spectroscopy
type: Class
subclass of: infrared emission spectroscopy
definition: IR emission spectroscopy where the spectrum is obtained by a single pulse of (UV) radiation, and is subject to a Fourier transform.
has exact synonym: FT-IRES
has exact synonym: FTIRES
has exact synonym: Fourier transform IRES
has exact synonym: Fourier transform infra-red emission spectrometry
has exact synonym: Fourier transform infra-red emission spectroscopy
has exact synonym: Fourier transform infrared emission spectrometry
has exact synonym: Fourier transform infrared emission spectroscopy
has exact synonym: Fourier-transform infrared spectroscopy
id: CHMO:0000652

Axiom
annotated source: Fourier transform infrared emission spectroscopy
annotated property: definition
annotated target: IR emission spectroscopy where the spectrum is obtained by a single pulse of (UV) radiation, and is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

mid-infrared emission spectroscopy
type: Class
subclass of: infrared emission spectroscopy
definition: Spectroscopy where the sample is heated and the mid infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has exact synonym: MIRES
has exact synonym: mid-infra-red emission spectrometry
has exact synonym: mid-infrared emission spectrometry
has exact synonym: mid-infrared emission spectroscopy
id: CHMO:0000653

Axiom
annotated source: mid-infrared emission spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is heated and the mid infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has db xref: ISBN:0-534-98144-5

planar array infrared emission spectroscopy
type: Class
subclass of: infrared emission spectroscopy
definition: Spectroscopy where the sample is heated and the infrared radiation (0.78–1000 μm) emitted during cooling is detected with a two-dimensional focal plane array infrared camera.
has exact synonym: PA IR
has exact synonym: PA IRES
has exact synonym: PA-IR
has exact synonym: PA-IRES
has exact synonym: planar array IR emission spectrometry
has exact synonym: planar array IR emission spectroscopy
has exact synonym: planar array IRES
has exact synonym: planar array infra-red emission spectrometry
has exact synonym: planar array infrared emission spectrometry
has exact synonym: planar array infrared emission spectroscopy
id: CHMO:0000654

Axiom
annotated source: planar array infrared emission spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is heated and the infrared radiation (0.78–1000 μm) emitted during cooling is detected with a two-dimensional focal plane array infrared camera.
has db xref: https://doi.org/10.1021/ac061799l

single-photon infrared emission spectroscopy
type: Class
subclass of: infrared emission spectroscopy
definition: Spectroscopy where the sample is heated using ultraviolet excitation (single photon) and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has exact synonym: SPIRES
has exact synonym: single photon infra-red emission spectrometry
has exact synonym: single photon infra-red emission spectroscopy
has exact synonym: single-photon infra-red emission spectrometry
has exact synonym: single-photon infrared emission spectroscopy
id: CHMO:0000655

Axiom
annotated source: single-photon infrared emission spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is heated using ultraviolet excitation (single photon) and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
has db xref: https://doi.org/10.1021/jp9724434

Raman spectroscopy
type: Class
subclass of: scattering spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range by a sample is detected.
has exact synonym: Raman scattering spectrometry
has exact synonym: Raman scattering spectroscopy
has exact synonym: Raman spectrometry
id: CHMO:0000656

Axiom
annotated source: Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range by a sample is detected.
has db xref: FIX:0000058
has db xref: https://orcid.org/0000-0002-0640-0422

chiral Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where vibrational optical activity is measured by means of a small difference in the intensity of Raman scattering from chiral molecules of right- and left-circularly polarised incident light.
has exact synonym: Raman optical activity
has exact synonym: chiral Raman
has exact synonym: chiral Raman spectrometry
id: CHMO:0000657

Axiom
annotated source: chiral Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where vibrational optical activity is measured by means of a small difference in the intensity of Raman scattering from chiral molecules of right- and left-circularly polarised incident light.
has db xref: https://doi.org/10.1016/j.vibspec.2006.04.020

coherent Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light from three lasers (known as pump, probe and Stokes/anti-Stokes) by a sample is detected. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
id: CHMO:0000658

Axiom
annotated source: coherent Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light from three lasers (known as pump, probe and Stokes/anti-Stokes) by a sample is detected. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
has db xref: https://orcid.org/0000-0002-0640-0422

coherent Stokes Raman spectroscopy
type: Class
subclass of: coherent Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. An anti-Stokes frequency stimulation beam is used and a Stokes frequency beam is observed. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
has exact synonym: CSRS
has exact synonym: coherent Stokes Raman scattering spectrometry
has exact synonym: coherent Stokes Raman scattering spectroscopy
has exact synonym: coherent Stokes Raman spectrometry
id: CHMO:0000659

Axiom
annotated source: coherent Stokes Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. An anti-Stokes frequency stimulation beam is used and a Stokes frequency beam is observed. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
has db xref: https://orcid.org/0000-0002-0640-0422

coherent Stokes resonance Raman spectroscopy
type: Class
subclass of: coherent Stokes Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. An anti-Stokes frequency stimulation beam is used and a Stokes frequency beam is observed and the difference between the pump and the Stokes beams coincides with the frequency of an electronic transition within the molecule. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
id: CHMO:0000660

Axiom
annotated source: coherent Stokes resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. An anti-Stokes frequency stimulation beam is used and a Stokes frequency beam is observed and the difference between the pump and the Stokes beams coincides with the frequency of an electronic transition within the molecule. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
has db xref: https://orcid.org/0000-0002-0640-0422

coherent anti-Stokes Raman spectroscopy
type: Class
subclass of: coherent Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. A Stokes frequency stimulation beam is used and an anti-Stokes frequency beam is observed. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
has exact synonym: CARS
has exact synonym: coherent anti-Stokes Raman scattering spectrometry
has exact synonym: coherent anti-Stokes Raman scattering spectroscopy
has exact synonym: coherent anti-Stokes Raman spectrometry
id: CHMO:0000661

Axiom
annotated source: coherent anti-Stokes Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. A Stokes frequency stimulation beam is used and an anti-Stokes frequency beam is observed. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
has db xref: FIX:0000075
has db xref: https://orcid.org/0000-0002-0640-0422

coherent anti-Stokes resonance Raman spectroscopy
type: Class
subclass of: coherent anti-Stokes Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. A Stokes frequency stimulation beam is used and an anti-Stokes frequency beam is observed and the difference between the pump and the anti-Stokes beams coincides with the frequency of an electronic transition within the molecule. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
id: CHMO:0000662

Axiom
annotated source: coherent anti-Stokes resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. A Stokes frequency stimulation beam is used and an anti-Stokes frequency beam is observed and the difference between the pump and the anti-Stokes beams coincides with the frequency of an electronic transition within the molecule. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
has db xref: https://orcid.org/0000-0002-0640-0422

confocal Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light is detected. An aperture is used to discriminate between Raman signal coming from the focused laser spot and Raman signal coming from the out-of-focus region of the sample.
has exact synonym: CRS
has exact synonym: confocal Raman spectrometry
id: CHMO:0000663

Axiom
annotated source: confocal Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light is detected. An aperture is used to discriminate between Raman signal coming from the focused laser spot and Raman signal coming from the out-of-focus region of the sample.
has db xref: ISBN:0824703693

confocal Raman microscopy
type: Class
subclass of: Raman microscopy
subclass of: confocal Raman spectroscopy
definition: The collection of spatially resolved Raman spectra of a sample during optical microscopy. An aperture is used to discriminate between Raman signal coming from the laser spot and that coming from the out-of-focus region of the sample.
has exact synonym: confocal Raman microanalysis
has exact synonym: confocal Raman microspectrometry
has exact synonym: confocal Raman microspectroscopy
has exact synonym: confocal micro Raman
id: CHMO:0000664

Axiom
annotated source: confocal Raman microscopy
annotated property: definition
annotated target: The collection of spatially resolved Raman spectra of a sample during optical microscopy. An aperture is used to discriminate between Raman signal coming from the laser spot and that coming from the out-of-focus region of the sample.
has db xref: ISBN:0824703693

Fourier transform Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of light (produced by a single laser pulse) by a sample is detected and the spectrum is subject to a Fourier transform.
has db xref: FIX:0000384
has exact synonym: FT-Raman
has exact synonym: Fourier transform Raman spectrometry
id: CHMO:0000665

Axiom
annotated source: Fourier transform Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of light (produced by a single laser pulse) by a sample is detected and the spectrum is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

hyper Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of light by a (liquid) sample is detected. During scattering, photons from the incident laser (with frequency ω) are scattered by sample into photons of the second harmonic (photons with frequency 2ω).
has exact synonym: hyper Raman scattering spectrometry
has exact synonym: hyper Raman scattering spectroscopy
has exact synonym: hyper Raman spectrometry
has exact synonym: hyper-Raman scattering spectrometry
has exact synonym: hyper-Raman scattering spectroscopy
has exact synonym: hyper-Raman spectrometry
has exact synonym: hyper-Raman spectroscopy
id: CHMO:0000666

Axiom
annotated source: hyper Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of light by a (liquid) sample is detected. During scattering, photons from the incident laser (with frequency ω) are scattered by sample into photons of the second harmonic (photons with frequency 2ω).
has db xref: https://orcid.org/0000-0002-0640-0422

polarised Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the polarisation of light which has been subjected to Raman scattering by a sample is determined.
has exact synonym: polarised Raman spectrometry
has exact synonym: polarized Raman spectrometry
has exact synonym: polarized Raman spectroscopy
id: CHMO:0000667

Axiom
annotated source: polarised Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the polarisation of light which has been subjected to Raman scattering by a sample is determined.
has db xref: https://orcid.org/0000-0002-0640-0422

resonance Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Raman spectroscopy where the energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition in the sample.
has db xref: FIX:0000060
has exact synonym: RR spectrometry
has exact synonym: RR spectroscopy
has exact synonym: resonance Raman spectrometry
has exact synonym: resonant Raman spectrometry
has exact synonym: resonant Raman spectroscopy
has related synonym: RRS
id: CHMO:0000668

Axiom
annotated source: resonance Raman spectroscopy
annotated property: definition
annotated target: Raman spectroscopy where the energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition in the sample.
has db xref: https://orcid.org/0000-0002-0640-0422

Kerr-gated resonance Raman spectroscopy
type: Class
subclass of: resonance Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample, and the laser is combined with a Kerr gate fluorescence rejection system.
has exact synonym: Kerr-gated Raman spectrometry
id: CHMO:0000669

Axiom
annotated source: Kerr-gated resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample, and the laser is combined with a Kerr gate fluorescence rejection system.
has db xref: https://orcid.org/0000-0002-0640-0422

surface-enhanced resonance Raman spectroscopy
type: Class
subclass of: resonance Raman spectroscopy
subclass of: surface-enhanced Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
has db xref: FIX:0000077
has exact synonym: SERRS
has exact synonym: surface enhanced resonance Raman scattering spectrometry
has exact synonym: surface enhanced resonance Raman scattering spectroscopy
has exact synonym: surface enhanced resonance Raman spectrometry
id: CHMO:0000670

Axiom
annotated source: surface-enhanced resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
has db xref: https://orcid.org/0000-0002-0640-0422

ultraviolet resonance Raman spectroscopy
type: Class
subclass of: resonance Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from an ultraviolet laser, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
has exact synonym: UVRR
has exact synonym: UVRRS
has exact synonym: ultra-violet resonance Raman spectroscopy
id: CHMO:0000671

Axiom
annotated source: ultraviolet resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from an ultraviolet laser, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
has db xref: https://doi.org/10.1039/b702944f

deep ultra-violet resonance Raman spectroscopy
type: Class
subclass of: ultraviolet resonance Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a deep ultraviolet (<300 nm) laser, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
id: CHMO:0000672

Axiom
annotated source: deep ultra-violet resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a deep ultraviolet (<300 nm) laser, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
has db xref: https://doi.org/10.1039/b702944f

spatially-offset Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a laser, by a sample is detected. Scattered light is collected from regions laterally offset from the excitation laser spot.
has exact synonym: SORS
has exact synonym: SORSS
has exact synonym: spatially offset Raman scattering spectrometry
has exact synonym: spatially offset Raman scattering spectroscopy
has exact synonym: spatially offset Raman spectrometry
has exact synonym: spatially offset Raman spectroscopy
id: CHMO:0000674

Axiom
annotated source: spatially-offset Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a laser, by a sample is detected. Scattered light is collected from regions laterally offset from the excitation laser spot.
has db xref: https://orcid.org/0000-0002-0640-0422

stimulated Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from two lasers ('pump' and 'probe') by a sample is detected.
has exact synonym: SRS
has exact synonym: stimulated Raman scattering spectroscopy
has exact synonym: stimulated Raman spectrometry
has exact synonym: stimulated scattering spectrometry
id: CHMO:0000675

Axiom
annotated source: stimulated Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from two lasers ('pump' and 'probe') by a sample is detected.
has db xref: ISBN:0-471-96523-5

femosecond stimulated Raman spectroscopy
type: Class
subclass of: stimulated Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a femtosecond laser pulse, by a sample is detected. The laser pulse is generated by the mixing of two lasers ('pump' and 'probe').
has exact synonym: FSRS
has exact synonym: FSRSS
has exact synonym: emtosecond broadband stimulated Raman scattering spectrometry
has exact synonym: femosecond stimulated Raman scattering spectrometry
has exact synonym: femosecond stimulated Raman scattering spectroscopy
has exact synonym: femosecond stimulated Raman spectrometry
has exact synonym: femtosecond broadband stimulated Raman scattering spectroscopy
has exact synonym: femtosecond broadband stimulated Raman spectrometry
has exact synonym: femtosecond broadband stimulated Raman spectroscopy
id: CHMO:0000676

Axiom
annotated source: femosecond stimulated Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a femtosecond laser pulse, by a sample is detected. The laser pulse is generated by the mixing of two lasers ('pump' and 'probe').
has db xref: https://doi.org/10.1088/1742-6596/28/1/007

surface-enhanced Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected.
has exact synonym: SERS
has exact synonym: SERS spectroscopy
has exact synonym: surface enhanced Raman scattering
has exact synonym: surface enhanced Raman spectrometry
has exact synonym: surface enhanced Raman spectroscopy
has exact synonym: surface-enhanced Raman scattering
has exact synonym: surface-enhanced Raman scattering (SERS) spectroscopy
has exact synonym: surface-enhanced Raman spectrometry
has exact synonym: surface-enhanced Raman spectroscopy
id: CHMO:0000677

Axiom
annotated source: surface-enhanced Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected.
has db xref: FIX:0000076
has db xref: https://orcid.org/0000-0002-0640-0422

tip-enhanced Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser (500–650 nm), by metal surfaces, where scattering is enhanced by the optical near-field of a metal-coated scanning probe microscopy tip, is detected.
has exact synonym: TERS
has exact synonym: tip-enhanced Raman scattering spectrometry
has exact synonym: tip-enhanced Raman scattering spectroscopy
id: CHMO:0000678

Axiom
annotated source: tip-enhanced Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser (500–650 nm), by metal surfaces, where scattering is enhanced by the optical near-field of a metal-coated scanning probe microscopy tip, is detected.
has db xref: https://doi.org/10.1002/anie.200460656
has db xref: https://doi.org/10.1039/b9nr00156e

ultra-high vacuum tip-enhanced Raman spectroscopy
type: Class
subclass of: tip-enhanced Raman spectroscopy
definition: Spectroscopy where the Raman scattering of visible laser light, by metal surfaces, where scattering is enhanced by the optical near field of a scanning tunnelling tip, under ultra-high vacuum is detected.
has exact synonym: UHV-TERS
id: CHMO:0000679

Axiom
annotated source: ultra-high vacuum tip-enhanced Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of visible laser light, by metal surfaces, where scattering is enhanced by the optical near field of a scanning tunnelling tip, under ultra-high vacuum is detected.
has db xref: https://orcid.org/0000-0002-0640-0422

ultraviolet Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from an ultraviolet laser, by a sample is detected.
has exact synonym: UVR
has exact synonym: ultra-violet Raman spectrometry
has exact synonym: ultra-violet Raman spectroscopy
has exact synonym: ultraviolet Raman spectrometry
has exact synonym: ultraviolet Raman spectroscopy
id: CHMO:0000680

Axiom
annotated source: ultraviolet Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from an ultraviolet laser, by a sample is detected.
has db xref: https://doi.org/10.1021/ja044708f

attenuated total reflectance Fourier transform infrared spectroscopy
type: Class
subclass of: attenuated total reflectance infrared spectroscopy
definition: Spectroscopy where infrared light is introduced into a prism at an angle exceeding the critical angle for internal reflection. This produces an evanescent wave at the reflecting surface (a surface which is transparent to infrared such as thallium bromide) on which the sample is supported. The distortion of the evanescent wave by the sample is measured producing a spectrum which is then subject to a Fourier transform.
has exact synonym: ATR FT-IR spectroscopy
has exact synonym: ATR FTIR spectroscopy
has exact synonym: ATR-FTIR
has exact synonym: ATR-FTIR spectroscopy
has exact synonym: FTIR-ATR
has exact synonym: Fourier transform attenuated total reflectance infra-red
has exact synonym: Fourier transform attenuated total reflectance infra-red spectroscopy
has exact synonym: Fourier transform attenuated total reflectance infrared
has exact synonym: Fourier transform attenuated total reflectance infrared spectroscopy
has exact synonym: Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy
has exact synonym: Fourier transform infrared attenuated total reflectance spectroscopy
has exact synonym: Fourier transform infrared attenuated total reflection (FTIR-ATR) spectroscopy
has exact synonym: attenuated total reflectance Fourier transform infra-red spectroscopy
has exact synonym: attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy
id: CHMO:0000763

Axiom
annotated source: attenuated total reflectance Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where infrared light is introduced into a prism at an angle exceeding the critical angle for internal reflection. This produces an evanescent wave at the reflecting surface (a surface which is transparent to infrared such as thallium bromide) on which the sample is supported. The distortion of the evanescent wave by the sample is measured producing a spectrum which is then subject to a Fourier transform.
has db xref: FIX:0000644
has db xref: ISBN:0-471-96523-5

single molecule surface-enhanced Raman spectroscopy
type: Class
subclass of: surface-enhanced Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a single molecule sample adsorbed onto a metal (Au, Ag or Cu) surface is detected.
has exact synonym: SM SERS
has exact synonym: SM-SERRS
has exact synonym: SM-SERS
has exact synonym: SM-SERS spectroscopy
has exact synonym: SMSERS
has exact synonym: single molecule surface enhanced Raman scattering
has exact synonym: single molecule surface enhanced Raman scattering spectroscopy
has exact synonym: single molecule surface-enhanced Raman scattering
has exact synonym: single molecule surface-enhanced Raman scattering spectroscopy
has exact synonym: single molecule surface-enhanced Raman spectroscopy
id: CHMO:0000770

Axiom
annotated source: single molecule surface-enhanced Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a single molecule sample adsorbed onto a metal (Au, Ag or Cu) surface is detected.
has db xref: https://doi.org/10.1021/cr980133r

assay output
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: assay
subclass of: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: assay
definition: An information content entity that is output by an assay.
has exact synonym: experimental data
id: CHMO:0000793

Axiom
annotated source: assay output
annotated property: definition
annotated target: An information content entity that is output by an assay.
has db xref: https://orcid.org/0000-0001-5985-7429
has db xref: https://orcid.org/0000-0002-0640-0422

spectrum
type: Class
subclass of: assay output
subclass of: Restriction
  on property: is_specified_output_of
  some values from: spectroscopy
definition: A plot of a measured quantity against some experimental parameter.
has exact synonym: spectra
has exact synonym: spectrum plot
id: CHMO:0000800

Axiom
annotated source: spectrum
annotated property: definition
annotated target: A plot of a measured quantity against some experimental parameter.
has db xref: https://orcid.org/0000-0001-5985-7429

Raman spectrum
type: Class
subclass of: spectrum
definition: A plot of intensity vs. Raman shift (cm-1) obtained by measuring the Raman scattering of monochromatic light from a sample.
has exact synonym: Raman spectra
id: CHMO:0000823

Axiom
annotated source: Raman spectrum
annotated property: definition
annotated target: A plot of intensity vs. Raman shift (cm-1) obtained by measuring the Raman scattering of monochromatic light from a sample.
has db xref: https://doi.org/10.1021/jp001661l

thermogravimetry-Fourier transform infrared spectroscopy
type: Class
subclass of: Fourier transform infrared spectroscopy
definition: The FTIR analysis of volatile compounds released during the measurement of the mass of a sample as a function of temperature.
has exact synonym: TG-FT-IR
has exact synonym: TG-FTIR
has exact synonym: TG/FTIR
has exact synonym: TGA-FT-IR
has exact synonym: TGA-FTIR
has exact synonym: thermogravimetry coupled to Fourier transform infrared spectroscopy
has exact synonym: thermogravimetry-FTIR
id: CHMO:0000859

Axiom
annotated source: thermogravimetry-Fourier transform infrared spectroscopy
annotated property: definition
annotated target: The FTIR analysis of volatile compounds released during the measurement of the mass of a sample as a function of temperature.
has db xref: https://orcid.org/0000-0002-0640-0422

near-infrared Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of near-infrared radiation (radiation in the range 0.8–2 μm) is detected.
has exact synonym: NIR Raman
has exact synonym: near-infrared Raman
id: CHMO:0000870

Axiom
annotated source: near-infrared Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of near-infrared radiation (radiation in the range 0.8–2 μm) is detected.
has db xref: https://orcid.org/0000-0002-0640-0422

electrochemical surface-enhanced Raman spectroscopy
type: Class
subclass of: surface-enhanced Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, at a metal (Au, Ag or Cu) electrochemcial interface is detected.
has exact synonym: EC-SERS
has exact synonym: electrochemical SERS
has exact synonym: electrochemical surface enhanced Raman scattering
has exact synonym: electrochemical surface-enhanced Raman scattering
has exact synonym: electrochemical surface-enhanced Raman spectroscopy
id: CHMO:0000875

Axiom
annotated source: electrochemical surface-enhanced Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, at a metal (Au, Ag or Cu) electrochemcial interface is detected.
has db xref: https://doi.org/jp809363m

surface-enhanced chiral Raman spectroscopy
type: Class
subclass of: chiral Raman spectroscopy
definition: Spectroscopy where vibrational optical activity from a sample absorbed onto a metal (Au, Ag or Cu) surface is measured by means of a small difference in the intensity of Raman scattering from chiral molecules of right- and left-circularly polarised incident light.
has exact synonym: SEROA
has exact synonym: surface enhanced Raman optical activity
has exact synonym: surface enhanced chiral Raman spectroscopy
has exact synonym: surface-enhanced Raman optical activity
id: CHMO:0000885

Axiom
annotated source: surface-enhanced chiral Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where vibrational optical activity from a sample absorbed onto a metal (Au, Ag or Cu) surface is measured by means of a small difference in the intensity of Raman scattering from chiral molecules of right- and left-circularly polarised incident light.
has db xref: https://orcid.org/0000-0002-0640-0422

microscope
type: Class
subclass of: device
definition: A piece of apparatus which is used to generate an image of the surface of a specimen, whether by focusing reflected light onto where it can be collected or by scanning a given area of the surface.
id: CHMO:0000953

Axiom
annotated source: microscope
annotated property: definition
annotated target: A piece of apparatus which is used to generate an image of the surface of a specimen, whether by focusing reflected light onto where it can be collected or by scanning a given area of the surface.
has db xref: https://orcid.org/0000-0001-5985-7429

polarization modulation infrared reflection–adsorption spectroscopy
type: Class
subclass of: reflection–absorption infrared spectroscopy
definition: Spectroscopy where the differential absorption and reflection of low incident angle p- and s-polarized infrared light by the surface molecules of a highly reflective or polished sample is measured. The ultra-thin layers on metal surfaces interact with the p-polarized component of light, but not with the s-polarized component.
has exact synonym: PM-IRRAS
has exact synonym: polarization modulation infrared reflection adsorption spectroscopy
has exact synonym: polarization modulation-infrared reflection-adsorption spectroscopy
id: CHMO:0001078

Axiom
annotated source: polarization modulation infrared reflection–adsorption spectroscopy
annotated property: definition
annotated target: Spectroscopy where the differential absorption and reflection of low incident angle p- and s-polarized infrared light by the surface molecules of a highly reflective or polished sample is measured. The ultra-thin layers on metal surfaces interact with the p-polarized component of light, but not with the s-polarized component.
has db xref: https://orcid.org/0000-0002-0640-0422

single pulse–pulsed laser polymerization–near-infrared technique
type: Class
subclass of: near-infrared absorption spectroscopy
definition: A technique for measuring the time-resolved concentration of monomers during polymerisation reactions. The polymerisation is initiated by a single pulse of laser radiation and the monomer concentration is monitored by measuring absorbance in the near-infrared (0.8–2 μm) region.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-03-13T11:42:53Z
has exact synonym: SP-PLP-NIR
has exact synonym: single pulse-pulsed laser polymerization-near-infrared
id: CHMO:0001157

Axiom
annotated source: single pulse–pulsed laser polymerization–near-infrared technique
annotated property: definition
annotated target: A technique for measuring the time-resolved concentration of monomers during polymerisation reactions. The polymerisation is initiated by a single pulse of laser radiation and the monomer concentration is monitored by measuring absorbance in the near-infrared (0.8–2 μm) region.
has db xref: ISBN:386727682X

spectrometer
type: Class
subclass of: sensor
definition: A piece of apparatus used to measure a spectrum.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-03-25T01:54:09Z
has exact synonym: spectrograph
has exact synonym: spectroscope
id: CHMO:0001234

Axiom
annotated source: spectrometer
annotated property: definition
annotated target: A piece of apparatus used to measure a spectrum.
has db xref: https://orcid.org/0000-0002-0640-0422

Raman spectrometer
type: Class
subclass of: spectrometer
definition: A piece of apparatus that consists of a laser, a beam splitter, an interferometer and a detector and is used to measure Raman spectra.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-03-25T01:55:39Z
id: CHMO:0001235

Axiom
annotated source: Raman spectrometer
annotated property: definition
annotated target: A piece of apparatus that consists of a laser, a beam splitter, an interferometer and a detector and is used to measure Raman spectra.
has db xref: https://orcid.org/0000-0002-0640-0422

gas chromatography-infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Any method where a sample mixture is first separated by column chromatography where the mobile phase is a gas, then the absorption of radiation from the infrared region by the sample is measured.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-04-06T11:47:54Z
has exact synonym: GC IR
has exact synonym: GC-IR
has exact synonym: GC/IR
has exact synonym: GCIR
has exact synonym: gas chromatography infrared spectrometry
has exact synonym: gas chromatography infrared spectroscopy
has exact synonym: gas chromatography-infrared spectrometry
id: CHMO:0001262

Axiom
annotated source: gas chromatography-infrared spectroscopy
annotated property: definition
annotated target: Any method where a sample mixture is first separated by column chromatography where the mobile phase is a gas, then the absorption of radiation from the infrared region by the sample is measured.
has db xref: https://orcid.org/0000-0002-0640-0422

pyrolysis gas chromatography-infrared spectroscopy
type: Class
subclass of: gas chromatography-infrared spectroscopy
definition: Any method where a sample mixture is first chemically degraded by heating then separated by column chromatography where the mobile phase is a gas, then the absorption of radiation from the infrared region by the sample is measured.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-04-06T11:52:44Z
has exact synonym: Py-GC-IR
has exact synonym: py-GC-IR
has exact synonym: pyrolysis gas chromatography infrared spectrometry
has exact synonym: pyrolysis gas chromatography infrared spectroscopy
has exact synonym: pyrolysis-gas chromatography-infrared spectrometry
has exact synonym: pyrolysis-gas chromatography-infrared spectroscopy
id: CHMO:0001263

Axiom
annotated source: pyrolysis gas chromatography-infrared spectroscopy
annotated property: definition
annotated target: Any method where a sample mixture is first chemically degraded by heating then separated by column chromatography where the mobile phase is a gas, then the absorption of radiation from the infrared region by the sample is measured.
has db xref: https://orcid.org/0000-0002-0640-0422

pyrolysis infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample is first chemically degraded by heating then its absorption of radiation from the infrared region (0.78–1000 μm) is measured.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-04-06T11:56:10Z
has exact synonym: Py-IR
has exact synonym: Py/IR
has exact synonym: py-IR
has exact synonym: pyrolysis IR
has exact synonym: pyrolysis-IR
id: CHMO:0001264

Axiom
annotated source: pyrolysis infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is first chemically degraded by heating then its absorption of radiation from the infrared region (0.78–1000 μm) is measured.
has db xref: OrangeBook:5.3

sum-frequency generation spectroscopy
type: Class
subclass of: vibrational spectroscopy
definition: A method for generating surface-specific vibrational spectra by mixing two light beams at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-07T03:31:21Z
has exact synonym: SFG
has exact synonym: SFG spectroscopy
has exact synonym: SFG vibrational spectroscopy
has exact synonym: VSFG spectroscopy
has exact synonym: sum frequency generation (SFG) spectroscopy
has exact synonym: sum frequency generation (SFG) vibrational spectroscopy
has exact synonym: sum frequency generation spectroscopy
has exact synonym: vibrational sum-frequency generation (VSFG) spectroscopy
has exact synonym: vibrational sum-frequency generation spectroscopy
id: CHMO:0001288

Axiom
annotated source: sum-frequency generation spectroscopy
annotated property: definition
annotated target: A method for generating surface-specific vibrational spectra by mixing two light beams at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
has db xref: https://doi.org/10.1021/ja9831453

transmission Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser, by a sample is detected. The light is collected from the non-illuminated side of the sample.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-20T10:12:23Z
has exact synonym: TRS
has exact synonym: transmission Raman
has exact synonym: transmission Raman scattering spectroscopy
has exact synonym: transmission Raman spectrometry
id: CHMO:0001766

Axiom
annotated source: transmission Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser, by a sample is detected. The light is collected from the non-illuminated side of the sample.
has db xref: https://orcid.org/0000-0002-0640-0422

optical tweezers Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser, by a sample (e.g. a biological cell) constrained using optical tweezers is detected.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-20T10:18:22Z
has exact synonym: OTRS
has exact synonym: Raman tweezers
id: CHMO:0001767

Axiom
annotated source: optical tweezers Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser, by a sample (e.g. a biological cell) constrained using optical tweezers is detected.
has db xref: https://doi.org/10.1039/b815253e

supercritical fluid extraction-Fourier transform infrared spectroscopy
type: Class
subclass of: Fourier transform infrared spectroscopy
definition: Fourier transform infrared spectroscopy where the sample is initially transferred from a matrix to a liquid phase using a supercritical fluid.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-20T02:49:54Z
has exact synonym: SFE-FTIR
has exact synonym: supercritical fluid extraction-Fourier transform infrared absorption spectroscopy
id: CHMO:0001794

Axiom
annotated source: supercritical fluid extraction-Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Fourier transform infrared spectroscopy where the sample is initially transferred from a matrix to a liquid phase using a supercritical fluid.
has db xref: https://orcid.org/0000-0002-0640-0422

reflection–absorption Fourier transform infrared spectroscopy
type: Class
subclass of: reflection–absorption infrared spectroscopy
definition: Spectroscopy where the absorption and reflection of low-incident-angle infrared light by the surface molecules of a highly reflective or polished sample is measured. The sample absorbs a single pulse of radiation and the spectrum obtained is subject to a Fourier transform.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-21T10:50:58Z
has exact synonym: FT-IRAS
has exact synonym: FT-IRRAS
has exact synonym: Fourier transform infrared reflection absorption spectrometry
has exact synonym: Fourier transform infrared reflection absorption spectroscopy
has exact synonym: RA FT-IR
has exact synonym: RA FTIR
has exact synonym: RA-FTIR
has exact synonym: reflection absorption (RA) FT-IR
has exact synonym: reflection absorption Fourier transform infra-red spectrometry
has exact synonym: reflection absorption Fourier transform infrared spectrometry
has exact synonym: reflection absorption Fourier transform infrared spectroscopy
has exact synonym: reflection-absorption Fourier transform infrared spectroscopy
id: CHMO:0001798

Axiom
annotated source: reflection–absorption Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the absorption and reflection of low-incident-angle infrared light by the surface molecules of a highly reflective or polished sample is measured. The sample absorbs a single pulse of radiation and the spectrum obtained is subject to a Fourier transform.
has db xref: ISBN:0-471-96523-5
has db xref: https://doi.org/10.1039/b821475a

Raman microscope
type: Class
subclass of: microscope
subclass of: Raman spectrometer
definition: A piece of apparatus, consisting of a laser beam (<10 μm diameter), a monochromator and a detector coupled to an optical microscope, which is used to measure Raman spectra.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-26T01:03:35Z
has alternative id: CHMO:0001236
has exact synonym: Raman microspectrometer
id: CHMO:0001814

Axiom
annotated source: Raman microscope
annotated property: definition
annotated target: A piece of apparatus, consisting of a laser beam (<10 μm diameter), a monochromator and a detector coupled to an optical microscope, which is used to measure Raman spectra.
has db xref: https://orcid.org/0000-0002-0640-0422

vibrational microscopy
type: Class
subclass of: microspectroscopy
definition: A type of chemical imaging spectroscopy where an optical microscope is used to image the sample and locate a small area for spectral analysis that probes the vibrational degrees of freedom of a molecule.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-28T10:08:22Z
has exact synonym: vibrational microspectroscopy
has exact synonym: vibrational spectroscopic imaging
id: CHMO:0001818

Axiom
annotated source: vibrational microscopy
annotated property: definition
annotated target: A type of chemical imaging spectroscopy where an optical microscope is used to image the sample and locate a small area for spectral analysis that probes the vibrational degrees of freedom of a molecule.
has db xref: FIX:0000695
has db xref: https://orcid.org/0000-0002-0640-0422

synchrotron Fourier transform infrared spectroscopy
type: Class
subclass of: Fourier transform infrared spectroscopy
definition: Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm), produced in a synchrotron, and the spectrum obtained is subject to a Fourier transform.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-05-28T10:47:32Z
has exact synonym: S-FTIR
has exact synonym: S-FTIR spectrometry
has exact synonym: S-FTIR spectroscopy
has exact synonym: SFT-IR
has exact synonym: SFTIR
has exact synonym: synchrotron Fourier transform infra-red absorption spectroscopy
has exact synonym: synchrotron Fourier transform infra-red spectrometry
has exact synonym: synchrotron Fourier transform infrared (FT-IR) spectroscopy
has exact synonym: synchrotron Fourier transform infrared (S-FTIR)
has exact synonym: synchrotron Fourier transform infrared spectrometry
has exact synonym: synchrotron Fourier transform infrared spectroscopy
has exact synonym: synchrotron-based FTIR
id: CHMO:0001821

Axiom
annotated source: synchrotron Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm), produced in a synchrotron, and the spectrum obtained is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

rapid-scan infrared absorption spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). Spectra are collected at a rate of approx. 0.05 s per spectrum.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-03T10:09:14Z
has exact synonym: rapid scan IR
has exact synonym: rapid scan IR spectroscopy
has exact synonym: rapid scan infrared absorption spectroscopy
has exact synonym: rapid scan infrared spectroscopy
has exact synonym: rapid-scan IR
has exact synonym: rapid-scan IR spectroscopy
has exact synonym: rapid-scan infrared spectroscopy
id: CHMO:0001907

Axiom
annotated source: rapid-scan infrared absorption spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). Spectra are collected at a rate of approx. 0.05 s per spectrum.
has db xref: ISBN:1574445391

ultra-rapid-scan infrared absorption spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). Spectra are collected at a rate of approx. 0.001 s per spectrum.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-03T10:12:17Z
has exact synonym: ultra rapid scan IR
has exact synonym: ultra rapid scan IR spectroscopy
has exact synonym: ultra rapid scan infrared absorption spectroscopy
has exact synonym: ultra rapid scan infrared spectroscopy
has exact synonym: ultra-rapid-scan IR
has exact synonym: ultra-rapid-scan IR spectroscopy
has exact synonym: ultra-rapid-scan infrared spectroscopy
id: CHMO:0001908

Axiom
annotated source: ultra-rapid-scan infrared absorption spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). Spectra are collected at a rate of approx. 0.001 s per spectrum.
has db xref: ISBN:1574445391

stimulated Raman gain spectroscopy
type: Class
subclass of: stimulated Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light from two lasers ('pump' and 'probe') by a sample is detected. In stimulated Raman gain spectroscopy the probe laser has a lower frequency than the pump laser.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-10T09:51:36Z
has exact synonym: Raman gain spectroscopy
has exact synonym: SRGS
id: CHMO:0001939

Axiom
annotated source: stimulated Raman gain spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light from two lasers ('pump' and 'probe') by a sample is detected. In stimulated Raman gain spectroscopy the probe laser has a lower frequency than the pump laser.
has db xref: ISBN:0824705572

stimulated Raman loss spectroscopy
type: Class
subclass of: stimulated Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light from two lasers ('pump' and 'probe') by a sample is detected. In stimulated Raman gain spectroscopy the pump laser has a lower frequency than the probe laser.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-10T09:55:17Z
has exact synonym: IRGS
has exact synonym: IRS
has exact synonym: Raman loss spectroscopy
has exact synonym: SRLS
has exact synonym: inverse Raman gain spectroscopy
has exact synonym: inverse Raman spectroscopy
id: CHMO:0001940

Axiom
annotated source: stimulated Raman loss spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light from two lasers ('pump' and 'probe') by a sample is detected. In stimulated Raman gain spectroscopy the pump laser has a lower frequency than the probe laser.
has db xref: ISBN:0824705572

photoacoustic Raman spectroscopy
type: Class
subclass of: stimulated Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. Two lasers ('pump and 'probe') are mixed and focused on the sample cell. When the frequency difference between the lasers corresponds to a Raman transition, an acoustic signal (a sound wave produced by an increase in pressure) is generated and detected by a sensitive microphone.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-10T10:02:35Z
has exact synonym: PARS
id: CHMO:0001941

Axiom
annotated source: photoacoustic Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. Two lasers ('pump and 'probe') are mixed and focused on the sample cell. When the frequency difference between the lasers corresponds to a Raman transition, an acoustic signal (a sound wave produced by an increase in pressure) is generated and detected by a sensitive microphone.
has db xref: ISBN:0824705572

ionisation-detected stimulated Raman spectroscopy
type: Class
subclass of: stimulated Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from two lasers ('pump' and 'probe') by a sample is detected. The molecules in the sample are ionised using an ultraviolet laser in order to improve the signal-to-noise ratio of the spectrum.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-10T10:14:20Z
has exact synonym: IDSRS
has exact synonym: ionization-detected stimulated Raman spectroscopy
id: CHMO:0001942

Axiom
annotated source: ionisation-detected stimulated Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from two lasers ('pump' and 'probe') by a sample is detected. The molecules in the sample are ionised using an ultraviolet laser in order to improve the signal-to-noise ratio of the spectrum.
has db xref: ISBN:0824705572

higher-order Raman spectral excitation spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a two-colour laser, by a sample is detected.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-10T10:23:02Z
has exact synonym: HORSES
has exact synonym: higher order Raman spectral excitation studies
has exact synonym: higher-order Raman spectral excitation spectroscopy
has exact synonym: higher-order Raman spectral excitation studies
id: CHMO:0001943

Axiom
annotated source: higher-order Raman spectral excitation spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a two-colour laser, by a sample is detected.
has db xref: https://doi.org/10.1007/BF00750953

non-resonance Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light does not coincide with an electronic transition in the sample.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-17T03:24:06Z
has exact synonym: non resonance Raman spectroscopy
has exact synonym: non resonant Raman spectroscopy
has exact synonym: non-resonance Raman
has exact synonym: non-resonant Raman
has exact synonym: non-resonant Raman spectroscopy
id: CHMO:0001986

Axiom
annotated source: non-resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light does not coincide with an electronic transition in the sample.
has db xref: FIX:0000026
has db xref: https://orcid.org/0000-0002-0640-0422

drop coating deposition Raman spectroscopy
type: Class
subclass of: Raman spectroscopy
definition: A type of Raman spectroscopy where the spectral signal is enhanced by pre-concentration of the sample. Drops of the sample in solution are deposited onto a surface and dry in a 'coffee-ring' pattern. Spectra are then obtained from this ring of excess of material, after evaporation has completed.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-14T10:12:49Z
has exact synonym: DCD Raman spectroscopy
has exact synonym: DCDR
has exact synonym: DCDR spectroscopy
has exact synonym: drop coating deposition Raman (DCDR) spectroscopy
has exact synonym: drop-coating deposition Raman spectroscopy
has exact synonym: drop-coating-deposition Raman spectroscopy
id: CHMO:0002165

Axiom
annotated source: drop coating deposition Raman spectroscopy
annotated property: definition
annotated target: A type of Raman spectroscopy where the spectral signal is enhanced by pre-concentration of the sample. Drops of the sample in solution are deposited onto a surface and dry in a 'coffee-ring' pattern. Spectra are then obtained from this ring of excess of material, after evaporation has completed.
has db xref: https://doi.org/10.1039/b701541k

polarised Fourier transform infrared spectroscopy
type: Class
subclass of: Fourier transform infrared spectroscopy
definition: Spectroscopy where the sample absorbs a single pulse of polarised radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a Fourier transform.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-08-24T12:48:20Z
has exact synonym: polarised FTIR
has exact synonym: polarised Fourier transform infra-red absorption spectroscopy
has exact synonym: polarised Fourier transform infra-red spectrometry
has exact synonym: polarised Fourier transform infrared (FT-IR) spectroscopy
has exact synonym: polarised Fourier transform infrared spectrometry
has exact synonym: polarised Fourier transform infrared spectroscopy
has exact synonym: polarized FTIR
has exact synonym: polarized Fourier transform infra-red absorption spectroscopy
has exact synonym: polarized Fourier transform infra-red spectrometry
has exact synonym: polarized Fourier transform infrared (FT-IR) spectroscopy
has exact synonym: polarized Fourier transform infrared spectrometry
has exact synonym: polarized Fourier transform infrared spectroscopy
id: CHMO:0002286

Axiom
annotated source: polarised Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs a single pulse of polarised radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

pyrolysis Fourier transform infrared spectroscopy
type: Class
subclass of: Fourier transform infrared spectroscopy
subclass of: pyrolysis infrared spectroscopy
definition: Spectroscopy where the sample is first chemically degraded by heating then its absorption of radiation from the infrared region (0.78–1000 μm) is measured and the spectrum obtained is subject to a Fourier transform.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-08-24T12:53:20Z
has exact synonym: P-FTIR
has exact synonym: P/FTIR
has exact synonym: PFTIR
has exact synonym: Py-FTIR
has exact synonym: Py/FTIR
has exact synonym: py-FTIR
has exact synonym: pyrolysis FTIR
has exact synonym: pyrolysis-FTIR
id: CHMO:0002287

Axiom
annotated source: pyrolysis Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample is first chemically degraded by heating then its absorption of radiation from the infrared region (0.78–1000 μm) is measured and the spectrum obtained is subject to a Fourier transform.
has db xref: https://doi.org/10.1021/jp972162w

time-resolved polarised Fourier transform infrared spectroscopy
type: Class
subclass of: polarised Fourier transform infrared spectroscopy
definition: Spectroscopy where the sample absorbs a single pulse of polarised radiation from the infrared region (0.78–1000 μm) and the spectrum obtained, recorded as a function of time, is subject to a Fourier transform.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-08-24T12:55:24Z
has exact synonym: time-resolved polarised FTIR
has exact synonym: time-resolved polarised Fourier transform infra-red absorption spectroscopy
has exact synonym: time-resolved polarised Fourier transform infra-red spectrometry
has exact synonym: time-resolved polarised Fourier transform infrared (FT-IR) spectroscopy
has exact synonym: time-resolved polarised Fourier transform infrared spectrometry
has exact synonym: time-resolved polarised Fourier transform infrared spectroscopy
has exact synonym: time-resolved polarized FTIR
has exact synonym: time-resolved polarized Fourier transform infra-red absorption spectroscopy
has exact synonym: time-resolved polarized Fourier transform infra-red spectrometry
has exact synonym: time-resolved polarized Fourier transform infrared (FT-IR) spectroscopy
has exact synonym: time-resolved polarized Fourier transform infrared spectrometry
has exact synonym: time-resolved polarized Fourier transform infrared spectroscopy
id: CHMO:0002288

Axiom
annotated source: time-resolved polarised Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs a single pulse of polarised radiation from the infrared region (0.78–1000 μm) and the spectrum obtained, recorded as a function of time, is subject to a Fourier transform.
has db xref: https://orcid.org/0000-0002-0640-0422

fast Fourier transform infrared spectroscopy
type: Class
subclass of: Fourier transform infrared spectroscopy
definition: Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a fast Fourier transform.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-08-24T01:00:06Z
has exact synonym: FFT-FTIR
has exact synonym: FFT/FTIR
id: CHMO:0002289

Axiom
annotated source: fast Fourier transform infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a fast Fourier transform.
has db xref: FIX:0000647
has db xref: https://doi.org/10.1021/ie960134e

infrared transmission spectroscopy
type: Class
subclass of: vibrational spectroscopy
definition: Spectroscopy where the transmission of infrared radiation (0.78–1000 μm) through a sample is detected.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-08-24T01:02:36Z
has exact synonym: IR transmission spectroscopy
has exact synonym: IR transmittance spectroscopy
has exact synonym: infrared transmittance spectroscopy
has exact synonym: transmission IR
id: CHMO:0002290

Axiom
annotated source: infrared transmission spectroscopy
annotated property: definition
annotated target: Spectroscopy where the transmission of infrared radiation (0.78–1000 μm) through a sample is detected.
has db xref: FIX:0000661

dispersive infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). The infrared beam is passed through a diffraction grating which separates (or disperses) the wavelength of the light and directs each wavelength individually through a slit to a detector.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-08-24T01:12:29Z
id: CHMO:0002291

Axiom
annotated source: dispersive infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). The infrared beam is passed through a diffraction grating which separates (or disperses) the wavelength of the light and directs each wavelength individually through a slit to a detector.
has db xref: FIX:0000649
has db xref: http://www.thermo.com/eThermo/CMA/PDFs/Product/productPDF_21615.pdf

surface-enhanced non-resonance Raman spectroscopy
type: Class
subclass of: resonance Raman spectroscopy
subclass of: surface-enhanced Raman spectroscopy
subclass of: non-resonance Raman spectroscopy
definition: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected. The energy of the incoming laser is adjusted such that it or the scattered light does not coincide with an electronic transition within the sample.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-09-15T05:14:57Z
has db xref: FIX:0000078
id: CHMO:0002373

Axiom
annotated source: surface-enhanced non-resonance Raman spectroscopy
annotated property: definition
annotated target: Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected. The energy of the incoming laser is adjusted such that it or the scattered light does not coincide with an electronic transition within the sample.
has db xref: https://orcid.org/0000-0002-0640-0422

scattering spectroscopy
type: Class
subclass of: spectroscopy
definition: Any method that measures the amount of light that a substance scatters at certain wavelengths, incident angles, and polarization angles.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-09-17T04:09:34Z
id: CHMO:0002414

Axiom
annotated source: scattering spectroscopy
annotated property: definition
annotated target: Any method that measures the amount of light that a substance scatters at certain wavelengths, incident angles, and polarization angles.
has db xref: FIX:0000057

infrared–visible sum-frequency generation spectroscopy
type: Class
subclass of: sum-frequency generation spectroscopy
definition: A method for generating surface-specific vibrational spectra by mixing two light beams (visible and IR) at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-12-01T09:35:28Z
has exact synonym: infrared-visible sum-frequency generation (SFG) spectroscopy
has exact synonym: infrared-visible sum-frequency generation spectroscopy
id: CHMO:0002627

Axiom
annotated source: infrared–visible sum-frequency generation spectroscopy
annotated property: definition
annotated target: A method for generating surface-specific vibrational spectra by mixing two light beams (visible and IR) at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
has db xref: https://doi.org/10.1021/ja9831453

thermogravimetry-differential thermal analysis
type: Class
subclass of: Fourier transform infrared spectroscopy
definition: The measurement of the temperature difference between the sample and a reference material during the measurement of the mass of the sample as a function of temperature.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2010-01-04T04:19:21Z
has exact synonym: DTA-TG
has exact synonym: DTA-TGA
has exact synonym: DTA/TG
has exact synonym: DTA/TGA
has exact synonym: TG-DTA
has exact synonym: TGA-DTA
has exact synonym: TGDTA
has exact synonym: differential thermal analysis and thermal gravimetry analysis
has exact synonym: differential thermalgravimetric analysis
has exact synonym: thermogravimetric and differential thermal analyses
has exact synonym: thermogravimetry coupled to differential thermal analysis
id: CHMO:0002651

Axiom
annotated source: thermogravimetry-differential thermal analysis
annotated property: definition
annotated target: The measurement of the temperature difference between the sample and a reference material during the measurement of the mass of the sample as a function of temperature.
has db xref: https://orcid.org/0000-0002-0640-0422

electronic sum-frequency generation spectroscopy
type: Class
subclass of: sum-frequency generation spectroscopy
definition: A method for generating surface-specific electronic spectra by mixing two light beams at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2010-01-13T04:01:47Z
has exact synonym: ESFG spectroscopy
has exact synonym: electronic sum frequency generation spectroscopy
has exact synonym: electronic sum-frequency generation (ESFG) spectroscopy
id: CHMO:0002675

Axiom
annotated source: electronic sum-frequency generation spectroscopy
annotated property: definition
annotated target: A method for generating surface-specific electronic spectra by mixing two light beams at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
has db xref: https://doi.org/10.1039/b908097j

two-dimensional infrared spectroscopy
type: Class
subclass of: infrared absorption spectroscopy
definition: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 \μm) over two frequency axes. Cross peaks in the spectrum encode the couplings and orientation between vibrations.
created by: Hils
creation date: 2010-07-24T11:15:46Z
has exact synonym: 2D IR
has exact synonym: 2D-IR
has exact synonym: 2DIR
has exact synonym: two dimensional infrared spectroscopy
has exact synonym: two-dimensional IR spectroscopy
has exact synonym: two-dimensional infrared (2D-IR) spectroscopy
id: CHMO:0002710

Axiom
annotated source: two-dimensional infrared spectroscopy
annotated property: definition
annotated target: Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 \μm) over two frequency axes. Cross peaks in the spectrum encode the couplings and orientation between vibrations.
has db xref: FIX:0001069

sensor
type: Class
subclass of: device
definition: A piece of apparatus that is used to measure a physical quantity.
id: CHMO:0002793

Axiom
annotated source: sensor
annotated property: definition
annotated target: A piece of apparatus that is used to measure a physical quantity.
has db xref: https://orcid.org/0000-0001-5985-7429

in situ diffuse reflectance infrared Fourier transform spectroscopy
type: Class
subclass of: diffuse reflectance infrared Fourier transform spectroscopy
definition: Diffuse reflectance infrared Fourier transform spectroscopy of a sample that is carried out in the environment where the sample might be used.
has exact synonym: in situ DRIFT
has exact synonym: in situ DRIFTS
id: CHMO:0002813
comment: For example, the sample might be a catalyst, so during those catalytic processes.

Axiom
annotated source: in situ diffuse reflectance infrared Fourier transform spectroscopy
annotated property: definition
annotated target: Diffuse reflectance infrared Fourier transform spectroscopy of a sample that is carried out in the environment where the sample might be used.
has db xref: https://orcid.org/0000-0001-5985-7429

concentration
type: Class
subclass of: assay output
subclass of: Restriction
  on property: is about
  some values from: mixture
definition: Experimental method output expressing the contribution of one constituent to the composition of a mixture.
id: CHMO:0002820
comment: based heavily on https://doi.org/10.1351/goldbook.C01222

Axiom
annotated source: concentration
annotated property: definition
annotated target: Experimental method output expressing the contribution of one constituent to the composition of a mixture.
has db xref: https://orcid.org/0000-0001-5985-7429

mass concentration
type: Class
subclass of: concentration
definition: Experimental method output expressing a concentration in terms of the mass of a constituent divided by the volume of the mixture.
id: CHMO:0002821
comment: based heavily on https://doi.org/10.1351/goldbook.M03713

Axiom
annotated source: mass concentration
annotated property: definition
annotated target: Experimental method output expressing a concentration in terms of the mass of a constituent divided by the volume of the mixture.
has db xref: https://orcid.org/0000-0001-5985-7429

amount concentration
type: Class
subclass of: concentration
definition: Experimental method output expressing a concentration in terms of the amount of a constituent divided by the volume of the mixture.
has exact synonym: amount-of-substance concentration
has exact synonym: molarity
has exact synonym: substance concentration
id: CHMO:0002822
comment: based heavily on https://doi.org/10.1351/goldbook.A00295

Axiom
annotated source: amount concentration
annotated property: definition
annotated target: Experimental method output expressing a concentration in terms of the amount of a constituent divided by the volume of the mixture.
has db xref: https://orcid.org/0000-0001-5985-7429

volume concentration
type: Class
subclass of: concentration
definition: Experimental method output expressing a concentration in terms of the volume of a constituent divided by the volume of the mixture.
id: CHMO:0002823
comment: based heavily on https://doi.org/10.1351/goldbook.C01222

Axiom
annotated source: volume concentration
annotated property: definition
annotated target: Experimental method output expressing a concentration in terms of the volume of a constituent divided by the volume of the mixture.
has db xref: https://orcid.org/0000-0001-5985-7429

number concentration
type: Class
subclass of: concentration
definition: Experimental method output expressing a concentration in terms of the number of entities of a constituent divided by the volume of the mixture.
id: CHMO:0002824
comment: based heavily on https://doi.org/10.1351/goldbook.N04260

Axiom
annotated source: number concentration
annotated property: definition
annotated target: Experimental method output expressing a concentration in terms of the number of entities of a constituent divided by the volume of the mixture.
has db xref: https://orcid.org/0000-0001-5985-7429

device specification
type: Class
subclass of: directive information entity
has curation status: requires discussion
definition: A directive information entity which specifies a device and its settings for use within a plan specification.
term editor: http://orcid.org/0000-0002-8844-9165
date: 2021-11-29T21:53:39Z

measurement unit label
type: Class
subclass of: datum label
editor preferred term: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: pending final vetting
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

objective specification
type: Class
subclass of: directive information entity
editor preferred term: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative label: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: ready for release
definition: A directive information entity that describes an action the bearer will take.
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch

datum label
type: Class
subclass of: information content entity
editor preferred term: datum label
has curation status: metadata incomplete
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: GROUP: IAO
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
subclass of: Restriction
  on property: concretizes
  some values from: information content entity
editor preferred term: information carrier
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
has curation status: pending final vetting
definition: A quality of an information bearer that imparts the information content
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

model number
type: Class
subclass of: symbol
editor preferred term: model number
has curation status: pending final vetting
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
term editor: Person: Alan Ruttenberg

data item
type: Class
subclass of: information content entity
editor preferred term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
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.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative label: data
imported from: ogms.owl

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

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred term: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: ogms.owl

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
has curation status: metadata complete
definition: A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters

graph
type: Class
subclass of: diagram
editor preferred term: graph
has curation status: pending final vetting
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
term editor: PERSON: Lawrence Hunter
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI

algorithm
type: Class
subclass of: plan specification
editor preferred term: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: metadata complete
definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred term: curation status specification
has curation status: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

image
type: Class
subclass of: figure
editor preferred term: image
has curation status: ready for release
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI

data about an ontology part
type: Class
subclass of: data item
editor preferred term: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred term: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
definition: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
term editor: Clint Dowland
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred term: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: pending final vetting
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI

setting datum
type: Class
subclass of: data item
has curation status: metadata incomplete
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: information content entity
editor preferred term: material information bearer
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
example of usage: a brain
example of usage: a hard drive
has curation status: ready for release
definition: A material entity in which a concretization of an information content entity inheres.
term editor: GROUP: IAO

scatter plot
type: Class
subclass of: graph
editor preferred term: scatter plot
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
has curation status: ready for release
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
alternative label: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
  one of: out of scope
subclass of: data about an ontology part
editor preferred term: obsolescence reason specification
has curation status: pending final vetting
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

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

figure
type: Class
subclass of: information content entity
editor preferred term: figure
example of usage: Any picture, diagram or table
has curation status: metadata complete
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
term editor: PERSON: Lawrence Hunter

diagram
type: Class
subclass of: figure
editor preferred term: diagram
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has curation status: metadata complete
definition: A figure that expresses one or more propositions
term editor: PERSON: Lawrence Hunter

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

publication
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: publishing process
subclass of: document
editor preferred term: publication
example of usage: journal article, newspaper story, book, etc.
has curation status: metadata complete
definition: A document that is the output of a publishing process.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
term editor: PERSON: Lawrence Hunter
alternative label: published document
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
comment: Revisit the term in Octorber 2020. Improve the defintion.

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: length unit
subclass of: Restriction
  on property: is quality measurement of
  some values from: length
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of length quality
term editor: Alan Ruttenberg

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
editor preferred term: denotator type
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: mass unit
  intersection of: Restriction
    on property: is quality measurement of
    all values from: mass
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of mass quality
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg

publishing process
type: Class
subclass of: planned process
has curation status: metadata complete
definition: A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
term editor: Person: Jie Zheng
definition source: https://en.wikipedia.org/wiki/Publishing
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
ontology term requester: VEuPathDB

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: pending final vetting
definition: A planned process in which a document is created or added to by including the specified input in it.
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting

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

centrally registered identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has curation status: metadata complete
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative label: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: code set
example of usage: PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
term editor: Justin Whorton
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative label: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237

identifier
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: denotes
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: identifier creating process
subclass of: information content entity
subclass of: Restriction
  on property: denotes
  some values from: entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: identifier creating process
editor preferred term: identifier
definition: An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
term editor: Justin Whorton
term editor: Mathias Brochhausen
alternative label: proper name
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen
comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)

identifier creating process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: identifier
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: identifier
definition: A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
term editor: Justin Whorton
term editor: Mathias Brochhausen
alternative label: dubbing process
alternative label: naming
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen

code set
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: identifier
definition: An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
term editor: Alan Ruttenberg
term editor: Justin Whorton
term editor: Mathias Brochhausen
alternative label: code map
alternative label: code system
alternative label: codeset
alternative label: coding system
alternative label: controlled vocabulary
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
contributor: Alan Ruttenberg
contributor: Clint Dowland
contributor: Matt Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: Code sets might include non-entities/things (e.g. missing thumbs).
comment: Does not imply absence vs. presence of any taxonomy.
comment: Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
comment: Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
comment: The information content entities do not denote each other.

ontology module
type: Class
subclass of: data about an ontology part
editor preferred term: ontology module
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative label: ontology file
curator note: This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.

base ontology module
type: Class
subclass of: ontology module
editor preferred term: base ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

editors ontology module
type: Class
subclass of: ontology module
editor preferred term: editors ontology module
definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative label: source ontology module

main release ontology module
type: Class
subclass of: ontology module
editor preferred term: main release ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

bridge ontology module
type: Class
subclass of: ontology module
editor preferred term: bridge ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

import ontology module
type: Class
subclass of: subset ontology module
editor preferred term: import ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative label: import file

subset ontology module
type: Class
subclass of: ontology module
editor preferred term: subset ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative label: ontology slim
alternative label: subset ontology

curation subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: curation subset ontology module
definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.

analysis subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: analysis ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.

single layer subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: single layer ontology module
definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative label: ribbon subset

exclusion subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: exclusion subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative label: antislim

external import ontology module
type: Class
subclass of: import ontology module
editor preferred term: external import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative label: external import

species subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: species subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative label: taxon subset

reasoned ontology module
type: Class
subclass of: ontology module
editor preferred term: reasoned ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

generated ontology module
type: Class
subclass of: ontology module
editor preferred term: generated ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

template generated ontology module
type: Class
subclass of: generated ontology module
editor preferred term: template generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
editor preferred term: taxonomic bridge ontology module

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
editor preferred term: ontology module subsetted by expressivity

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: obo basic subset ontology module
definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: ontology module subsetted by OWL profile

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
editor preferred term: EL++ ontology module

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

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: obi.owl

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred term: 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

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
editor preferred term: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: ready for release
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
term editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
OBI_0001847: study

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred term: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: ready for release
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
disjoint with: planning
disjoint with: data transformation
editor preferred term: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
definition: A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
editor note: Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
term editor: PlanAndPlannedProcess Branch
alternative label: measuring
alternative label: scientific observation
definition source: OBI branch derived
OBI_0001847: study assay
OBI_9991118: any method

sample preparation for assay
type: Class
subclass of: material processing
editor preferred term: sample preparation for assay
has curation status: pending final vetting
definition: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
term editor: PlanAndPlannedProcess Branch
alternative label: study
definition source: OBI branch derived

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred term: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: ready for release
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative label: material transformation
definition source: OBI branch derived

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred term: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: ready for release
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
term editor: GROUP: Role Branch
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/1013

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: image
editor preferred term: imaging assay
has curation status: pending final vetting
definition: An assay that produces a picture of an entity.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes
        some values from: Restriction
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: Restriction
        on property: objective_achieved_by
        some values from: Restriction
subclass of: Restriction
  on property: realized in
  all values from: investigation
editor preferred term: investigation agent role
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: ready for release
definition: A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
editor note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
editor note: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
term editor: GROUP: Role Branch
alternative label: investigator
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
OBI_0001847: study person role
comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)

organization
type: Class
subclass of: material entity
editor preferred term: 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

protocol
type: Class
subclass of: plan specification
editor preferred term: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: ready for release
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
OBI_0001847: study protocol

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
editor preferred term: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: ready for release
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters

planning
type: Class
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor preferred term: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has curation status: ready for release
definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
term editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch

magnify function
type: Class
subclass of: function
editor preferred term: magnify function
has curation status: ready for release
definition: A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

excitation function
type: Class
subclass of: function
editor preferred term: excitation function
has curation status: ready for release
definition: A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

image acquisition function
type: Class
subclass of: measure function
subclass of: Restriction
  on property: characteristic of
  some values from: image creation device
subclass of: Restriction
  on property: realized in
  all values from: image creation
editor preferred term: image acquisition function
has curation status: ready for release
definition: An image acquisition function is a function to acquire an image of a material
term editor: Frank Gibson

image creation device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: image acquisition function
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
editor preferred term: image acquisition device
has curation status: metadata incomplete
definition: An image creation device is a device which captures a digitized image of an object
term editor: Frank Gibson
alternative label: image acquisition device
definition source: sep:00096

solid support function
type: Class
subclass of: function
editor preferred term: solid support function
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
has curation status: ready for release
definition: A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

assay objective
type: Class
subclass of: objective specification
editor preferred term: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: ready for release
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
term editor: PPPB branch
definition source: PPPB branch

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement datum
editor preferred term: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: ready for release
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson

material transformation objective
type: Class
subclass of: objective specification
editor preferred term: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: ready for release
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative label: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
editor preferred term: manufacturing
has curation status: ready for release
definition: A planned process with the objective to produce a processed material which will have a function for future use.
editor note: A person or organization (having manufacturer role) is a participant in this process
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred term: manufacturing objective
has curation status: ready for release
definition: is the objective to manufacture a material of a certain function (device)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: study design
editor preferred term: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: ready for release
definition: a planned process that carries out a study design
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
definition source: branch derived
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
imported from: obi.owl

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred term: manufacturer role
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
has curation status: metadata incomplete
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
term editor: GROUP: Role Branch
definition source: OBI

device setting
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: processed material
editor preferred term: device setting
example of usage: Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
has curation status: metadata incomplete
definition: a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
editor note: There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133
term editor: PERSON: Frank Gibson

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred term: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
has curation status: ready for release
definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative label: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop

center value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: center calculation data transformation
subclass of: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: center calculation data transformation
editor preferred term: center value
has curation status: pending final vetting
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: median

specimen collection objective
type: Class
subclass of: objective specification
editor preferred term: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: ready for release
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters

material sample role
type: Class
subclass of: specimen role
editor preferred term: material sample role
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: pending final vetting
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
term tracker item: https://github.com/obi-ontology/obi/issues/1013

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection process
  intersection of: Restriction
    on property: has_specified_input
    some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: material sample
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_output
  some values from: material sample
editor preferred term: material sampling process
has curation status: metadata incomplete
definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
alternative label: sample collection
alternative label: sampling
term tracker item: https://github.com/obi-ontology/obi/issues/1002

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
subclass of: Restriction
  on property: has role
  some values from: material sample role
editor preferred term: material sample
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: metadata incomplete
definition: A material entity that has the material sample role
term editor: OBI: workshop
alternative label: sample population
term tracker item: https://github.com/obi-ontology/obi/issues/1013
OBI_0001847: sample

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
has curation status: ready for release
definition: A device in which a measure function inheres.
term editor: GROUP:OBI Philly workshop
definition source: OBI

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: manufacturer role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred term: manufacturer
has curation status: metadata incomplete
definition: A person or organization that has a manufacturer role.

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred term: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
has curation status: ready for release
definition: A specimen that has been intentionally physically modified.
term editor: Bjoern Peters
definition source: Bjoern Peters
comment: A tissue sample that has been sliced and stained for a histology study.

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred term: 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.

image creation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: image
editor preferred term: image acquisition
example of usage: Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
has curation status: metadata incomplete
definition: A planned process that captures an image of an object.
term editor: PERSON: Jie Zheng
alternative label: image acquisition

investigation assay specification
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: part of
  some values from: study design
subclass of: Restriction
  on property: is about
  some values from: assay
editor preferred term: investigation assay specification
example of usage: Some examples of Project Method are Sequence, Array, Mass Spectrometry
has curation status: metadata complete
definition: A plan specification which indicates the assay type used to obtain data.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
OBI_0001886: Project Method
source: NIAID GSCID-BRC

categorical value specification
type: Class
subclass of: value specification
editor preferred term: categorical value specification
has curation status: metadata incomplete
definition: A value specification that is specifies one category out of a fixed number of nominal categories
term editor: PERSON:Bjoern Peters

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has specified numeric value
  min cardinality: 1
editor preferred term: scalar value specification
has curation status: metadata incomplete
definition: A value specification that consists of two parts: a numeral and a unit label
term editor: PERSON:Bjoern Peters

value specification
type: Class
subclass of: information content entity
editor preferred term: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
term editor: PERSON:Bjoern Peters

collection of specimens
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: material entity
editor preferred term: collection of specimens
example of usage: Blood cells collected from multiple donors over the course of a study.
has curation status: pending final vetting
definition: A material entity that has two or more specimens as its parts.
editor note: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: OBIB, OBI
source: Biobank

microscopy assay
type: Class
equivalent class: Class
  intersection of: imaging assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: microscope
subclass of: imaging assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: characteristic of
      some values from: microscope
subclass of: Restriction
  on property: has_specified_input
  some values from: microscope
editor preferred term: microscopy assay
example of usage: Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy.
has curation status: metadata complete
definition: An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
term editor: ImmPort
definition source: PMID:21685355

organism
type: Class
subclass of: material entity
editor preferred term: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
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

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: specimen role
editor preferred term: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: ready for release
definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
term tracker item: https://github.com/obi-ontology/obi/issues/1013

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
editor preferred term: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: ready for release
definition: A planned process that produces output data from input data.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative label: data analysis
alternative label: data processing
definition source: Branch editors
imported from: obi.owl

data transformation objective
type: Class
subclass of: objective specification
editor preferred term: data transformation objective
example of usage: normalize objective
has curation status: ready for release
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
term editor: James Malone
definition source: PERSON: James Malone

center calculation objective
type: Class
subclass of: data transformation objective
editor preferred term: center calculation objective
example of usage: A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
has curation status: ready for release
definition: A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
term editor: James Malone
definition source: PERSON: James Malone

center calculation data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: center value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: center calculation objective
subclass of: data transformation
editor preferred term: center calculation data transformation
has curation status: metadata incomplete
definition: A center calculation data transformation is a data transformation that has objective of center calculation.
term editor: James Malone
definition source: PERSON: James Malone

microscope
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: magnify function
editor preferred term: microscope
example of usage: PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
has curation status: metadata incomplete
definition: A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
term editor: PERSON: Phillippe Rocca-Serra
definition source: wikipedia

microscope slide
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: solid support function
editor preferred term: microscope slide
example of usage: PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
has curation status: metadata incomplete
definition: A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
term editor: PERSON: Phillippe Rocca-Serra
definition source: OBI biomaterial branch

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred term: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: ready for release
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
term editor: PERSON: Chris Stoeckert
alternative label: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has alternative id: PATO:0000072
has OBO namespace: quality
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has db xref: PATOC:GVG

concentration of
type: Class
subclass of: amount
definition: A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
has exact synonym: concentration
has OBO namespace: quality
id: PATO:0000033
in subset: attribute slim
in subset: relational slim
in subset: scalar slim

Axiom
annotated source: concentration of
annotated property: definition
annotated target: A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
has db xref: Wikipedia:http://en.wikipedia.org/wiki/concentration

morphology
type: Class
subclass of: physical object quality
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has OBO namespace: quality
id: PATO:0000051
in subset: attribute slim

Axiom
annotated source: morphology
annotated property: definition
annotated target: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has db xref: PATOC:GVG

amount
type: Class
subclass of: quantitative
subclass of: Restriction
  on property: RO_0015012
  some values from: has number of
definition: The number of entities of this type that are part of the whole organism.
has alternative id: PATO:0000053
has alternative id: PATO:0000071
has alternative id: PATO:0001169
has alternative id: PATO:0001226
has exact synonym: presence or absence in organism
has exact synonym: quantitative
has OBO namespace: quality
has related synonym: count in organism
has related synonym: number
has related synonym: presence
id: PATO:0000070
in subset: attribute slim
comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.

Axiom
annotated source: amount
annotated property: definition
annotated target: The number of entities of this type that are part of the whole organism.
has db xref: PATOC:GVG

size
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
has OBO namespace: quality
id: PATO:0000117
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: size
annotated property: definition
annotated target: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
has db xref: WordNet:WordNet

height
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
has OBO namespace: quality
id: PATO:0000119
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: height
annotated property: definition
annotated target: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
has db xref: PATOC:GVG

length
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality which is equal to the distance between two points.
see also: https://github.com/pato-ontology/pato/issues/337
has OBO namespace: quality
id: PATO:0000122
in subset: attribute slim
in subset: mpath slim
in subset: scalar slim
comment: Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion.

Axiom
annotated source: length
annotated property: definition
annotated target: A 1-D extent quality which is equal to the distance between two points.
has db xref: PATOC:GVG

mass
type: Class
subclass of: physical quality
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
has OBO namespace: quality
id: PATO:0000125
in subset: attribute slim
in subset: relational slim
in subset: scalar slim
comment: For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.

Axiom
annotated source: mass
annotated property: definition
annotated target: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
has db xref: PATOC:GVG

orientation
type: Class
subclass of: position
definition: A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object.
has alternative id: PATO:0000137
has exact synonym: angular placement
has OBO namespace: quality
has related synonym: amount of rotation
has related synonym: angle
has related synonym: angular magnitude
has related synonym: plane angle
id: PATO:0000133
in subset: attribute slim
in subset: relational slim

Axiom
annotated source: orientation
annotated property: definition
annotated target: A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object.
has db xref: PATOC:JE

position
type: Class
subclass of: physical quality
definition: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
has alternative id: PATO:0001032
has alternative id: PATO:0001631
has exact synonym: location
has exact synonym: placement
has exact synonym: relational spatial quality
has OBO namespace: quality
id: PATO:0000140
in subset: attribute slim

Axiom
annotated source: position
annotated property: definition
annotated target: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
has db xref: PATOC:GVG

temperature
type: Class
subclass of: physical quality
definition: A physical quality of the thermal energy of a system.
has OBO namespace: quality
id: PATO:0000146
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: temperature
annotated property: definition
annotated target: A physical quality of the thermal energy of a system.
has db xref: PATOC:GVG

width
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
see also: https://github.com/pato-ontology/pato/issues/337
has OBO namespace: quality
has related synonym: breadth
id: PATO:0000921
in subset: attribute slim
in subset: scalar slim
comment: Width often refers to the dimension that is greater than the extent in only one of the other two orthogonal dimensions, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion.

Axiom
annotated source: width
annotated property: definition
annotated target: A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
has db xref: PATOC:GVG

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has alternative id: PATO:0002079
has db xref: Wikipedia:Physical_property
has exact synonym: relational physical quality
has OBO namespace: quality
id: PATO:0001018
in subset: attribute slim

Axiom
annotated source: physical quality
annotated property: definition
annotated target: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has db xref: PATOC:GVG

mass density
type: Class
subclass of: physical quality
definition: A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
has OBO namespace: quality
has related synonym: density
id: PATO:0001019
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: mass density
annotated property: definition
annotated target: A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
has db xref: WordNet:WordNet

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
has alternative id: PATO:0001237
has alternative id: PATO:0001238
has db xref: snap:Quality
has exact synonym: monadic quality of a continuant
has exact synonym: multiply inhering quality of a physical entity
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has OBO namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

Axiom
annotated source: physical object quality
annotated property: definition
annotated target: A quality which inheres in a continuant.
has db xref: PATOC:GVG

wavelength
type: Class
subclass of: physical quality
definition: A physical quality which is equal to the distance between repeating units of a wave pattern.
has OBO namespace: quality
id: PATO:0001242
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: wavelength
annotated property: definition
annotated target: A physical quality which is equal to the distance between repeating units of a wave pattern.
has db xref: PATOC:GVG

has number of
type: Class
subclass of: amount
definition: The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
has db xref: OBO_REL:has_part
has exact synonym: extra or missing physical or functional parts
has exact synonym: has or lacks parts of type
has exact synonym: mereological quality
has exact synonym: number of
has OBO namespace: quality
has related synonym: cardinality
has related synonym: number
id: PATO:0001555
in subset: attribute slim
in subset: relational slim

Axiom
annotated source: has number of
annotated property: definition
annotated target: The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
has db xref: PATOC:CJM

depth
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension.
has OBO namespace: quality
id: PATO:0001595
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: depth
annotated property: definition
annotated target: A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension.
has db xref: WordNet:WordNet

1-D extent
type: Class
subclass of: size
definition: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
has exact synonym: 1-D size
has OBO namespace: quality
id: PATO:0001708
in subset: attribute slim

Axiom
annotated source: 1-D extent
annotated property: definition
annotated target: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
has db xref: PATOC:GVG

lateral orientation
type: Class
subclass of: orientation
definition: An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed laterally.
contributor: 0000-0002-2061-091X
creation date: 2013-10-10T05:16:45Z
has exact synonym: laterally directed
has OBO namespace: quality
id: PATO:0002497
in subset: value slim

Axiom
annotated source: lateral orientation
annotated property: definition
annotated target: An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed laterally.
has db xref: PATOC:WD

longitudinal orientation
type: Class
subclass of: orientation
definition: An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis.
contributor: https://orcid.org/0000-0003-3162-7490
creation date: 2014-10-17T14:24:19Z
has OBO namespace: quality
id: PATO:0005024
in subset: value slim

Axiom
annotated source: longitudinal orientation
annotated property: definition
annotated target: An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis.
has db xref: PATOC:WD

quantitative
type: Class
subclass of: quality
definition: A quality of an entity that can be represented numerically, including anything that can be counted, measured, or given a numerical value.
created by: https://orcid.org/0000-0001-8314-2140
has OBO namespace: quality
id: PATO:0103000

Axiom
annotated source: quantitative
annotated property: definition
annotated target: A quality of an entity that can be represented numerically, including anything that can be counted, measured, or given a numerical value.
has db xref: https://libguides.macalester.edu/c.php
has db xref: https://www.nnlm.gov/guides/data-glossary/quantitative-data

statistic
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: IAO_0000100
has curation status: ready for release
definition: a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
STATO_0000032: statistic

signal to noise ratio
type: Class
subclass of: ratio
has curation status: ready for release
definition: signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition last accessed: 2013-10-18
STATO_0000032: S/N
STATO_0000032: SNR
STATO_0000391: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.signaltonoise.html#scipy.stats.signaltonoise

ratio
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has numerator
    some values from: data item
  intersection of: Restriction
    on property: has denominator
    some values from: data item
subclass of: statistic
subclass of: Restriction
  on property: has numerator
  some values from: data item
subclass of: Restriction
  on property: has denominator
  some values from: data item
has curation status: pending final vetting
definition: A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
editor note: review formal definition as both numerator and denominator should be of the same type, not just some data item
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7

length unit
type: Class
subclass of: measurement unit label
comment: "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]

mass unit
type: Class
subclass of: measurement unit label
comment: "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia]

meter
type: Class
equivalent class: Class
  one of: meter
subclass of: meter based unit
type: NamedIndividual
has exact synonym: m
has exact synonym: metre
comment: "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST]

kilogram
type: Class
equivalent class: Class
  one of: kilogram
subclass of: gram based unit
type: NamedIndividual
has exact synonym: kg
comment: "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [BIPM:BIPM, NIST:NIST]

centimeter
type: Class
equivalent class: Class
  one of: centimeter
subclass of: meter based unit
type: NamedIndividual
has exact synonym: centimetre
has exact synonym: cm
comment: "A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST]

millimeter
type: Class
equivalent class: Class
  one of: millimeter
subclass of: meter based unit
type: NamedIndividual
has exact synonym: millimetre
has exact synonym: mm
comment: "A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST]

micrometer
type: Class
equivalent class: Class
  one of: micrometer
subclass of: meter based unit
type: NamedIndividual
has exact synonym: micrometre
has exact synonym: micron
has exact synonym: um
comment: "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST]

nanometer
type: Class
equivalent class: Class
  one of: nanometer
subclass of: meter based unit
type: NamedIndividual
has exact synonym: nanometre
has exact synonym: nm
comment: "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST]

angstrom
type: Class
equivalent class: Class
  one of: angstrom
subclass of: angstrom based unit
type: NamedIndividual
has exact synonym: Å
comment: "A length unit which is equal to 10 [-10] m." [NIST:NIST]

picometer
type: Class
equivalent class: Class
  one of: picometer
subclass of: meter based unit
type: NamedIndividual
has exact synonym: picometre
has exact synonym: pm
comment: "A length unit which is equal to 10^[-12] m." [NIST:NIST]

gram
type: Class
equivalent class: Class
  one of: gram
subclass of: gram based unit
type: NamedIndividual
has exact synonym: g
comment: "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST]

milligram
type: Class
equivalent class: Class
  one of: milligram
subclass of: gram based unit
type: NamedIndividual
has exact synonym: mg
comment: "A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [UOC:GVG]

microgram
type: Class
equivalent class: Class
  one of: microgram
subclass of: gram based unit
type: NamedIndividual
has exact synonym: ug
comment: "A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG]

nanogram
type: Class
equivalent class: Class
  one of: nanogram
subclass of: gram based unit
type: NamedIndividual
has exact synonym: ng
comment: "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG]

picogram
type: Class
equivalent class: Class
  one of: picogram
subclass of: gram based unit
type: NamedIndividual
has exact synonym: pg
comment: "A mass unit which is equal to 10^[-12] g." [UOC:GVG]

femtogram
type: Class
equivalent class: Class
  one of: femtogram
subclass of: gram based unit
type: NamedIndividual
has exact synonym: fg
comment: "A mass unit which is equal to 10^[-15] g." [NIST:NIST]

concentration unit
type: Class
subclass of: measurement unit label
comment: "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG]

molar mass unit
type: Class
subclass of: mass unit
comment: "A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia]

unit of molarity
type: Class
subclass of: concentration unit
comment: "A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution." [UOC:GVG]

molar
type: Class
equivalent class: Class
  one of: molar
subclass of: molar based unit
type: NamedIndividual
has exact synonym: M
comment: "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [UOC:GVG]

millimolar
type: Class
equivalent class: Class
  one of: millimolar
subclass of: molar based unit
type: NamedIndividual
has exact synonym: mM
comment: "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [UOC:GVG]

micromolar
type: Class
equivalent class: Class
  one of: micromolar
subclass of: molar based unit
type: NamedIndividual
has exact synonym: uM
comment: "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [UOC:GVG]

nanomolar
type: Class
equivalent class: Class
  one of: nanomolar
subclass of: molar based unit
type: NamedIndividual
has exact synonym: nM
comment: "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [UOC:GVG]

picomolar
type: Class
equivalent class: Class
  one of: picomolar
subclass of: molar based unit
type: NamedIndividual
has exact synonym: pM
comment: "A unit of molarity which is equal to 10^[-12] M." [UOC:GVG]

unit of molality
type: Class
subclass of: concentration unit
comment: "A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG]

molal
type: Class
equivalent class: Class
  one of: molal
subclass of: molal based unit
type: NamedIndividual
has exact synonym: m
comment: "A unit of concentration which expresses a concentration of a solution of 1 mole per kilogram of solvent (mol/kg)." [UOC:GVG]

millimolal
type: Class
equivalent class: Class
  one of: millimolal
subclass of: molal based unit
type: NamedIndividual
has exact synonym: mm
comment: "A molality unit which is equal to one thousandth of a molal or 10^[-3] m." [UOC:GVG]

micromolal
type: Class
equivalent class: Class
  one of: micromolal
subclass of: molal based unit
type: NamedIndividual
has exact synonym: um
comment: "A molality unit which is equal to one millionth of a molal or 10^[-6] m." [UOC:GVG]

nanomolal
type: Class
equivalent class: Class
  one of: nanomolal
subclass of: molal based unit
type: NamedIndividual
has exact synonym: nm
comment: "A molality unit which is equal to one thousandth of one millionth of a molal or 10^[-9] m." [UOC:GVG]

picomolal
type: Class
equivalent class: Class
  one of: picomolal
subclass of: molal based unit
type: NamedIndividual
has exact synonym: pm
comment: "A molality unit which is equal to 10^[-12] m." [UOC:GVG]

femtomolar
type: Class
equivalent class: Class
  one of: femtomolar
subclass of: molar based unit
type: NamedIndividual
has exact synonym: fM
comment: "A unit of molarity which is equal to 10^[-15] M." [UOC:GVG]

unit of normality
type: Class
subclass of: concentration unit
comment: "A unit of concentration which highlights the chemical nature of salts." [Wikipedia:Wikipedia]

normal
type: Class
equivalent class: Class
  one of: normal
subclass of: normal based unit
type: NamedIndividual
has exact synonym: N
comment: "A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule." [Wikipedia:Wikipedia]

mole fraction
type: Class
equivalent class: Class
  one of: mole fraction
subclass of: mole fraction based unit
type: NamedIndividual
has exact synonym: (x)
has exact synonym: chi
comment: "A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia]

kilogram per mole
type: Class
equivalent class: Class
  one of: kilogram per mole
subclass of: gram per mole based unit
type: NamedIndividual
has exact synonym: kg/mol
comment: "A molar mass unit which is equal to one kilogram of mass of one mole of chemical element or chemical compound." [NIST:NIST]

gram per mole
type: Class
equivalent class: Class
  one of: gram per mole
subclass of: gram per mole based unit
type: NamedIndividual
has exact synonym: g/mol
comment: "A molar mass unit which is equal to one gram of mass of one mole of chemical element or chemical compound." [NIST:NIST]

mass percentage
type: Class
equivalent class: Class
  one of: mass percentage
subclass of: mass percentage based unit
type: NamedIndividual
has exact synonym: w/w
has exact synonym: weight-weight percentage
comment: "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia]

mass volume percentage
type: Class
equivalent class: Class
  one of: mass volume percentage
subclass of: mass volume percentage based unit
type: NamedIndividual
has exact synonym: (w/v)
has exact synonym: weight-volume percentage
comment: "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG]

volume percentage
type: Class
equivalent class: Class
  one of: volume percentage
subclass of: volume percentage based unit
type: NamedIndividual
has exact synonym: % (v/v)
comment: "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG]

unit per volume unit
type: Class
subclass of: concentration unit
comment: "A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution." [Webmd:Webmd]

unit per milliliter
type: Class
equivalent class: Class
  one of: unit per milliliter
subclass of: unit per milliliter based unit
type: NamedIndividual
has exact synonym: U/ml
has exact synonym: unit per millilitre
comment: "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one milliliter." [Webmd:Webmd]

unit per liter
type: Class
equivalent class: Class
  one of: unit per liter
subclass of: unit per liter based unit
type: NamedIndividual
has exact synonym: U/l
has exact synonym: unit per litre
comment: "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter." [UOC:GVG]

mass per unit volume
type: Class
equivalent class: Class
  one of: mass per unit volume
subclass of: mass per unit volume based unit
type: NamedIndividual
comment: "A concentration unit which is a standard measure of the mass of a substance in a given volume (density)." [Wikipedia:Wikipedia]

pH
type: Class
equivalent class: Class
  one of: pH
subclass of: pH based unit
type: NamedIndividual
comment: "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia]

cell concentration unit
type: Class
subclass of: concentration unit
comment: "A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline]

cells per milliliter
type: Class
equivalent class: Class
  one of: cells per milliliter
subclass of: cells per milliliter based unit
type: NamedIndividual
has exact synonym: cells per millilitre
has exact synonym: cells per ml
comment: "A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline]

catalytic (activity) concentration unit
type: Class
subclass of: concentration unit
comment: "A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG]

katal per cubic meter
type: Class
equivalent class: Class
  one of: katal per cubic meter
subclass of: katal per cubic meter based unit
type: NamedIndividual
has exact synonym: kat/m^[3]
has exact synonym: katal per cubic metre
comment: "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST]

katal per liter
type: Class
equivalent class: Class
  one of: katal per liter
subclass of: katal per liter based unit
type: NamedIndividual
has exact synonym: kat/l
has exact synonym: katal per litre
comment: "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST]

volume per unit volume
type: Class
subclass of: concentration unit
comment: "A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST]

milliliter per cubic meter
type: Class
equivalent class: Class
  one of: milliliter per cubic meter
subclass of: volume per unit volume
type: NamedIndividual
has exact synonym: millilitre per cubic metre
has exact synonym: ml/m^[3]
comment: "A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST]

milliliter per liter
type: Class
equivalent class: Class
  one of: milliliter per liter
subclass of: volume per unit volume
type: NamedIndividual
has exact synonym: millilitre per litre
has exact synonym: ml/l
comment: "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST]

colony forming unit per volume
type: Class
subclass of: concentration unit
comment: "A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia]

colony forming unit per milliliter
type: Class
equivalent class: Class
  one of: colony forming unit per milliliter
subclass of: colony forming unit per milliliter based unit
type: NamedIndividual
has exact synonym: cfu/ml
has exact synonym: colony forming unit per millilitre
comment: "A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia]

plaque forming unit per volume
type: Class
subclass of: concentration unit
comment: "A concentration unit which a measure of plaque forming units in a given volume." [UOC:GVG]

plaque forming unit per milliliter
type: Class
equivalent class: Class
  one of: plaque forming unit per milliliter
subclass of: plaque forming unit per milliliter based unit
type: NamedIndividual
has exact synonym: pfu/ml
has exact synonym: plaque forming unit per millilitre
comment: "A concentration unit which a measure of plaque forming units in one milliliter." [UOC:GVG]

dalton
type: Class
equivalent class: Class
  one of: dalton
subclass of: dalton based unit
type: NamedIndividual
has exact synonym: Da
has exact synonym: amu
has exact synonym: u
has exact synonym: unified atomic mass unit
comment: "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia]

kilodalton
type: Class
equivalent class: Class
  one of: kilodalton
subclass of: dalton based unit
type: NamedIndividual
has exact synonym: kDa
comment: "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia]

amount per container
type: Class
subclass of: concentration unit
comment: "A concentration unit which is a standard measure of the amount of a substance in a given container." [UOC:GVG]

ug/disk
type: Class
subclass of: amount per container
comment: "A unit which is equal to one microgram per disk, where a disk is some physical surface/container upon which the substance is deposited." [UOC:MD]

nmole/disk
type: Class
subclass of: amount per container
comment: "A unit which is equal to one nanomole per disk, where a disk is some physical surface/container upon which the substance is deposited." [UOC:MD]

milliunits per milliliter
type: Class
equivalent class: Class
  one of: milliunits per milliliter
subclass of: unit per volume unit
type: NamedIndividual
has exact synonym: mU/ml
has exact synonym: milliunits per millilitre
comment: "A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter." [UOC:GVG]

dose unit
type: Class
subclass of: concentration unit
comment: "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC]

milligram per kilogram
type: Class
equivalent class: Class
  one of: milligram per kilogram
subclass of: dose unit
type: NamedIndividual
comment: "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]

milligram per square meter
type: Class
equivalent class: Class
  one of: milligram per square meter
subclass of: dose unit
type: NamedIndividual
comment: "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC]

dosage unit
type: Class
equivalent class: Class
  one of: dosage unit
subclass of: dosage unit based unit
type: NamedIndividual
comment: "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered over time to a recipient subject, expressed in terms of the size of the subject." [UO:PC]

milligram per kilogram per day
type: Class
equivalent class: Class
  one of: milligram per kilogram per day
subclass of: dosage unit
type: NamedIndividual
comment: "A dosage unit which is equal to 1 milligram per day of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]

cells per microliter
type: Class
subclass of: cell concentration unit
has exact synonym: cells per microlitre
has exact synonym: cells per ul
comment: "A unit of cell concentration which is equal to one cell in a volume of 1 microliter." [UO:GVG]

cells per well
type: Class
subclass of: cell concentration unit
comment: "A unit of cell concentration which is equal to 1 cell in a well or discrete container of arbitrary volume." [UO:PC]

radioactivity concentration
type: Class
subclass of: concentration unit
comment: "A concentration unit which is a standard measure of the amount of radioactivity in a given volume." [UO:GVG]

curie per liter
type: Class
subclass of: radioactivity concentration
has exact synonym: curie per litre
comment: "A unit of radioactivity concentration which is equal to one curie in a volume of 1 liter." [UO:GVG]

microcurie per milliliter
type: Class
subclass of: radioactivity concentration
has exact synonym: microcurie per millilitre
comment: "A unit of radioactivity concentration which is equal to one micro curie in a volume of 1 liter." [UO:GVG]

centiMorgan
type: Class
equivalent class: Class
  one of: centiMorgan
subclass of: length unit
type: NamedIndividual
has exact synonym: cM
comment: "A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]

centiRay
type: Class
equivalent class: Class
  one of: centiRay
subclass of: length unit
type: NamedIndividual
has exact synonym: cR
comment: "A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]

micromole per litre
type: Class
equivalent class: Class
  one of: micromole per litre
subclass of: unit of molality
type: NamedIndividual
comment: "A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST]

micromole per kilogram
type: Class
equivalent class: Class
  one of: micromole per kilogram
subclass of: unit of molality
type: NamedIndividual
comment: "A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR]

milli
type: Class
equivalent class: Class
  one of: milli
subclass of: mass unit
type: NamedIndividual
has exact synonym: mDa
has exact synonym: milli unified atomic mass unit
has exact synonym: millidalton
has exact synonym: mmu
comment: "A mass unit which is equal to 1/12 the mass of 12C" [Wikipedia:Wikipedia]

inch
type: Class
equivalent class: Class
  one of: inch
subclass of: inch based unit
type: NamedIndividual
has exact synonym: in
comment: "A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia]

thou
type: Class
equivalent class: Class
  one of: thou
subclass of: thou based unit
type: NamedIndividual
has exact synonym: mil
has exact synonym: th
comment: "A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia]

foot
type: Class
equivalent class: Class
  one of: foot
subclass of: foot based unit
type: NamedIndividual
has exact synonym: ft
comment: "A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia]

yard
type: Class
equivalent class: Class
  one of: yard
subclass of: yard based unit
type: NamedIndividual
has exact synonym: yd
comment: "A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia]

chain
type: Class
equivalent class: Class
  one of: chain
subclass of: chain based unit
type: NamedIndividual
has exact synonym: ch
comment: "A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia]

furlong
type: Class
equivalent class: Class
  one of: furlong
subclass of: furlong based unit
type: NamedIndividual
has exact synonym: fur
comment: "A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia]

mile
type: Class
equivalent class: Class
  one of: mile
subclass of: mile based unit
type: NamedIndividual
has exact synonym: mi
comment: "A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia]

league
type: Class
equivalent class: Class
  one of: league
subclass of: league based unit
type: NamedIndividual
has exact synonym: lea
comment: "A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia]

maritime length unit
type: Class
equivalent class: Class
  one of: maritime length unit
subclass of: maritime length unit based unit
type: NamedIndividual
comment: "A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia]

fathom
type: Class
equivalent class: Class
  one of: fathom
subclass of: fathom based unit
type: NamedIndividual
has exact synonym: ftm
comment: "A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia]

cable
type: Class
equivalent class: Class
  one of: cable
subclass of: cable based unit
type: NamedIndividual
comment: "A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia]

nautical mile
type: Class
equivalent class: Class
  one of: nautical mile
subclass of: nautical mile based unit
type: NamedIndividual
comment: "A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia]

grain
type: Class
equivalent class: Class
  one of: grain
subclass of: grain based unit
type: NamedIndividual
has exact synonym: gr
comment: "An imperial mass unit which is equivalent to 64.798,91 milligrams." [Wikipedia:Wikipedia]

drachm
type: Class
equivalent class: Class
  one of: drachm
subclass of: drachm based unit
type: NamedIndividual
has exact synonym: dr
comment: "An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound." [Wikipedia:Wikipedia]

ounce
type: Class
equivalent class: Class
  one of: ounce
subclass of: ounce based unit
type: NamedIndividual
has exact synonym: oz
comment: "An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound." [Wikipedia:Wikipedia]

pound
type: Class
equivalent class: Class
  one of: pound
subclass of: pound based unit
type: NamedIndividual
has exact synonym: lb
comment: "An imperial mass unit which is equivalent to 453.592,37 grams." [Wikipedia:Wikipedia]

stone
type: Class
equivalent class: Class
  one of: stone
subclass of: stone based unit
type: NamedIndividual
has exact synonym: st
comment: "An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds." [Wikipedia:Wikipedia]

quarter
type: Class
equivalent class: Class
  one of: quarter
subclass of: quarter based unit
type: NamedIndividual
has exact synonym: qr
has exact synonym: qtr
comment: "An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds." [Wikipedia:Wikipedia]

hundredweight
type: Class
equivalent class: Class
  one of: hundredweight
subclass of: hundredweight based unit
type: NamedIndividual
has exact synonym: cwt
comment: "An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone." [Wikipedia:Wikipedia]

ton
type: Class
equivalent class: Class
  one of: ton
subclass of: ton based unit
type: NamedIndividual
has exact synonym: t
comment: "An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds." [Wikipedia:Wikipedia]

kilometer
type: Class
equivalent class: Class
  one of: kilometer
subclass of: meter based unit
type: NamedIndividual
has exact synonym: kilometre
has exact synonym: km
comment: "A length unit which is equal to one thousand meters." [UOB:LKSR]

titer
type: Class
subclass of: concentration unit
comment: A concentration unit which denotes the minimum amount of a substance in a solution that still yields a positive reading, as determined by serial dilution.

meter based unit
type: Class
subclass of: length unit

angstrom based unit
type: Class
subclass of: length unit

gram based unit
type: Class
subclass of: mass unit

molar based unit
type: Class
subclass of: unit of molarity

molal based unit
type: Class
subclass of: unit of molality

normal based unit
type: Class
subclass of: unit of normality

mole fraction based unit
type: Class
subclass of: concentration unit

gram per mole based unit
type: Class
subclass of: molar mass unit

mass percentage based unit
type: Class
subclass of: concentration unit

mass volume percentage based unit
type: Class
subclass of: concentration unit

volume percentage based unit
type: Class
subclass of: volume per unit volume

unit per milliliter based unit
type: Class
subclass of: unit per volume unit

unit per liter based unit
type: Class
subclass of: unit per volume unit

mass per unit volume based unit
type: Class
subclass of: concentration unit

pH based unit
type: Class
subclass of: concentration unit

cells per milliliter based unit
type: Class
subclass of: cell concentration unit

katal per cubic meter based unit
type: Class
subclass of: catalytic (activity) concentration unit

katal per liter based unit
type: Class
subclass of: catalytic (activity) concentration unit

colony forming unit per milliliter based unit
type: Class
subclass of: colony forming unit per volume

plaque forming unit per milliliter based unit
type: Class
subclass of: plaque forming unit per volume

dalton based unit
type: Class
subclass of: mass unit

dosage unit based unit
type: Class
subclass of: concentration unit

inch based unit
type: Class
subclass of: length unit

thou based unit
type: Class
subclass of: length unit

foot based unit
type: Class
subclass of: length unit

yard based unit
type: Class
subclass of: length unit

chain based unit
type: Class
subclass of: length unit

furlong based unit
type: Class
subclass of: length unit

mile based unit
type: Class
subclass of: length unit

league based unit
type: Class
subclass of: length unit

maritime length unit based unit
type: Class
subclass of: length unit

fathom based unit
type: Class
subclass of: maritime length unit

cable based unit
type: Class
subclass of: maritime length unit

nautical mile based unit
type: Class
subclass of: maritime length unit

grain based unit
type: Class
subclass of: mass unit

drachm based unit
type: Class
subclass of: mass unit

ounce based unit
type: Class
subclass of: mass unit

pound based unit
type: Class
subclass of: mass unit

stone based unit
type: Class
subclass of: mass unit

quarter based unit
type: Class
subclass of: mass unit

hundredweight based unit
type: Class
subclass of: mass unit

ton based unit
type: Class
subclass of: mass unit

vibrational spectrometer configuration specification
type: Class
subclass of: setting datum
definition: A setting datum that specifies the needed settings of a spectrometer used in vibrational spectroscopy.
contributor: http://orcid.org/0000-0002-1595-3213

Raman spectrometer configuration
type: Class
subclass of: device setting
example of usage: The set of meassured configuration characteristics of a Raman spectrometer, like the operating temperature of a Raman spectrometer.
definition: A device setting that represents the measured or set physical qualities which make up the configuration state of a Raman spectrometer at the time of a measurement (e.g. operating temperature, exitation wavelength, groove density, ...).
contributor: http://orcid.org/0000-0002-1595-3213

integration time setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed.
editor note: This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
alternative label: integration period setting
alternative label: integration time
contributor: http://orcid.org/0000-0002-1595-3213

Axiom
annotated source: integration time setting
annotated property: definition
annotated target: A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed.
source: https://www.oceaninsight.com/knowledge-hub/glossary/#i

preamplifier gain setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the preamplifier gain in CCD sensors.
editor note: This class should better be defined in a more general device ontology.
contributor: http://orcid.org/0000-0002-1595-3213

horizontal shift speed setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the horizontal shift speed in CCD sensors.
editor note: This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
contributor: http://orcid.org/0000-0002-1595-3213

vertical shift speed setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the vertical shift speed in CCD sensors.
editor note: This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
contributor: http://orcid.org/0000-0002-1595-3213

device temperature setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the operating temperature of a device.
editor note: This class should better be defined in a more general device ontology.
contributor: http://orcid.org/0000-0002-1595-3213

number of accumulations
type: Class
subclass of: setting datum
definition: A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio.
editor note: This class might better be defined in a more general device ontology.
alternative label: number of acquisitions
contributor: http://orcid.org/0000-0002-1595-3213

CCD sensor binning read mode setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the binning read mode of a device with a CCD sensor.
editor note: This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
contributor: http://orcid.org/0000-0002-1595-3213

groove density
type: Class
subclass of: physical quality
definition: A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter.
editor note: temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541)
alternative label: groove frequency
contributor: http://orcid.org/0000-0002-1595-3213

Axiom
annotated source: groove density
annotated property: definition
annotated target: A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter.
source: Diffraction grating
source: https://www.meetoptics.com/academy/groove-density

groove density setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the number of grooves in a diffraction grating device.
editor note: This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
alternative label: grating
alternative label: grating setting
contributor: http://orcid.org/0000-0002-1595-3213

diffraction grating
type: Class
subclass of: device
definition: A device that is an optical component with a periodic structure that diffracts light into several beams travelling in different directions (i.e. different diffraction angles)
editor note: This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
contributor: http://orcid.org/0000-0002-1595-3213

Axiom
annotated source: diffraction grating
annotated property: definition
annotated target: A device that is an optical component with a periodic structure that diffracts light into several beams travelling in different directions (i.e. different diffraction angles)
source: Diffraction grating

deprecated_excitation wavelength
type: Class
definition: A physical quality of the light source that is used used to excite a system to a higher energy state.
editor note: This class is not needed, as PATO:wavelength is sufficient, if this quality of a Raman device is really needed.
has obsolescence reason: failed exploratory term
term replaced by: wavelength
contributor: http://orcid.org/0000-0002-1595-3213
deprecated: true

excitation wavelength setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the wavelength of an electromagnetic radiation source (e.g. a laser) which has the function to excite the energy state of a target material.
editor note: This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
contributor: http://orcid.org/0000-0002-1595-3213

objective magnification factor setting
type: Class
subclass of: setting datum
example of usage: 100x
definition: A setting datum that specifies the magnification factor of the objective collecting the scattered light.
alternative label: magnification
alternative label: magnification setting
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-1595-3213
contributor: http://orcid.org/0000-0002-2239-3955

spectral window range maximum
type: Class
subclass of: setting datum
example of usage: 210 cm^-1
definition: A setting datum that specifies the upper boundary of the spectral window range utilized during the acquisition of spectroscopic data.
editor note: It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived.
alternative label: acquisition band maximum
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-1595-3213

spectral window range minimum
type: Class
subclass of: setting datum
example of usage: 1960 cm^-1
definition: A setting datum that specifies the lower boundary of the spectral window range utilized during the acquisition of spectroscopic data.
editor note: It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived.
alternative label: acquisition band minimum
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-1595-3213

incident light power datum
type: Class
subclass of: scalar measurement datum
example of usage: 200 mW
definition: A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components.
alternative label: excitation light power
alternative label: light power on the sample
contributor: http://orcid.org/0000-0001-7694-5519
comment: The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot.

region of interest
type: Class
subclass of: site
definition: A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded.
editor note: See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402
alternative label: ROI
alternative label: imaging region of interest
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955

Axiom
annotated source: region of interest
annotated property: definition
annotated target: A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded.
source: Item:Q57

region of interest width
type: Class
subclass of: setting datum
example of usage: 1 mm
definition: A setting datum that specifies the width (length in the X direction) of the region of interest.
alternative label: ROI horizontal length
alternative label: ROI width
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: region of interest width = (point distance X) * (number of measurements X)

region of interest breadth
type: Class
subclass of: setting datum
example of usage: 0.5 mm
definition: A setting datum that specifies the height (length in the Y direction) of the region of interest.
alternative label: ROI breadth
alternative label: ROI lateral length
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: region of interest breadth = (point distance Y) * (number of measurements Y)

region of interest depth
type: Class
subclass of: setting datum
example of usage: 0.1 mm
definition: A setting datum that specifies the depth (length in the Z direction) of the region of interest.
alternative label: ROI depth
alternative label: ROI vertical length
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: region of interest depth = (point distance Z) * (number of measurements Z)

point distance X
type: Class
subclass of: setting datum
example of usage: 20 µm
definition: A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy.
alternative label: sampling pace in the X direction
alternative label: sampling step in the X direction
alternative label: voxel distance in the X direction
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: point distance X = (region of interest width) / (number of measurements X)

point distance Y
type: Class
subclass of: setting datum
example of usage: 10 µm
definition: A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy.
alternative label: sampling pace in the Y direction
alternative label: sampling step in the Y direction
alternative label: voxel distance in the Y direction
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: point distance Y = (region of interest breadth) / (number of measurements Y)

point distance Z
type: Class
subclass of: setting datum
example of usage: 10 µm
definition: A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy.
alternative label: axial mapping distance
alternative label: sampling pace in the Z direction
alternative label: sampling step in the Z direction
alternative label: vertical mapping distance
alternative label: voxel distance in the Z direction
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: point distance Z = (region of interest depth) / (number of measurements Z)

number of measurements X
type: Class
subclass of: setting datum
example of usage: 50
definition: A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width.
alternative label: number of points in the X direction
alternative label: number of points per line
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: number of measurements X = (region of interest width) / (point distance X)

number of measurements Y
type: Class
subclass of: setting datum
example of usage: 100
definition: A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth.
alternative label: number of lines per layer
alternative label: number of points in the Y direction
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3955
comment: number of measurements = (region of interest breadth) / (point distance Y)

number of measurements Z
type: Class
subclass of: setting datum
example of usage: 10
definition: A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth.
alternative label: number of layers per acquisition
alternative label: number of points in the Z direction
contributor: http://orcid.org/0000-0001-7694-5519
contributor: http://orcid.org/0000-0002-2239-3956
comment: number of measurements Z = (region of interest depth) / (point distance Z)

Raman raw data
type: Class
subclass of: measurement datum
definition: A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam.
alternative label: raw Raman data
contributor: http://orcid.org/0000-0002-2239-3955

Axiom
annotated source: Raman raw data
annotated property: definition
annotated target: A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam.
source: Item:Q64

lens numerical aperture
type: Class
subclass of: setting datum
example of usage: The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm.
definition: A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located.
editor note: possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA
alternative label: numerical aperture
contributor: http://orcid.org/0000-0002-1595-3213
contributor: http://orcid.org/0000-0002-2239-3955

Axiom
annotated source: lens numerical aperture
annotated property: definition
annotated target: A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located.
source: Numerical aperture
source: Item:Q385

primary Raman data
type: Class
subclass of: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data transformation
    intersection of: Restriction
      on property: has_specified_input
      some values from: Raman raw data
definition: A data item that is obtained by processing raw Raman data.
contributor: http://orcid.org/0000-0002-1595-3213
contributor: http://orcid.org/0000-0002-2239-3955

resolution
type: Class
subclass of: physical quality
definition: A physical quality of a measurement device that expresses (realizes) the device's capacity to distinguish between two distinct but closely related measurements of the same physical quality or type, often quantified as the smallest detectable difference (resolution interval) between measured values.
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin

resolution interval
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: resolution
subclass of: Restriction
  on property: has value specification
  some values from: value specification
definition: A data item that quantifies a resolution, by representing the minimum measurable difference between two measurements of the same physical quality or type, such that the measurements can be distinguished as different.
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin

resolution power
type: Class
subclass of: ratio
definition: A ratio that quantifies the ability of a measurement device to distinguish between small differences in measurement values, expressed as the ratio between a typical measurement datum and the corresponding resolution interval.
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin

Axiom
annotated source: resolution power
annotated property: definition
annotated target: A ratio that quantifies the ability of a measurement device to distinguish between small differences in measurement values, expressed as the ratio between a typical measurement datum and the corresponding resolution interval.
source: ISBN 081946043-5

spatial resolution interval
type: Class
subclass of: resolution interval
definition: A resolution interval that quantifies the minimum distance between two points such that they can be considered two separate points in a given microscope under specific experimental parameters.
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin

Axiom
annotated source: spatial resolution interval
annotated property: definition
annotated target: A resolution interval that quantifies the minimum distance between two points such that they can be considered two separate points in a given microscope under specific experimental parameters.
source: ISBN 081946043-5

lateral resolution interval as angle
type: Class
subclass of: spatial resolution interval
definition: A spatial resolution interval that quantifies the minimum angular separation between two points on a plane orthogonal to the light ray, expressed as an angle centered in the lens (Formula: δθ = 1.22 * λ / D).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: $δθ = 1.22cdotλ/D$

Axiom
annotated source: lateral resolution interval as angle
annotated property: definition
annotated target: A spatial resolution interval that quantifies the minimum angular separation between two points on a plane orthogonal to the light ray, expressed as an angle centered in the lens (Formula: δθ = 1.22 * λ / D).
source: ISBN 081946043-5

lateral resolution interval as length
type: Class
subclass of: spatial resolution interval
definition: A spatial resolution interval that quantifies the minimum linear separation between two points on a plane orthogonal to the light ray, expressed as the distance from the center of the optical spot (Formula: δr = 0.61 * λ / NA).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: $δr = 0.61cdotλ/NA$ (Abbe formula, derived from the Rayleigh criterion with the Kirchhoff, Debye and paraxial approximation) $= 1.22 λcdot(f/sharp)$

Axiom
annotated source: lateral resolution interval as length
annotated property: definition
annotated target: A spatial resolution interval that quantifies the minimum linear separation between two points on a plane orthogonal to the light ray, expressed as the distance from the center of the optical spot (Formula: δr = 0.61 * λ / NA).
source: ISBN 081946043-5

axial resolution interval as length
type: Class
subclass of: spatial resolution interval
definition: A spatial resolution interval that quantifies the minimum measurable separation between two points along the axis of propagation of the light ray, expressed as a linear distance (Formula: δz = 2 ⋅ n ⋅ λ / NA²).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: $δz = 2cdot ncdotλ/NA²$

Axiom
annotated source: axial resolution interval as length
annotated property: definition
annotated target: A spatial resolution interval that quantifies the minimum measurable separation between two points along the axis of propagation of the light ray, expressed as a linear distance (Formula: δz = 2 ⋅ n ⋅ λ / NA²).
source: ISBN 081946043-5

spectral resolution interval
type: Class
subclass of: resolution interval
definition: A resolution interval that quantifies the minimum separation between two narrow peaks in a spectrum such that they can be distinguished as two separate peaks.
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin

Axiom
annotated source: spectral resolution interval
annotated property: definition
annotated target: A resolution interval that quantifies the minimum separation between two narrow peaks in a spectrum such that they can be distinguished as two separate peaks.
source: ISBN 081946043-5

spectral resolution interval as wavelength
type: Class
subclass of: spectral resolution interval
definition: A spectral resolution interval that quantifies the minimum separation between two wavelengths such that they can be distinguished as different (Formula: δλ = λ / (n * N)).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: $δλ = λ / (ncdot N) = RFcdot Δλcdot WS / n$

Axiom
annotated source: spectral resolution interval as wavelength
annotated property: definition
annotated target: A spectral resolution interval that quantifies the minimum separation between two wavelengths such that they can be distinguished as different (Formula: δλ = λ / (n * N)).
source: ISBN 081946043-5
source: Item:Q200
source: Item:Q22

spectral resolution interval as wavenumber
type: Class
subclass of: spectral resolution interval
definition: A spectral resolution interval that quantifies the minimum separation between two wavenumbers such that they can be distinguished as different (Formula: δν~ = δλ / λ²).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: $δbarν$

Axiom
annotated source: spectral resolution interval as wavenumber
annotated property: definition
annotated target: A spectral resolution interval that quantifies the minimum separation between two wavenumbers such that they can be distinguished as different (Formula: δν~ = δλ / λ²).
source: ISBN 081946043-5

spectral resolution interval as frequency
type: Class
subclass of: spectral resolution interval
definition: A spectral resolution interval that quantifies the minimum separation between two frequencies such that they can be distinguished as different (Formula: δν = c * δν~ = c * δλ / λ²).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: $δν$

Axiom
annotated source: spectral resolution interval as frequency
annotated property: definition
annotated target: A spectral resolution interval that quantifies the minimum separation between two frequencies such that they can be distinguished as different (Formula: δν = c * δν~ = c * δλ / λ²).
source: ISBN 081946043-5

spectral resolution interval as energy
type: Class
subclass of: spectral resolution interval
definition: A spectral resolution interval that quantifies the minimum separation between two energy levels such that they can be distinguished as different (Formula: δE = h * δν = h * c * δν~ = h * c * δλ / λ²).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: $δE$

Axiom
annotated source: spectral resolution interval as energy
annotated property: definition
annotated target: A spectral resolution interval that quantifies the minimum separation between two energy levels such that they can be distinguished as different (Formula: δE = h * δν = h * c * δν~ = h * c * δλ / λ²).
source: ISBN 081946043-5

radiometric resolution interval
type: Class
subclass of: resolution interval
definition: A resolution interval that quantifies the minimum difference in irradiated energy, often coded as gray level in a grayscale or look-up-table (LUT).
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin

Axiom
annotated source: radiometric resolution interval
annotated property: definition
annotated target: A resolution interval that quantifies the minimum difference in irradiated energy, often coded as gray level in a grayscale or look-up-table (LUT).
source: ISBN 081946043-5

temporal resolution interval
type: Class
subclass of: resolution interval
definition: A resolution interval that quantifies the temporal separation between two measurements or frames, often expressed as the inverse of the frame rate. In techniques where temporal resolution is not directly derived from frame rate, it quantifies the minimum temporal interval between two resolvable events.
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: In techniques where the temporal resolution is not given directly from a temporal distance between subsequent measurements (e.g., pulsed time resolved pump-probe techniques), it can be used more properly as defined above

Axiom
annotated source: temporal resolution interval
annotated property: definition
annotated target: A resolution interval that quantifies the temporal separation between two measurements or frames, often expressed as the inverse of the frame rate. In techniques where temporal resolution is not directly derived from frame rate, it quantifies the minimum temporal interval between two resolvable events.
source: ISBN 081946043-5

diffraction limit
type: Class
subclass of: spatial resolution interval
definition: A spatial resolution interval that quantifies the theoretical maximum spatial resolution achievable by an optical system, constrained by the diffraction of light.
editor note: This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
contributor: http://orcid.org/0000-0002-2239-3955
contributor: Stefano Luin
comment: The Abbe diffraction limit, is defined as λ/ (2 NA) in which λ is the wavelength of the illuminating light and NA is the numerical aperture.

Axiom
annotated source: diffraction limit
annotated property: definition
annotated target: A spatial resolution interval that quantifies the theoretical maximum spatial resolution achievable by an optical system, constrained by the diffraction of light.
source: http://www.w3.org/2002/07/ISO/DIS%2018115-3,%20https:/www.iso.org/obp/ui#d25805417e256

spectral window center
type: Class
subclass of: setting datum
subclass of: center value
example of usage: 560 cm^-1
definition: A setting datum that specifies the middle wavelength/wavenumber of a spectrum, equal to the average of the maximum and minimum of the spectral window range utilized during the acquisition of spectroscopic data. It corresponds to the optimal alignment or centering of the spectrometer to ensure that the most relevant spectral features are captured effectively within the defined acquisition range.
contributor: http://orcid.org/0000-0002-1595-3213
contributor: http://orcid.org/0000-0002-2239-3955

Stefano Luin
type: NamedIndividual
type: Homo sapiens
affiliation: VIBSO Working Group

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred term: example to be eventually removed

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: 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
type: curation status specification
editor preferred term: 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
type: curation status specification
editor preferred term: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release
term editor: PERSON:Alan Ruttenberg

ready for release
type: NamedIndividual
type: curation status specification
editor preferred term: 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
type: curation status specification
editor preferred term: 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
type: curation status specification
editor preferred term: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
editor preferred term: 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.

obsolete_core
type: NamedIndividual
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
has obsolescence reason: placeholder removed
deprecated: true

placeholder removed
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: placeholder removed

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

term imported
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: 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
type: obsolescence reason specification
editor preferred term: 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
type: denotator type
editor preferred term: 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
type: denotator type
editor preferred term: 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
type: denotator type
editor preferred term: 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
type: curation status specification
editor preferred term: 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
type: curation status specification
editor preferred term: 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
type: obsolescence reason specification
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
type: obsolescence reason specification
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

Assay A
type: NamedIndividual
type: assay
realizes: EvaluantRole R
has_specified_input: MaterialEntity M
has_specified_output: DataItem D
achieves_planned_objective: AssayObjective O
description: The assay A is planned to produce as a specified output the data item D which is a specific kind of information about the material entity M, which has the evaluant role R that gets realized in this planned observation process. This example instance is part of the ontology to demonstrate the OBI assay pattern. The type and number of relations between this instance and other example instances are based on the subclassOf and equivalentTo axioms asserted on OBI's assay.

_Laser_Wavelength_1
type: NamedIndividual
type: wavelength
quality of: _Raman_Spectrometer_1
description: The laser wavelength of _Raman_Spectrometer_1 which is a general attribute (aka quality/characteristic) of _Raman_Spectrometer_1. The quantity of this attribute is represented by the _Wavelength_Value_Specification_1.

_Raman_Spectrometer_1
type: NamedIndividual
type: Raman spectrometer
description: The Raman spectrometer that is used in _RamanAssay_1.

_Raman_Spectroscopy_1
type: NamedIndividual
type: Raman spectroscopy
has_specified_input: _Raman_Spectrometer_1
has_specified_input: _Sample_1
has_specified_input: _Wavelength_Setting_Info_1
has_specified_output: _Raman_Spectrum_1
achieves_planned_objective: _Raman_Spectrum_Objective_1
executes: _Raman_Spectroscopy_Method_1
description: The Raman spectroscopy in which _Sample_1 is being assayed according to _Raman_Spectroscopy_Method_1 in order to achieve _Raman_Spectrum_Objective_1.

_Raman_Spectroscopy_Method_1
type: NamedIndividual
type: investigation assay specification
has part: _Raman_Spectrum_Objective_1
has part: _Wavelength_Setting_Info_1
is about: _Raman_Spectrometer_1
is about: _Raman_Spectroscopy_1
description: The information that indicates the type of _Raman_Spectroscopy_1 by describing its method, specifying its inputs and outputs, as well as the necessary steps and actions that have to be taken in order to achieve _Raman_Spectrum_Objective_1. For the sake of keeping it simple, not all parts of this assay specification will be provided as assertions on this example.

_Raman_Spectrum_1
type: NamedIndividual
type: data item
is about: _Sample_1
description: The Raman spectrum (the data outputed by _RamanSpectrometer_1 NOT the plot) of _Sample_1 created by _RamanAssay_1. Currently classified as an IAO:'data item' as a more specific subclass thereof has yet to be minted in VIBSO (see alos: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77)

_Raman_Spectrum_Objective_1
type: NamedIndividual
type: assay objective
description: The information that specifies the intended outcome of _Raman_Spectroscopy_1 to be the creation of a Raman Spectrum.

_Sample_1
type: NamedIndividual
type: material sample
description: The material entity that is being evaluated in _RamanAssay_1.

_Wavelength_Setting_Info_1
type: NamedIndividual
type: excitation wavelength setting
has value specification: _Wavelength_Value_Specification_1
RO_0002566: _Laser_Wavelength_1
description: The information that determines the wavelength of the laser of _Raman_Spectrometer_1 which is used to excite the sample. This information gets encoded by the _Laser_Value_Specification_1.

_Wavelength_Value_Specification_1
type: NamedIndividual
type: scalar value specification
has measurement unit label: nanometer
specifies value of: _Laser_Wavelength_1
has specified value: 555.0
description: The encoding of the value determined by _Wavelength_Setting_Info_1, which consists of the unit label and the literal value of the laser wavelength of _Raman_Spectrometer_1.

Rainer Stosch
type: NamedIndividual
type: Homo sapiens
affiliation: German National Metrology Institute
affiliation: NFDI4Chem
affiliation: VIBSO Working Group

Philip Strömert
type: NamedIndividual
type: Homo sapiens
affiliation: German National Library of Science and Technology Hannover
affiliation: NFDI4Chem
affiliation: VIBSO Working Group

Giacomo Lanza
type: NamedIndividual
type: Homo sapiens
affiliation: German National Metrology Institute
affiliation: NFDI4Chem
affiliation: VIBSO Working Group

Johannes Hunold
type: NamedIndividual
type: Homo sapiens
affiliation: German National Library of Science and Technology Hannover
affiliation: NFDI4Chem
affiliation: VIBSO Working Group

German National Library of Science and Technology Hannover
type: NamedIndividual
type: organization
label: Technische Informationsbibliothek (TIB) @de

German National Metrology Institute
type: NamedIndividual
type: organization
label: Physikalisch-Technische Bundesanstalt (PTB) @de

NFDI4Chem
type: NamedIndividual