Metabolomics Standards Initiative Ontology (MSIO)
type: Ontology
Format: OWL
bug-database: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues
homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
rights: http://creativecommons.org/licenses/by/3.0/
version info: 1.0.1
Contributor: Silvia Marin
Contributor: Vitaly Selivanov
Contributor: Marta Cascante
Contributor: Pedro Ramon de Atauri Carulla
Contributor: Teresa Fan
description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.
Contributor: Andrew Lane
Contributor: Hunter Moseley
creator: Philippe Rocca-Serra
Contributor: Alejandra Gonzalez-Beltran

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

example of usage
type: AnnotationProperty
editor preferred label: example
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>

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

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

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

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

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

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: ready for release
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

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

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

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

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

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

has axiom label
type: AnnotationProperty

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: ready for release
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
term editor: Person: Alejandra Gonzalez-Beltran
term editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
sub property of: alternative term

IEDB alternative term
type: AnnotationProperty
editor preferred label: IEDB alternative term
has curation status: ready for release
definition: An alternative term used by the IEDB.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
sub property of: alternative term

temporal interpretation
type: AnnotationProperty

Contributor
type: AnnotationProperty
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
comment: An entity responsible for making contributions to the content of the resource.

Creator
type: AnnotationProperty
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
comment: An entity primarily responsible for making the content of the resource.

Date
type: AnnotationProperty
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
comment: A date associated with an event in the life cycle of the resource.

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
comment: An account of the content of the resource.

Format
type: AnnotationProperty
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
comment: The physical or digital manifestation of the resource.

Source
type: AnnotationProperty
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
comment: The topic of the content of the resource.

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

has_alternative_id
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

label
type: AnnotationProperty
editor preferred label: label

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
imported from: Ontology for Biomedical Investigation
temporal interpretation: axiom holds for all times

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
sub property of: topObjectProperty
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
imported from: Ontology for Biomedical Investigation
temporal interpretation: axiom holds for all times

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: Ontology for Biomedical Investigation
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
equivalent property:
  inverse of: realized in
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: Ontology for Biomedical Investigation
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

preceded by
type: ObjectProperty
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: preceded by
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
imported from: Ontology for Biomedical Investigation
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: precedes
imported from: Ontology for Biomedical Investigation

is restricted to
type: ObjectProperty
definition: An object property linking a consent code to a specific restriction which further constrains it, such as research should be restricted to a specific disease or geographical location.
id: DUO:0000010

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: unit
imported from: Ontology for Biomedical Investigation

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: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: Ontology for Biomedical Investigation

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

is quality measurement of
type: ObjectProperty
equivalent property:
  inverse of: is quality measured as
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
imported from: Ontology for Biomedical Investigation

has coordinate unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: length unit
imported from: Ontology for Biomedical Investigation
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
has curation status: metadata complete
definition: relates a process to a time-measurement-datum that represents the duration of the process
term editor: Person:Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

is quality measured as
type: ObjectProperty
equivalent property:
  inverse of: is quality measurement of
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
imported from: Ontology for Biomedical Investigation

has time stamp
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
term editor: Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

has measurement datum
type: ObjectProperty
sub property of: has part
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the measurement datum that was measured
term editor: Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

is isotopomer of
type: ObjectProperty
has curation status: requires discussion
definition: a chemical entity is said to be an isotopomer of another one if it has the same number of each isotopic atom but differs in their positions. isotopomer is a contraction of isotopic isomer
term editor: CH2DCH=0 is isotopomer of CH3CD=0
definition source: IUPAC compendium of chemical terminology (2nd edition, 1997)

is isotopologue of
type: ObjectProperty
example of usage: CH4 is isotopologue of CH3D which is isotopologue of CH2D2
has curation status: requires discussion
definition: a molecular entity which differs only in isotopic composition (i.e the number of isotopic substitution differs but the overall chemical structure is unchanged) is said to be an isotologue
term editor: Philippe Rocca-Serra
definition source: IUPAC compendium of chemical terminology (2nd edition, 1997)

manufactured by
type: ObjectProperty
sub property of: topObjectProperty
definition: A relation associating a product to its manufacturer.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

is_supported_by_data
type: ObjectProperty
domain: conclusion based on data
range: data item
editor preferred label: is_supported_by_data
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
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
imported from: Ontology for Biomedical Investigation

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 label: has_specified_input
example of usage: see is_input_of example_of_usage
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.
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: Ontology for Biomedical Investigation

is_specified_input_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_input
sub property of: participates in
range: planned process
editor preferred label: is_specified_input_of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: 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
imported from: Ontology for Biomedical Investigation

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 label: has_specified_output
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: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: Ontology for Biomedical Investigation

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred label: 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: Ontology for Biomedical Investigation

is_proxy_for
type: ObjectProperty
domain: continuant
range: continuant
editor preferred label: is_proxy_for
example of usage: position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity
has curation status: metadata incomplete
definition: A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
editor note: A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition)
term editor: Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

has grain
type: ObjectProperty
sub property of: has part
editor preferred label: has grain
has curation status: metadata complete
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
term editor: PERSON: Alan Ruttenberg
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: Ontology for Biomedical Investigation

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

is member of organization
type: ObjectProperty
inverse of: has organization member
domain: Class
  union of: Homo sapiens
  union of: organization
range: organization
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

specifies value of
type: ObjectProperty
sub property of: is about
domain: value specification
editor preferred label: specifies value of
has curation status: metadata incomplete
definition: A relation between a value specification and an entity which the specification is about.
imported from: Ontology for Biomedical Investigation

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
inverse of: bearer of
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
imported from: Ontology for Biomedical Investigation
temporal interpretation: axiom holds for all times

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
imported from: Ontology for Biomedical Investigation
temporal interpretation: axiom holds for all times

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

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

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
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.
imported from: Ontology for Biomedical Investigation

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
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.
imported from: Ontology for Biomedical Investigation

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of
imported from: Ontology for Biomedical Investigation

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

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of
imported from: Ontology for Biomedical Investigation

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

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

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
sub property of: topObjectProperty
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role
imported from: Ontology for Biomedical Investigation
label: has_role

derives from
type: ObjectProperty
equivalent property:
  inverse of: derives into
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from
imported from: Ontology for Biomedical Investigation
imported from: ro.owl

derives into
type: ObjectProperty
equivalent property:
  inverse of: derives from
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative term: derives_into
imported from: Ontology for Biomedical Investigation

temporal relation
type: ObjectProperty
range: occurrent
has curation status: pending final vetting
editor note: move to BFO?
definition source: Allen
imported from: Ontology for Biomedical Investigation
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has measurement value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
imported from: Ontology for Biomedical Investigation

has x coordinate value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float
imported from: Ontology for Biomedical Investigation

has y coordinate value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float
imported from: Ontology for Biomedical Investigation

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: value specification
range: real
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

has specified value
type: DatatypeProperty
domain: value specification
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

integer32
type: Class
subclass of: byte format
coverage: For 1r/1i spectra and for Bruker, this term describe an array of integers (32bits).

sample number
type: Class
subclass of: sample attribute
definition: A reference number relevant to the sample under study.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000001

Axiom
annotated source: sample number
annotated property: definition
annotated target: A reference number relevant to the sample under study.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

long64
type: Class
subclass of: byte format
coverage: For 1r/1i spectra and for Bruker, this term describe an array of longs (64bits).

sample state information
type: Class
subclass of: sample attribute
definition: The chemical phase of a pure sample, or the state of a mixed sample.
has_obo_namespace: NMR
id: NMR:1000003

Axiom
annotated source: sample state information
annotated property: definition
annotated target: The chemical phase of a pure sample, or the state of a mixed sample.
database_cross_reference: MSI:NMR

sample mass information
type: Class
subclass of: sample attribute
definition: Total mass of sample used.
database_cross_reference: value-type:xsd:float
has_obo_namespace: NMR
id: NMR:1000004

Axiom
annotated source: sample mass information
annotated property: definition
annotated target: Total mass of sample used.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample mass information
annotated property: database_cross_reference
annotated target: value-type:xsd:float

sample volume
type: Class
subclass of: sample attribute
definition: Total volume of solution used.
database_cross_reference: value-type:xsd:float
has_obo_namespace: NMR
id: NMR:1000005

Axiom
annotated source: sample volume
annotated property: definition
annotated target: Total volume of solution used.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample volume
annotated property: database_cross_reference
annotated target: value-type:xsd:float

sample concentration
type: Class
subclass of: sample attribute
definition: Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
database_cross_reference: value-type:xsd:float
has_obo_namespace: NMR
id: NMR:1000006

Axiom
annotated source: sample concentration
annotated property: definition
annotated target: Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample concentration
annotated property: database_cross_reference
annotated target: value-type:xsd:float

quadrature detection
type: Class
subclass of: NMR data processing
comment: One of the problems that should be apparent after observing the spectrum and the FID is that it is not possible to determine if the frequency is positive or negative. The instrument uses a spectrometer frequency and all signal frequencies are measured relative to the spectrometer frequency. If a molecule produces two signals, one at 300,000,001 Hz and another at 299,999,999 Hz, and the spectrometer frequency is 300,000,000 Hz, the first signal is at +1 Hz and the second is at -1 Hz. Electronically the lower frequency signals are very easy frequency to detect, transmit, amplify and sample. The complication with this rotating frame of reference is that a single detector can not distinguish positive and negative frequencies. This problem is why quadrature detection is important. Quadrature detection uses two detector channels separated by 90 degrees. These are referred to as the real channel and the imaginary channel. Using these two channels, it is possible to distinguish positive and negative frequencies. This section shows how the quadrature signal is processed to obtain an NMR spectrum. The Fourier transform produces a complex number with a real and an imaginary component. The Re function extracts the real spectrum and the Im function extracts the imaginary spectrum from the complex number.

contact role
type: Class
subclass of: contact attribute

data file attribute
type: Class
subclass of: generically dependent continuant

NMR instrument type
type: Class
subclass of: instrument attribute

1D spectrum coordinate system descriptor
type: Class
subclass of: NMR spectrum descriptor

pre-acquisition solvent suppression
type: Class
subclass of: data transformation

peak processing
type: Class
subclass of: frequency domain data processing

Hexafluorobenzene
type: Class
subclass of: concentration standard
subclass of: NMR solvent

Chloroform-d
type: Class
subclass of: NMR solvent
has_exact_synonym: CDCl3

heavy water
type: Class
subclass of: NMR solvent
consider: CHEBI:41981
has_exact_synonym: D2O

sample pH
type: Class
subclass of: pH

post buffer pH
type: Class
subclass of: pH

apodization
type: Class
subclass of: time domain data processing
term editor: Philippe Rocca-Serra
definition source: http://www.scs.illinois.edu/nmr/handouts/general_pdf/ugi034.pdf
definition: Apodization is an umbrella term that is used to refer to signal processing covering the manipulation of the FID to either increase signal-to-noise (S/N) or resolution. it is usually possible to gain either S/N or resolution, but not both. Apodization is usually performed by applying a window function to the FID

metabolomics database identifier
type: Class
subclass of: external reference identifier
Source: http://www.metabolomicssociety.org/databases
comment: PRS: rename 'reference' to 'identifier'

Metabolights identifier
type: Class
subclass of: metabolomics database identifier

acetonitrile
type: Class
subclass of: 1H spectrum reference compound

1,4-Dioxane
type: Class
subclass of: 1H spectrum reference compound
subclass of: 13C spectrum reference compound

1H spectrum reference compound
type: Class
subclass of: chemical shift standard

2,2-Dimethyl-2-silapentane-5-sulfonate
type: Class
subclass of: 1H spectrum reference compound
has_exact_synonym: DSS

sodium acetate
type: Class
subclass of: 1H spectrum reference compound

tetramethylsilane
type: Class
subclass of: 1H spectrum reference compound
subclass of: 13C spectrum reference compound
has_exact_synonym: TMS

13C spectrum reference compound
type: Class
subclass of: chemical shift standard

NMR instrument model
type: Class
subclass of: instrument attribute
definition: Instrument model name not including the vendor's name.
has_obo_namespace: NMR
id: NMR:1000031

Axiom
annotated source: NMR instrument model
annotated property: definition
annotated target: Instrument model name not including the vendor's name.
database_cross_reference: MSI:NMR

instrument customization
type: Class
subclass of: instrument attribute
definition: Free text description of a single customization made to the instrument; for several modifications, use several entries.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000032

Axiom
annotated source: instrument customization
annotated property: definition
annotated target: Free text description of a single customization made to the instrument; for several modifications, use several entries.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: instrument customization
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Chloroform-d1
type: Class
subclass of: 13C spectrum reference compound
subclass of: 2H spectrum reference compound

keyword
type: Class
subclass of: reference

tetramethylammonium bromide
type: Class
subclass of: 13C spectrum reference compound
subclass of: 15N spectrum reference compound

15N spectrum reference compound
type: Class
subclass of: chemical shift standard

ammonia (liquid)
type: Class
subclass of: 15N spectrum reference compound

ammonium bromide
type: Class
subclass of: 15N spectrum reference compound

1,4-morpholine
type: Class
subclass of: 15N spectrum reference compound

nitromethane
type: Class
subclass of: 15N spectrum reference compound

pyridine
type: Class
subclass of: 15N spectrum reference compound

sodium nitrate
type: Class
subclass of: 15N spectrum reference compound

post-acquisition solvent suppression
type: Class
subclass of: spectral denoising
has_exact_synonym: solvent filtering

decoupling method
type: Class
subclass of: NMR acquisition parameter
definition: Nuclear magnetic resonance decoupling (NMR decoupling for short) is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate fully or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks which are up to several hertz frequency from each other. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds.
Source: http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_decoupling

homonuclear decoupling
type: Class
subclass of: decoupling method

heteronuclear decoupling
type: Class
subclass of: decoupling method

emulsion
type: Class
subclass of: liquid
definition: State if the sample is in emulsion form.
has_obo_namespace: NMR
id: NMR:1000047

Axiom
annotated source: emulsion
annotated property: definition
annotated target: State if the sample is in emulsion form.
database_cross_reference: MSI:NMR

gas
type: Class
subclass of: sample state information
definition: State if the sample is in gaseous form.
has_obo_namespace: NMR
id: NMR:1000048

Axiom
annotated source: gas
annotated property: definition
annotated target: State if the sample is in gaseous form.
database_cross_reference: MSI:NMR

liquid
type: Class
subclass of: sample state information
definition: State if the sample is in liquid form.
has_obo_namespace: NMR
id: NMR:1000049

Axiom
annotated source: liquid
annotated property: definition
annotated target: State if the sample is in liquid form.
database_cross_reference: MSI:NMR

solid
type: Class
subclass of: sample state information
definition: State if the sample is in solid form.
has_obo_namespace: NMR
id: NMR:1000050

Axiom
annotated source: solid
annotated property: definition
annotated target: State if the sample is in solid form.
database_cross_reference: MSI:NMR

solution
type: Class
subclass of: liquid
definition: State if the sample is in solution form.
has_obo_namespace: NMR
id: NMR:1000051

Axiom
annotated source: solution
annotated property: definition
annotated target: State if the sample is in solution form.
database_cross_reference: MSI:NMR

suspension
type: Class
subclass of: liquid
definition: State if the sample is in suspension form.
has_obo_namespace: NMR
id: NMR:1000052

Axiom
annotated source: suspension
annotated property: definition
annotated target: State if the sample is in suspension form.
database_cross_reference: MSI:NMR

sample batch information
type: Class
subclass of: sample attribute
definition: Sample batch lot identifier.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000053

Axiom
annotated source: sample batch information
annotated property: definition
annotated target: Sample batch lot identifier.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample batch information
annotated property: database_cross_reference
annotated target: value-type:xsd:string

broad band decoupling
type: Class
subclass of: decoupling method

off resonance decoupling
type: Class
subclass of: decoupling method

specific decoupling
type: Class
subclass of: decoupling method
has_exact_synonym: band-selective decoupling
has_exact_synonym: narowband decoupling

angle of sinusoid
type: Class
subclass of: window function parameter

31P spectrum reference compound
type: Class
subclass of: chemical shift standard

phosphoric acid
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: H3PO4

phosphorus
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: P4

trimethyl phosphate
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: (CH3O)3PO

triphenylphosphine
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: P(C6H5)3

triphenylphosphine oxide
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: O=P(C6H5)3

co-dissolved internal reference
type: Class
subclass of: chemical shift reference

synthetic reference signal
type: Class
subclass of: chemical shift reference

residual solvent signal
type: Class
subclass of: chemical shift reference

FID zero filling
type: Class
subclass of: time domain data processing

data extrapolation using linear prediction
type: Class
subclass of: FID zero filling

multiplying FID by window function
type: Class
subclass of: time domain data processing

FID fourier transformation
type: Class
subclass of: time domain data processing
definition: The mathematical conversion of time-resolved FID raw data into frequency resolved NMR spectra (frequency-resolved NMR data) by means of fourier transformation of coordinate systems.

phase correction
type: Class
subclass of: frequency domain data processing
has_exact_synonym: phasing
has_exact_synonym: spectral phasing

peak integration
type: Class
subclass of: peak processing

peak alignment
type: Class
subclass of: peak processing

peak shape fitting
type: Class
subclass of: peak fitting

spectral referencing
type: Class
subclass of: frequency domain data processing

sodium trimethylsilyl-propionate
type: Class
subclass of: 13C spectrum reference compound
Source: Pohl, L.; Eckle, M. (1969). "Sodium 3-(trimethylsilyl)tetradeuteriopropionate, a new water-soluble standard for 1H.N.M.R.". Angewandte Chemie, International Edition in English 8 (5): 381. doi:10.1002/anie.196903811
has_exact_synonym: TMSP
has_exact_synonym: trimethylsilyl propanoic acid

linear scaling
type: Class
subclass of: scaling
comment: used to be 'linear scaling algorithm'

scaling
type: Class
subclass of: frequency domain data processing
comment: used to be called 'scaling algorithm'

non-linear scaling
type: Class
subclass of: scaling
comment: used to be postfixed with algorithm

total spectral area scaling
type: Class
subclass of: linear scaling

probabilistic quotient normalization
type: Class
subclass of: linear scaling
Source: Dieterle F, Ross A, Schlotterbeck G, Senn H: Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem 2006, 78(13):4281-90.

scaling by generalized logarithmic transformation
type: Class
subclass of: non-linear scaling
has_exact_synonym: glog scaling

pareto scaling
type: Class
subclass of: non-linear scaling

autoscaling
type: Class
subclass of: non-linear scaling

2D J-resolved spectrum
type: Class
subclass of: 2D spectrum
has_exact_synonym: JRES spectrum

MetaboLab software
type: Class
subclass of: open source NMR software
Source: http://www.biomedcentral.com/1471-2105/12/366#B2

Metaboquant software
type: Class
subclass of: open source NMR software

rNMR software
type: Class
subclass of: open source NMR software

open source NMR software
type: Class
subclass of: NMR software

commercial NMR software
type: Class
subclass of: NMR software

NMRLab software
type: Class
subclass of: open source NMR software
Source: Günther U, Ludwig C, Rüterjans H: NMRLAB - advanced NMR data processing in Matlab., J Magn Reson 2000, 145(2):201-208.

NMRPipe software
type: Class
subclass of: open source NMR software
Source: Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995, 6(3):277-293.

matNMR software
type: Class
subclass of: open source NMR software
Source: van Beek JD: matNMR: a flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab. J Magn Reson 2007, 187:19-26.

concentration of chemical compound
type: Class
subclass of: chemical compound attribute

manual phase correction
type: Class
subclass of: phase correction

automatic phase correction
type: Class
subclass of: phase correction

DC offset correction
type: Class
subclass of: phase correction

Gibbs multiplication
type: Class
subclass of: frequency domain data processing
Source: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-366

skyline projection
type: Class
subclass of: spectral projection

shifted sine window function
type: Class
subclass of: sine window function
has_exact_synonym: shifted sine apodization

sinc window multiplication of FID (1D)
type: Class
subclass of: window function for apodization
has_exact_synonym: SINC
has_exact_synonym: Sinc window multiplication

SEM window function
type: Class
subclass of: window function for apodization
Source: http://www.sciencedirect.com/science/article/pii/S0003267008000950
bug-database: https://github.com/nmrML/nmrML/issues/36
has_exact_synonym: combined sine-bell–exponential window function

trapezoid window function
type: Class
subclass of: window function for apodization
has_exact_synonym: TRAP
has_exact_synonym: trapezoid apodization
comment: Functional form ( 0:t1 linear increase from 0.0 to 1.0, t1:size-t2 1.0 -t2: linear decrease from 1.0 to 0.0 / Parameters ( * data Array of spectral data., * t1 Left ramp length., * t2 Right ramp length., * inv Set True for inverse apodization.

shifted gaussian window function
type: Class
subclass of: Gaussian window function

baseline correction using spline function
type: Class
subclass of: baseline correction

heteronuclear single quantum coherence spectrum
type: Class
subclass of: 2D spectrum
has_exact_synonym: HSQC NMR spectrum

Zangger-Sterk pulse sequence
type: Class
subclass of: NMR pulse sequence

pure shift 1D Zangger-Sterk pulse sequence
type: Class
subclass of: Zangger-Sterk pulse sequence
Source: http://nmr.chemistry.manchester.ac.uk/

oneshot pulse sequence
type: Class
subclass of: NMR pulse sequence
Source: http://nmr.chemistry.manchester.ac.uk/

pure shift oneshot pulse sequence
type: Class
subclass of: oneshot pulse sequence
Source: http://nmr.chemistry.manchester.ac.uk/

perfect echo watergate pulse sequence
type: Class
subclass of: NMR pulse sequence
Source: http://nmr.chemistry.manchester.ac.uk/
has_exact_synonym: PE Watergate pulse sequence

NMR Star 3.1 file format
type: Class
subclass of: NMR software data format

NMR Star 2.1 file format
type: Class
subclass of: NMR software data format

3D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
has_exact_synonym: three dimensional spectrum

4D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
has_exact_synonym: four dimensional spectrum

NMR spectrum by dimensionality
type: Class
subclass of: NMR spectrum

homonuclear chemical shift spectrum
type: Class
subclass of: NMR spectrum

heteronuclear chemical shift spectrum
type: Class
subclass of: NMR spectrum

Bruker instrument model
type: Class
subclass of: NMR instrument model
definition: Bruker instrument model.
has_obo_namespace: NMR
id: NMR:1000122

Axiom
annotated source: Bruker instrument model
annotated property: definition
annotated target: Bruker instrument model.
database_cross_reference: MSI:NMR

homonuclear exchange spectroscopy spectrum
type: Class
subclass of: NMR spectrum

heteronuclear exchange spectroscopy spectrum
type: Class
subclass of: NMR spectrum

homonuclear J-resolved spectrum
type: Class
subclass of: 2D J-resolved spectrum

heteronuclear J-resolved spectrum
type: Class
subclass of: 2D J-resolved spectrum

calibration test spectrum
type: Class
subclass of: NMR spectrum by processing step

NMR star software
type: Class
subclass of: open source NMR software

Felix software
type: Class
subclass of: commercial NMR software
Source: http://www.felixnmr.com/

PIPP software
type: Class
subclass of: NMR software

TALOS+ software
type: Class
subclass of: NMR software

CYANA software
type: Class
subclass of: open source NMR software
Source: http://www.cyana.org/wiki/index.php/Main_Page

XPLOR-NIH software
type: Class
subclass of: NMR software
Source: http://nmr.cit.nih.gov/xplor-nih/

computed concentration
type: Class
subclass of: concentration of chemical compound
editorial note: request these in UO ?

XEASY software
type: Class
subclass of: open source NMR software
Source: http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/XEASY

sparky software
type: Class
subclass of: open source NMR software

CARA software
type: Class
subclass of: open source NMR software
Source: http://nmr-software.blogspot.de/2007/04/cara.html

Wattos software
type: Class
subclass of: open source NMR software

MADNMR software
type: Class
subclass of: NMR software

Pronto software
type: Class
subclass of: NMR software

TRIAD NMR software
type: Class
subclass of: NMR software

library based computed concentration
type: Class
subclass of: computed concentration

Lorenzian estimated concentration
type: Class
subclass of: computed concentration
has_exact_synonym: Lorenzian (-Integration) (Modeled Area) Estimated Concentration
comment: https://docs.google.com/spreadsheets/d/1egsLQWoQuCxAYPr9MIo-F0A5K9RCbJSC8yWZyYq_fiQ/edit

measured area based concentration
type: Class
subclass of: computed concentration
has_exact_synonym: Measured Area (Integration) based Concentration

time-domain amplitude computed concentration
type: Class
subclass of: computed concentration

group time delay compensation
type: Class
subclass of: time domain data processing
definition: This is independent of the bruker acquisition parameter named "GRPDLY" (Group Delay), but this is a "shift" applied on the fid to calibrate its zero

scaling by forward linear prediction
type: Class
subclass of: data extrapolation using linear prediction

back calculation of first points by linear-prediction
type: Class
subclass of: data extrapolation using linear prediction

scaling by mirror image linear prediction
type: Class
subclass of: data extrapolation using linear prediction

digital filtering
type: Class
subclass of: NMR acquisition parameter

3D strip plot generation
type: Class
subclass of: plot and graph generation
definition source: Daniel Schober
Source: http://jjhelmus.github.io/nmrglue/current/jbnmr_examples/s11_strip_plots.html
definition: A spectrum vizualization method for 3D nmr spectra, assisting assignments for large sequential molecules, i.e. Proteins. The first two axis in the plot represent the ppms along the two acquisition nuclei, and a third dimension captures the sequential molecule order for the third nucleus.

Batman software
type: Class
subclass of: open source NMR software

JEOL instrument model
type: Class
subclass of: NMR instrument model

tecmag instrument model
type: Class
subclass of: NMR instrument model

automatic baseline recognition
type: Class
subclass of: baseline correction
Source: Bao et al. (2013) A new automatic baseline correction method based on iterative method, J. Magn. Res. 218:35-43
Source: Golotvin & Williams (2000), Improved baseline recognition and modeling of FT NMR spectra, J. Magn. Res. 146:122-125

Trimethylsilyl propionate
type: Class
subclass of: 1H spectrum reference compound
has_exact_synonym: TSP

TMIC lab pulse sequence
type: Class
subclass of: NMR pulse sequence
has_exact_synonym: pulse sequence from Wishart lab library

probe gradient strength
type: Class
subclass of: field strength

NMR acquisition computer operating system
type: Class
subclass of: NMR software
coverage: e.g. Linux or Windows, ...

NMR autosampler software
type: Class
subclass of: NMR software
coverage: e.g. Bruker Biospin ICON-NMR

Bruker Biospin ICON-NMR software
type: Class
subclass of: NMR autosampler software

buffer pH
type: Class
subclass of: pH

field frequency lock
type: Class
subclass of: sample attribute
coverage: e.g. heavy water (D2O)
has_exact_synonym: lock frequency

concentration standard
type: Class
subclass of: calibration compound
has_exact_synonym: quantitation standard

NMR acquisition software
type: Class
subclass of: NMR software

CIMR MI standard
type: Class
subclass of: minimum information standard

signal line width
type: Class
subclass of: NMR quality check

signal line width at five percent intensity
type: Class
subclass of: signal line width

NMR spectrum descriptor
type: Class
subclass of: generically dependent continuant

pulse width
type: Class
subclass of: pulse parameter

hard pulse width
type: Class
subclass of: pulse width

sweep width
type: Class
subclass of: NMR acquisition parameter
has_exact_synonym: spectrum width

number of data points
type: Class
subclass of: 1D spectrum coordinate system descriptor
has_exact_synonym: number of data points in spectrum
has_exact_synonym: number of first dimension data points

x end value
type: Class
subclass of: 1D spectrum coordinate system descriptor
definition: tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.

y-axis type
type: Class
subclass of: 1D spectrum coordinate system descriptor

center of bin on x-axis
type: Class
subclass of: binned spectrum descriptor
has_exact_synonym: bucket x center

spectral quantitation algorithm
type: Class
subclass of: binned spectrum descriptor
has_exact_synonym: NMR spectrum quantification method

NMRProcFlow software
type: Class
subclass of: open source NMR software
definition: The NMRProcFlow open source software provides a complete set of tools for processing (e.g. Bucketing) and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization.

Bayesil software
type: Class
subclass of: open source NMR software
definition: Bayesil is a web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum or cerebrospinal fluid. The NMR spectra must be collected in a standardized fashion for Bayesil to perform optimally. Bayesil first performs all spectral processing steps, including Fourier transformation, phasing, solvent filtering, chemical shift referencing, baseline correction and reference line shape convolution automatically. It then deconvolutes the resulting NMR spectrum using a reference spectral library, which here contains the signatures of more than 60 metabolites. This deconvolution process determines both the identity and quantity of the compounds in the biofluid mixture.
Source: Ravanbakhsh S, Liu P, Bjorndahl TC, Mandal R, Grant JR, Wilson M, Eisner R, Sinelnikov I, Hu X, Luchinat C, Greiner R, Wishart DS. (2015) Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics. PLoS ONE 10(5): e0124219.

nmrML Assign
type: Class
subclass of: Bayesil software
definition: nmrML-Assign is a web server for creating an nmrML file from a FID and a structure. The FID is first automatically processed with Bayesil. The resulting interactive spectrum allows assigning peaks to specific atoms in the structure and the assignments are saved in the nmrML format. For more information about nmrML please visit nmrML.org. nmrML-Assign works with 1H and 13C NMR spectra in Bruker or Agilent/Varian format.
comment: Uses JspectraView Software

doublet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: d

triplet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: t

quatruplet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: q

cluster of peaks across samples
type: Class
subclass of: data file content
definition: a set of peaks that are highly correlated in a series of samples
coverage: a feature request by Daniel Jacob inserted at IBP hackathon

simulated spectrum
type: Class
subclass of: NMR spectrum by processing step

pulse parameter
type: Class
subclass of: parameter

JEOL FID format
type: Class
subclass of: FID format

doublet of doublets feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: dd

ABX multiplet pattern
type: Class
subclass of: multiplet feature
definition: AMX, ABX and ABC patterns, and various related spin systems are very common in Proton NMR of organic molecules.When two of the protons of an AMX pattern approach each other to form an ABX pattern, the characteristic changes in intensities of a strongly coupled system (leaning) are seen, and, as the size of J approaches the value of νAB more complicated changes arise, so that the pattern can no longer be analyzed correctly by first order methods.

singlet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: s

quintet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: qi

doublet of triplets
type: Class
subclass of: multiplicity feature
has_exact_synonym: dt

triplet of douplets
type: Class
subclass of: multiplicity feature
has_exact_synonym: td

triplet of triplets
type: Class
subclass of: multiplicity feature
has_exact_synonym: tt

NMR spectrum by pulse sequence
type: Class
subclass of: NMR spectrum

NMR spectrum by processing step
type: Class
subclass of: NMR spectrum

2D spectrum coordinate system descriptor
type: Class
subclass of: NMR spectrum descriptor

y-axis value type
type: Class
subclass of: 2D spectrum coordinate system descriptor
see also: the subclasses come from the Rubtsov specification

power value type
type: Class
subclass of: y-axis value type

magnitude value type
type: Class
subclass of: y-axis value type

real value type
type: Class
subclass of: y-axis value type

imaginary value type
type: Class
subclass of: y-axis value type

complex value types
type: Class
subclass of: y-axis value type

spectral projection axis
type: Class
subclass of: NMR spectrum descriptor

f1 axis
type: Class
subclass of: spectral projection axis

f2 axis
type: Class
subclass of: spectral projection axis

NMR Format converter
type: Class
subclass of: NMR software

BML-NMR identifier
type: Class
subclass of: metabolomics database identifier

creatinine
type: Class
subclass of: concentration standard
comment: will be further specified via a concentration value

2D pulse sequence
type: Class
subclass of: NMR pulse sequence

data simulation
type: Class
subclass of: data transformation
comment: used to be labeled 'NMR spectrum simulation'

dynamic nuclear polarization NMR
type: Class
subclass of: NMR instrument type
has_exact_synonym: DNP NMR
has_exact_synonym: dynamic nuclear polarization enhanced NMR system

chemical shift
type: Class
subclass of: NMR spectrum descriptor
definition: Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis
Source: http://en.wikipedia.org/wiki/Chemical_shift

nmr signal intensity
type: Class
subclass of: NMR spectrum descriptor
definition: an information object that describes the strength of the NMR signal

baseline correction using polynomial function
type: Class
subclass of: baseline correction

first transient of the tnnoesy-presaturation pulse sequence
type: Class
subclass of: 2D pulse sequence

Varian acquisition parameter file
type: Class
subclass of: acquisition parameter file

procpar
type: Class
subclass of: Varian processing parameter file

acqus
type: Class
subclass of: Bruker acquisition parameter file

Bruker acquisition parameter file
type: Class
subclass of: acquisition parameter file

peak feature
type: Class
subclass of: NMR spectrum descriptor
has_obo_namespace: NMR
id: NMR:1000231

global
type: Class
subclass of: Varian acquisition parameter file

Varian autosampler
type: Class
subclass of: autosampler

Varian SMS 50
type: Class
subclass of: Varian autosampler

Varian probe
type: Class
subclass of: NMR probe

5mm HCN probe
type: Class
subclass of: Varian liquid cold probe

Varian liquid cold probe
type: Class
subclass of: Varian probe

reference compound NMR spectrum
type: Class
subclass of: NMR spectrum
comment: e.g as in HMDB

Mestrelab software
type: Class
subclass of: NMR software

ACD spectrus software
type: Class
subclass of: NMR software

Mat NMR 3 software
type: Class
subclass of: NMR software

NMRLab software
type: Class
subclass of: software

Spinworks NMR software
type: Class
subclass of: software

NMR software vendor
type: Class
subclass of: software vendor

Spinworks
type: Class
subclass of: NMR software vendor

iNMR software
type: Class
subclass of: NMR software

NMR pipe
type: Class
subclass of: NMR software

cule NMR software
type: Class
subclass of: NMR software

Matlab to nmrML converter
type: Class
subclass of: NMR Format converter
Source: Git: nmrML\tools\Parser_and_Converters\Matlab
comment: By Batman/ Tim Ebbels Group

Bruker processing parameter file
type: Class
subclass of: processing parameter file

procs
type: Class
subclass of: Bruker processing parameter file

Varian processing parameter file
type: Class
subclass of: processing parameter file

Madison Metabolomics Consortium Database MMCD identifier
type: Class
subclass of: metabolomics database identifier
Source: http://mmcd.nmrfam.wisc.edu/
comment: PRS: rename 'identifyer' to 'identifier'

Bigg metabolomics database identifier
type: Class
subclass of: metabolomics database identifier
Source: http://bigg.ucsd.edu/
comment: PRS: rename 'identifyer' to 'identifier'

Lorentz Gaussian window function
type: Class
subclass of: window function for apodization
has_exact_synonym: Lorentz-to-Gauss apodization
comment: Functional form: gm(x_i) = exp(e - g*g) Where: e = pi*i*g1 g = 0.6*pi*g2*(g3*(size-1)-i) Parameters: * data Array of spectral data. * g1 Inverse exponential width. * g2 Gaussian broaden width. * g3 Location of gauss maximum. * inv Set True for inverse apodization.

traf window function
type: Class
subclass of: window function for apodization
has_exact_synonym: TRAF
has_exact_synonym: Transform of Reverse Added FIDs
definition: A Window function described by Daniel Traficante in their original paper.

trafs window function
type: Class
subclass of: window function for apodization
has_exact_synonym: TRAFS

peak fitting
type: Class
subclass of: peak processing

peak assignment
type: Class
subclass of: peak processing

deconvolution
type: Class
subclass of: peak processing

chemical shift sorting
type: Class
subclass of: frequency domain data processing
definition: A method of sorting multiple spectra by position of chemical shift peaks. This method is used in Batman and improves the fit for shifted/overlapped peaks.

fid file
type: Class
subclass of: Bruker FID file

Varian FID file
type: Class
subclass of: FID file

Bruker FID file
type: Class
subclass of: FID file

ERVA-based bucketing
type: Class
subclass of: bucketing
Source: Jacob D. et al (2013) Analytical and Bioanalytical Chemistry, 405, 5049-5061

cluster of peaks
type: Class
subclass of: binned spectrum descriptor

Match NMR tube
type: Class
subclass of: Bruker tube

shaped tube
type: Class
subclass of: Bruker tube

Shigemi tube
type: Class
subclass of: NMR sample tube

standard tube
type: Class
subclass of: Bruker tube

Bruker tube
type: Class
subclass of: NMR sample tube

JEOL magnet
type: Class
subclass of: NMR magnet

JEOL ECS magnet
type: Class
subclass of: JEOL magnet

JEOL ECA magnet
type: Class
subclass of: JEOL magnet

JEOL ECX magnet
type: Class
subclass of: JEOL magnet

Varian NMR software
type: Class
subclass of: commercial NMR software

VnmrJ software
type: Class
subclass of: Varian NMR software

Wilmad tube
type: Class
subclass of: NMR sample tube

4mm Match tube
type: Class
subclass of: Match NMR tube

2.5mm Match tube
type: Class
subclass of: Match NMR tube

3mm Match tube
type: Class
subclass of: Match NMR tube

5mm Match tube
type: Class
subclass of: Match NMR tube

1mm Match tube
type: Class
subclass of: Match NMR tube

1.7mm Match tube
type: Class
subclass of: Match NMR tube

2mm Match tube
type: Class
subclass of: Match NMR tube

4.25mm Match tube
type: Class
subclass of: Match NMR tube

3mm standard tube
type: Class
subclass of: standard tube

5mm standard tube
type: Class
subclass of: standard tube

1mm standard tube
type: Class
subclass of: standard tube

1.7mm standard tube
type: Class
subclass of: standard tube

Wilmad economy tube
type: Class
subclass of: Wilmad tube

Wilmad precision tube
type: Class
subclass of: Wilmad tube

Norell tube
type: Class
subclass of: NMR sample tube

JEOL FID file
type: Class
subclass of: FID file

nmRIO
type: Class
subclass of: NMR Format converter
Source: Git: nmrML\tools\Parser_and_Converters\R
comment: R statistics to nmrML. Developed by Steffen Neumann, IPB-Halle.de

rNMR-IO
type: Class
subclass of: NMR Format converter
Source: Git: nmrML\tools\Parser_and_Converters\R\rNMR-IO

Vendor2nmrML_Java
type: Class
subclass of: NMR Format converter
definition: Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors. The choice of Java was guided by i) the JAXB framework (Java Architecture for XML Binding), ii) its OS-platform independence and iii) strengthened by the existence of a useful java library (i.e [nmr-fid-tool](https://github.com/LuisFF/nmr-fid-tool)) for further processing and visualisation of the resulting nmrML data. As nmrML intents to gather and integrate several types of data and corresponding metadata in a single file, it is necessary to process each data source separately. Thus, two command tools were developed. The first one, nmrMLcreate allows to create a new nmrML file, based on available Bruker or Varian/Agilent raw files. The second one, nmrMLproc allows to add and fill in additional sections corresponding to the data processing step.
Source: Git: nmrML\tools\Parser_and_Converters\Java\converter
comment: Developed by Daniel Jacob at INRA Bordeaux. The recommended converter for Bruker and Varian/Agilent vendor format conversion.

Varian magnet
type: Class
subclass of: NMR magnet
has_exact_synonym: Agilent magnet

premium compact narrow bore magnet
type: Class
subclass of: Varian magnet

premium shielded narrow bore magnet
type: Class
subclass of: Varian magnet

premium shielded wide bore magnet
type: Class
subclass of: Varian magnet

modified Gaussian window function
type: Class
subclass of: Gaussian window function
has_exact_synonym: modified gaussian apodization
comment: Functional form: gmb(x_i) = exp(-a*i - b*i*i) Parameters: * data Array of spectral data. * a Exponential term. * b Gaussian term. * inv Set True for inverse apodization.

exponentially damped J-modulation window function
type: Class
subclass of: window function for apodization
has_exact_synonym: exponentially damped J-modulation apodization
comment: Functional form: jmod(x_i) = exp(-e)*sin( pi*off + pi*(end-off)*i/(size-1)) Parameters: * data Array of spectral data. * e Exponential term. * off Start of modulation in fraction of pi radians. * end End of modulation in fraction of pi radians. * inv Set True for inverse apodization

shifted sine bell window function
type: Class
subclass of: sine window function
has_exact_synonym: shifted sine-bell apodization
comment: Functional form: sp(x_i) = sin( (pi*off + pi*(end-off)*i/(size-1) )**pow Parameters: * data Array of spectral data. * start Start of Sine-Bell as percent of vector (0.0 -> 1.0) * end End of Sine-Bell as percent of vector (0.0 -> 1.0 ) * pow Power of Sine-Bell * inv Set True for inverse apodization.

triangle window function
type: Class
subclass of: window function for apodization
has_exact_synonym: triangle apodization
comment: Functional form: 0:loc linear increase/decrease from lHi to 1.0 loc: linear increase/decrease from 1.0 to rHi Parameters: * data Array of spectral data. * loc Location of apex, "auto" sets to middle. * lHi Left side starting height. * rHi Right side starting height. * inv Set True for inverse apodization.

acquisition log file
type: Class
subclass of: data file
definition: The acquisition log file is a created during an acquisition and could useful for debugging an acquisition that has gone awry.

PynmrML
type: Class
subclass of: NMR Format converter
Source: Git: nmrML\tools\Parser_and_Converters\python
comment: A Python based vendor to nmrML converter developed by MIchael Wilson at TMIC Edmonton.

MetaboAnalyst software
type: Class
subclass of: NMR software
definition: A web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources.
comment: Jianguo Xia, Igor V. Sinelnikov, Beomsoo Han and David S. Wishart, MetaboAnalyst 3.0—making metabolomics more meaningful, Nucl. Acids Res. (1 July 2015) 43 (W1): W251-W257. doi: 10.1093/nar/gkv380

acqu2s
type: Class
subclass of: Bruker acquisition parameter file

acqu3s
type: Class
subclass of: Bruker acquisition parameter file

proc2s
type: Class
subclass of: Bruker processing parameter file

proc3s
type: Class
subclass of: Bruker processing parameter file

NMR spectrum file
type: Class
subclass of: data file

Bruker NMR spectrum file
type: Class
subclass of: NMR spectrum file

1R file
type: Class
subclass of: Bruker NMR spectrum file

title file
type: Class
subclass of: Bruker processing parameter file

XEASY software
type: Class
subclass of: NMR software
definition: A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes.
Source: Christian Bartels, Tai-he Xia, Martin Billeter, Peter Güntert, Kurt Wüthrich, The program XEASY for computer-supported NMR spectral analysis of biological macromolecules, J Biomol NMR (1995) 6: 1. doi:10.1007/BF00417486

NMR spectrum vizualisation software
type: Class
subclass of: NMR software

JspectraView software
type: Class
subclass of: NMR spectrum vizualisation software
comment: Used in NMR Assign tool for Baysil

cryoprobe
type: Class
subclass of: NMR probe

inverse detection NMR probe
type: Class
subclass of: NMR probe

5mm inverse detection cryoprobe
type: Class
subclass of: 5mm HCN probe
subclass of: cryoprobe
subclass of: inverse detection NMR probe
subclass of: solid NMR probe

NMRViewer software
type: Class
subclass of: NMR spectrum vizualisation software
Source: Git: nmrML\tools\Visualizers\PMB_NMRviewer
comment: Developed by Daniel Jacob, INRA Bordeaux
example: http://services.cbib.u-bordeaux2.fr/SPECNMR/examples

AB multiplet pattern
type: Class
subclass of: multiplet feature
Source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

NMR solvent
type: Class
subclass of: object
comment: Use Chebi entities here.

NMR buffer
type: Class
subclass of: object
comment: Use Chebi entities here.

presat water suppression
type: Class
subclass of: pre-acquisition water suppression

Varian VNMRS 600
type: Class
subclass of: Varian VNMRS instrument

data content encoding
type: Class
subclass of: data encoding parameter

data compression scheme
type: Class
subclass of: data encoding parameter

byte format
type: Class
subclass of: data content encoding

zlib
type: Class
subclass of: binary data compression type

complex64
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 32bit float numbers to represent the real and imaginary part of the complex values.

complex128
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 64bit double precision values to represent the real and imaginary part of the complex values.

binary data compression type
type: Class
subclass of: data compression scheme

AB2 multiplet pattern
type: Class
subclass of: multiplet feature
Source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

data encoding parameter
type: Class
subclass of: parameter

uncompressed data
type: Class
subclass of: binary data compression type

digital signal processing firmware version
type: Class
subclass of: instrument attribute
definition: DSPFVS - DSP (Digital signal processing) firmware version corresponds to the version of the digital filter, a hardware component used by the spectrometer
has_exact_synonym: DSPFVS

decimation factor
type: Class
subclass of: NMR acquisition parameter
definition: DECIM - decimation factor is a (bruker) acquisition parameter that captures the number of raw analog points that are averaged in order to obtain a digital signal recorded in the fid.
has_exact_synonym: DECIM

group time delay
type: Class
subclass of: NMR acquisition parameter
definition: GRPDLY - is the time delay (in number of points?) between acquiring the analog signal and producing the digital signal (i.e. "The group delay is the time necessary for the digital filter function to “walk into” the raw FID and start generating significant intensity.")
has_exact_synonym: GRPDLY

NMR sampling strategy
type: Class
subclass of: NMR acquisition parameter
definition: a type of data acquisition parameter (when recording the FID) which can be continuous/uniform or sparse/non-uniform signal acquisition.

uniform sampling
type: Class
subclass of: NMR sampling strategy
has_exact_synonym: continuous sampling
definition: With uniform sampling, each sample is separated by the "dwell time".
editorial note: With uniform sampling we don't need to record the time points because we know the dwell time. We may add named strategies to the CV over time that are more specific than non-uniform

non-uniform sampling
type: Class
subclass of: NMR sampling strategy
Source: http://link.springer.com/chapter/10.1007%2F1-4020-3910-7_142#page-1
has_exact_synonym: sparse sampling
definition: with non-uniform, some samples are skipped, there are different strategies for which to skip, but we can simply record the time point as well as the complex data point in order to represent this type of data.
editorial note: Non-uniform sampling is something likely to become more important in the future, because it allows you to capture higher dimension spectra much more quickly

Bruker XWIN-NMR software
type: Class
subclass of: NMR acquisition software

software attribute
type: Class
subclass of: generically dependent continuant

NMR software version
type: Class
subclass of: software attribute

ABX3 multiplet pattern
type: Class
subclass of: multiplet feature
Source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

AA'BB' multiplet pattern
type: Class
subclass of: multiplet feature
Source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

AA'XX' multiplet pattern
type: Class
subclass of: multiplet feature
Source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

variable size bucketing
type: Class
subclass of: bucketing

uniform bucketing
type: Class
subclass of: bucketing

intelligent bucketing
type: Class
subclass of: bucketing

bucket importing
type: Class
subclass of: bucketing

bucket resetting
type: Class
subclass of: bucketing
comment: put in as reqired by NMRProcFlow tool

global baseline correction
type: Class
subclass of: baseline correction
comment: as needed for nmrProcFlow

local baseline correction
type: Class
subclass of: baseline correction
comment: as needed for nmrProcFlow

bucket fusioning
type: Class
subclass of: bucket resetting

JNM-ECX Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument

JNM-ECZR Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: JNM-ECZR series is a new system that fully incorporates the latest digital and high frequency technologies. Improved reliability and a more compact size make possible by incorporating more advanced integrated circuits, it supports even greater expandability options than current models for multi-channel operation, high power amplifiers and other accessories. The bus line for control of attachments has been upgraded to high speed and enables highly accurate and rapid control. 400 MHz - 1 GHz

JNM-ECZS Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: The entry model ECZS spectrometer has the same basic functions, performance and capability of high-end model. The main console is amazingly small, less than 1/2 that of the current ECS series spectrometer. Coupling the use of advanced software with highly reliable automation, all routine daily measurements can be automated, while the use of the autotune Supercool probe realizes the world’s highest sensitivity in its class. Whatever your application field ECZS can demonstrate its power. 400 MHz

AVANCE III HD
type: Class
subclass of: Bruker NMR instrument

NanoBay400 MHz
type: Class
subclass of: Bruker NMR instrument

Fourier 300HD
type: Class
subclass of: Bruker NMR instrument

DNP-NMR
type: Class
subclass of: Bruker NMR instrument

LC-NMR instrument
type: Class
subclass of: Bruker NMR instrument

LC-NMR/MS instrument
type: Class
subclass of: Bruker NMR instrument

Food-Screener instrument
type: Class
subclass of: Bruker NMR instrument

AVANCE IVDr
type: Class
subclass of: Bruker NMR instrument

JEOL Resonance 400MHz YH magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 500MHz magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 600MHz magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 700MHz magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 800MHz magnet
type: Class
subclass of: JEOL magnet

single peak feature
type: Class
subclass of: peak feature

NMR instrument vendor
type: Class
subclass of: instrument attribute
definition: Any organisation ort person that sells NMR instruments to customers.

Avance I spectrometer
type: Class
subclass of: Bruker NMR instrument

Oxford Instruments
type: Class
subclass of: NMR instrument manufacturer

Spinlock SRL
type: Class
subclass of: NMR instrument manufacturer

General Electric
type: Class
subclass of: NMR instrument manufacturer

Kimble Chase
type: Class
subclass of: NMR instrument manufacturer

Phillips
type: Class
subclass of: NMR instrument manufacturer

Siemens AG
type: Class
subclass of: NMR instrument manufacturer

Varian Inova 500
type: Class
subclass of: Varian INOVA

Varian VNMRS instrument
type: Class
subclass of: Varian NMR instrument

Varian Mercury plus
type: Class
subclass of: Varian MERCURY

Varian UnityInova instrument
type: Class
subclass of: Varian NMR instrument

Varian 400-MR NMR instrument
type: Class
subclass of: Varian NMR instrument

Varian DDR2 instrument
type: Class
subclass of: Varian NMR instrument

Agilent NMR instrument
type: Class
subclass of: NMR instrument

Agilent 400-MR NMR instrument
type: Class
subclass of: Agilent NMR instrument

Varian Mercury 400
type: Class
subclass of: Varian MERCURY

Agilent Au 400 (DDR2 Console)
type: Class
subclass of: Agilent NMR instrument

Agilent DDR 2 w/ HCN cryoprobe
type: Class
subclass of: Agilent NMR instrument

BMRB identifier
type: Class
subclass of: metabolomics database identifier

left trapezoid limit
type: Class
subclass of: trapezoid window function parameter
has_exact_synonym: TM1
comment: 0<TM1<1

trapezoid window function parameter
type: Class
subclass of: window function parameter

complex64 Integer
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 32bit integer numbers to represent the real and imaginary part of the complex values (2x32bits=>2x4bytes=> 2 integers) for the FID datatype.

complex128 Integer
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 64bit long integer numbers to represent the real and imaginary part of the complex values (2x64bits => 2x8bytes => 2 longs) for the FID datatype.

right trapezoid limit
type: Class
subclass of: trapezoid window function parameter
has_exact_synonym: TM2
comment: 0<TM2<1

thirty degree pulse duration
type: Class
subclass of: pulse parameter
has_exact_synonym: 30 degree pulse duration
definition: The duration of the excitation pulse needed to rotate the magnetisation vector by 30 degrees.

InChi
type: Class
subclass of: line representation

inchikey
type: Class
subclass of: line representation

Wiswesser Line Notation
type: Class
subclass of: line representation
has_exact_synonym: WLN

ROSDAL
type: Class
subclass of: line representation

SLN-Tripos
type: Class
subclass of: line representation

smarts
type: Class
subclass of: SMILES string

line representation
type: Class
subclass of: chemical compound formula

2D topological molecule representation
type: Class
subclass of: chemical compound formula

2D bond line structure
type: Class
subclass of: 2D topological molecule representation

3D geometrical molecule representation
type: Class
subclass of: chemical compound formula

3D bond line structure
type: Class
subclass of: 3D geometrical molecule representation

CAS number
type: Class
subclass of: chemical compound attribute

fingerprint model
type: Class
subclass of: chemical compound attribute

molfile
type: Class
subclass of: chemical compound attribute

compound similarity measure
type: Class
subclass of: chemical compound attribute

Tanimoto similarity
type: Class
subclass of: compound similarity measure

Gaussian window function parameter
type: Class
subclass of: window function parameter

2,2-Dimethyl-2-silapentane-5-sulfonate
type: Class
subclass of: concentration standard
has_exact_synonym: DSS

Gaussian maximum position
type: Class
subclass of: Gaussian window function parameter

2H spectrum reference compound
type: Class
subclass of: chemical shift standard

ABX2 multiplet pattern
type: Class
subclass of: multiplet feature

DRX 600 instrument
type: Class
subclass of: Bruker NMR instrument

plot and graph generation
type: Class
subclass of: frequency domain data processing

reference deconvolution
type: Class
subclass of: deconvolution
definition: vertical alignment of on and offset of the peak of the reference compound.

spectral smoothing
type: Class
subclass of: spectral denoising
definition: the process of removing noisy jitters in a spectral curve to get clearer and more meaningful signals and peaks.

NMR database format
type: Class
subclass of: data file format

BMRB/XML file format
type: Class
subclass of: NMR database format
Source: M. Yokochi, N. Kobayashi, E. L. Ulrich, A. R. Kinjo, T. Iwata, Y. E. Ioannidis, M. Livny, J. L. Markley, H. Nakamura, C. Kojima, T. Fujiwara, “Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins,” Journal of Biomedical Semantics, 5:7:16 (2016)

nD spectrum
type: Class
subclass of: NMR spectrum by dimensionality

NMR data conversion
type: Class
subclass of: file format conversion
definition: Terms used to describe types of data processing.
has_exact_synonym: data processing
has_obo_namespace: NMR
id: NMR:1000452

Axiom
annotated source: NMR data conversion
annotated property: definition
annotated target: Terms used to describe types of data processing.
database_cross_reference: MSI:NMR

sample
type: Class
subclass of: object
definition: tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source. defprov: Daniel Schober
has_obo_namespace: NMR
id: NMR:1000457

Axiom
annotated source: sample
annotated property: definition
annotated target: tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source. defprov: Daniel Schober
database_cross_reference: MSI:NMR

instrument
type: Class
subclass of: object
definition: Description of the instrument or the mass spectrometer.
has_exact_synonym: instrument configuration
has_obo_namespace: NMR
id: NMR:1000463

Axiom
annotated source: instrument
annotated property: definition
annotated target: Description of the instrument or the mass spectrometer.
database_cross_reference: MSI:NMR

Varian/Agilent instrument model
type: Class
subclass of: NMR instrument model
definition: Varian instrument model.
has_obo_namespace: NMR
id: NMR:1000489

Axiom
annotated source: Varian/Agilent instrument model
annotated property: definition
annotated target: Varian instrument model.
database_cross_reference: MSI:NMR

instrument attribute
type: Class
subclass of: object attribute
definition: Instrument properties that are associated with a value.
has_obo_namespace: NMR
id: NMR:1000496

Axiom
annotated source: instrument attribute
annotated property: definition
annotated target: Instrument properties that are associated with a value.
database_cross_reference: MSI:NMR

data file content
type: Class
subclass of: data file attribute
definition: Describes the data content on the file.
has_obo_namespace: NMR
id: NMR:1000524

Axiom
annotated source: data file content
annotated property: definition
annotated target: Describes the data content on the file.
database_cross_reference: MSI:NMR

instrument serial number
type: Class
subclass of: instrument attribute
definition: Serial Number of the instrument.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000529

Axiom
annotated source: instrument serial number
annotated property: definition
annotated target: Serial Number of the instrument.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: instrument serial number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

file format conversion
type: Class
subclass of: data transformation
definition: Conversion of one file format to another.
has_obo_namespace: NMR
id: NMR:1000530

Axiom
annotated source: file format conversion
annotated property: definition
annotated target: Conversion of one file format to another.
database_cross_reference: MSI:NMR

object attribute
type: Class
subclass of: generically dependent continuant
definition: Object Attribute.
has_obo_namespace: NMR
id: NMR:1000547

Axiom
annotated source: object attribute
annotated property: definition
annotated target: Object Attribute.
database_cross_reference: MSI:NMR

sample attribute
type: Class
subclass of: object attribute
definition: Sample properties that are associated with a value.
has_obo_namespace: NMR
id: NMR:1000548

Axiom
annotated source: sample attribute
annotated property: definition
annotated target: Sample properties that are associated with a value.
database_cross_reference: MSI:NMR

data file checksum type
type: Class
subclass of: data file attribute
definition: Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
has_obo_namespace: NMR
id: NMR:1000561

Axiom
annotated source: data file checksum type
annotated property: definition
annotated target: Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
database_cross_reference: MSI:NMR

MD5
type: Class
subclass of: data file checksum type
definition: MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000568

Axiom
annotated source: MD5
annotated property: definition
annotated target: MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: MD5
annotated property: database_cross_reference
annotated target: value-type:xsd:string

SHA-1
type: Class
subclass of: data file checksum type
definition: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000569

Axiom
annotated source: SHA-1
annotated property: definition
annotated target: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: SHA-1
annotated property: database_cross_reference
annotated target: value-type:xsd:string

NMR raw data file format
type: Class
subclass of: data file format
definition: Describes the type of file and its content.
has_exact_synonym: source file
has_obo_namespace: NMR
id: NMR:1000577

Axiom
annotated source: NMR raw data file format
annotated property: definition
annotated target: Describes the type of file and its content.
database_cross_reference: MSI:NMR

contact attribute
type: Class
subclass of: object attribute
definition: Details about a person or organization to contact in case of concern or discussion about the file.
has_obo_namespace: NMR
id: NMR:1000585

Axiom
annotated source: contact attribute
annotated property: definition
annotated target: Details about a person or organization to contact in case of concern or discussion about the file.
database_cross_reference: MSI:NMR

contact name
type: Class
subclass of: contact attribute
definition: Name of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000586

Axiom
annotated source: contact name
annotated property: definition
annotated target: Name of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact address
type: Class
subclass of: contact attribute
definition: Postal address of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000587

Axiom
annotated source: contact address
annotated property: definition
annotated target: Postal address of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact address
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact URL
type: Class
subclass of: contact attribute
definition: Uniform Resource Locator related to the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000588

Axiom
annotated source: contact URL
annotated property: definition
annotated target: Uniform Resource Locator related to the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact URL
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact email
type: Class
subclass of: contact attribute
definition: Email address of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000589

Axiom
annotated source: contact email
annotated property: definition
annotated target: Email address of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact email
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact organization
type: Class
subclass of: contact attribute
definition: Home institution of the contact person.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000590

Axiom
annotated source: contact organization
annotated property: definition
annotated target: Home institution of the contact person.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact organization
annotated property: database_cross_reference
annotated target: value-type:xsd:string

data processing parameter
type: Class
subclass of: parameter
definition: Data processing parameter used in the data processing performed on the data file.
has_obo_namespace: NMR
id: NMR:1000630

Axiom
annotated source: data processing parameter
annotated property: definition
annotated target: Data processing parameter used in the data processing performed on the data file.
database_cross_reference: MSI:NMR

data processing completion time
type: Class
subclass of: quality
definition: The time that a data processing action was finished.
database_cross_reference: value-type:xsd:date
has_obo_namespace: NMR
id: NMR:1000747

Axiom
annotated source: data processing completion time
annotated property: definition
annotated target: The time that a data processing action was finished.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: data processing completion time
annotated property: database_cross_reference
annotated target: value-type:xsd:date

FID format
type: Class
subclass of: NMR raw data file format
definition: Describes how the native spectrum identifiers are formated.
has_exact_synonym: nativeID format
has_obo_namespace: NMR
id: NMR:1000767

Axiom
annotated source: FID format
annotated property: definition
annotated target: Describes how the native spectrum identifiers are formated.
database_cross_reference: MSI:NMR

Bruker FID format
type: Class
subclass of: FID format
definition: file=xsd:IDREF.
has_obo_namespace: NMR
id: NMR:1000773
comment: The nativeID must be the same as the source file ID.

Axiom
annotated source: Bruker FID format
annotated property: definition
annotated target: file=xsd:IDREF.
database_cross_reference: MSI:NMR

custom unreleased software
type: Class
subclass of: software
definition: A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000799

Axiom
annotated source: custom unreleased software
annotated property: definition
annotated target: A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: custom unreleased software
annotated property: database_cross_reference
annotated target: value-type:xsd:string

sample preparation information
type: Class
subclass of: sample attribute
definition: Description of the preparation steps which took place before the measurement was performed.
has_obo_namespace: NMR
id: NMR:1000831

Axiom
annotated source: sample preparation information
annotated property: definition
annotated target: Description of the preparation steps which took place before the measurement was performed.
database_cross_reference: MSI:NMR

molecule
type: Class
subclass of: chemical compound
definition: A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
has_obo_namespace: NMR
id: NMR:1000859

Axiom
annotated source: molecule
annotated property: definition
annotated target: A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
database_cross_reference: MSI:NMR

peptide
type: Class
subclass of: chemical compound
definition: A compound of low molecular weight that is composed of two or more amino acids.
has_obo_namespace: NMR
id: NMR:1000860

Axiom
annotated source: peptide
annotated property: definition
annotated target: A compound of low molecular weight that is composed of two or more amino acids.
database_cross_reference: MSI:NMR

chemical compound attribute
type: Class
subclass of: object attribute
definition: A describable property of a chemical compound.
has_obo_namespace: NMR
id: NMR:1000861

Axiom
annotated source: chemical compound attribute
annotated property: definition
annotated target: A describable property of a chemical compound.
database_cross_reference: MSI:NMR

isoelectric point
type: Class
subclass of: chemical compound attribute
definition: The pH of a solution at which a charged molecule does not migrate in an electric field.
database_cross_reference: value-type:xsd:float
has_exact_synonym: pI
has_obo_namespace: NMR
id: NMR:1000862

Axiom
annotated source: isoelectric point
annotated property: definition
annotated target: The pH of a solution at which a charged molecule does not migrate in an electric field.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: isoelectric point
annotated property: database_cross_reference
annotated target: value-type:xsd:float

predicted isoelectric point
type: Class
subclass of: chemical compound attribute
definition: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
database_cross_reference: value-type:xsd:float
has_exact_synonym: predicted pI
has_obo_namespace: NMR
id: NMR:1000863

Axiom
annotated source: predicted isoelectric point
annotated property: definition
annotated target: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: predicted isoelectric point
annotated property: database_cross_reference
annotated target: value-type:xsd:float

chemical compound formula
type: Class
subclass of: chemical compound attribute
definition: A combination of symbols used to express the chemical composition of a compound.
has_obo_namespace: NMR
id: NMR:1000864

Axiom
annotated source: chemical compound formula
annotated property: definition
annotated target: A combination of symbols used to express the chemical composition of a compound.
database_cross_reference: MSI:NMR

empirical formula
type: Class
subclass of: chemical compound formula
definition: A chemical formula which expresses the proportions of the elements present in a substance.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000865

Axiom
annotated source: empirical formula
annotated property: definition
annotated target: A chemical formula which expresses the proportions of the elements present in a substance.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: empirical formula
annotated property: database_cross_reference
annotated target: value-type:xsd:string

molecular formula
type: Class
subclass of: line representation
definition: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000866

Axiom
annotated source: molecular formula
annotated property: definition
annotated target: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: molecular formula
annotated property: database_cross_reference
annotated target: value-type:xsd:string

structural formula
type: Class
subclass of: chemical compound formula
definition: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000867

Axiom
annotated source: structural formula
annotated property: definition
annotated target: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: structural formula
annotated property: database_cross_reference
annotated target: value-type:xsd:string

SMILES string
type: Class
subclass of: line representation
definition: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000868

Axiom
annotated source: SMILES string
annotated property: definition
annotated target: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: SMILES string
annotated property: database_cross_reference
annotated target: value-type:xsd:string

external reference identifier
type: Class
subclass of: reference
definition: An identifier/accession number to an external reference database.
has_obo_namespace: NMR
id: NMR:1000878

Axiom
annotated source: external reference identifier
annotated property: definition
annotated target: An identifier/accession number to an external reference database.
database_cross_reference: MSI:NMR

PubMed identifier
type: Class
subclass of: external reference identifier
definition: A unique identifier for a publication in the PubMed database (MIR:00000015).
database_cross_reference: value-type:xsd:integer
has_obo_namespace: NMR
id: NMR:1000879

Axiom
annotated source: PubMed identifier
annotated property: definition
annotated target: A unique identifier for a publication in the PubMed database (MIR:00000015).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: PubMed identifier
annotated property: database_cross_reference
annotated target: value-type:xsd:integer

chemical compound
type: Class
subclass of: object
definition: A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
has_obo_namespace: NMR
id: NMR:1000881
comment: Use Chebi entities here.

Axiom
annotated source: chemical compound
annotated property: definition
annotated target: A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
database_cross_reference: MSI:NMR

protein
type: Class
subclass of: chemical compound
definition: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
has_obo_namespace: NMR
id: NMR:1000882

Axiom
annotated source: protein
annotated property: definition
annotated target: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
database_cross_reference: MSI:NMR

protein short name
type: Class
subclass of: protein attribute
definition: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000883

Axiom
annotated source: protein short name
annotated property: definition
annotated target: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein short name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

protein attribute
type: Class
subclass of: object attribute
definition: An nonphysical attribute describing a specific protein.
has_obo_namespace: NMR
id: NMR:1000884

Axiom
annotated source: protein attribute
annotated property: definition
annotated target: An nonphysical attribute describing a specific protein.
database_cross_reference: MSI:NMR

protein accession
type: Class
subclass of: protein attribute
definition: Accession number for a specific protein in a database.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000885

Axiom
annotated source: protein accession
annotated property: definition
annotated target: Accession number for a specific protein in a database.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein accession
annotated property: database_cross_reference
annotated target: value-type:xsd:string

protein name
type: Class
subclass of: protein attribute
definition: A long name describing the function of the protein.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000886

Axiom
annotated source: protein name
annotated property: definition
annotated target: A long name describing the function of the protein.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

peptide attribute
type: Class
subclass of: object attribute
definition: An nonphysical attribute that can be used to describe a peptide.
has_obo_namespace: NMR
id: NMR:1000887

Axiom
annotated source: peptide attribute
annotated property: definition
annotated target: An nonphysical attribute that can be used to describe a peptide.
database_cross_reference: MSI:NMR

unmodified peptide sequence
type: Class
subclass of: peptide attribute
definition: A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000888

Axiom
annotated source: unmodified peptide sequence
annotated property: definition
annotated target: A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: unmodified peptide sequence
annotated property: database_cross_reference
annotated target: value-type:xsd:string

modified peptide sequence
type: Class
subclass of: peptide attribute
definition: A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu).
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000889

Axiom
annotated source: modified peptide sequence
annotated property: definition
annotated target: A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: modified peptide sequence
annotated property: database_cross_reference
annotated target: value-type:xsd:string

peptide labeling state
type: Class
subclass of: peptide attribute
definition: A state description of how a peptide might be isotopically or isobarically labelled.
has_obo_namespace: NMR
id: NMR:1000890

Axiom
annotated source: peptide labeling state
annotated property: definition
annotated target: A state description of how a peptide might be isotopically or isobarically labelled.
database_cross_reference: MSI:NMR

heavy labeled peptide
type: Class
subclass of: peptide attribute
definition: A peptide that has been created or labeled with some heavier-than-usual isotopes.
has_obo_namespace: NMR
id: NMR:1000891

Axiom
annotated source: heavy labeled peptide
annotated property: definition
annotated target: A peptide that has been created or labeled with some heavier-than-usual isotopes.
database_cross_reference: MSI:NMR

unlabeled peptide
type: Class
subclass of: peptide attribute
definition: A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
has_exact_synonym: light labeled peptide
has_obo_namespace: NMR
id: NMR:1000892

Axiom
annotated source: unlabeled peptide
annotated property: definition
annotated target: A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
database_cross_reference: MSI:NMR

peptide group label
type: Class
subclass of: peptide attribute
definition: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000893

Axiom
annotated source: peptide group label
annotated property: definition
annotated target: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: peptide group label
annotated property: database_cross_reference
annotated target: value-type:xsd:string

data standard
type: Class
subclass of: generically dependent continuant
definition: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
has_obo_namespace: NMR
id: NMR:1000898

Axiom
annotated source: data standard
annotated property: definition
annotated target: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
database_cross_reference: MSI:NMR

de facto standard
type: Class
subclass of: data standard
definition: A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
database_cross_reference: MS_1000899
has_obo_namespace: NMR
id: NMR:1000899

Axiom
annotated source: de facto standard
annotated property: definition
annotated target: A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
database_cross_reference: MSI:NMR

minimum information standard
type: Class
subclass of: data standard
definition: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
database_cross_reference: MS_1000899
has_obo_namespace: NMR
id: NMR:1000900

Axiom
annotated source: minimum information standard
annotated property: definition
annotated target: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
database_cross_reference: MSI:NMR

tab delimited text file
type: Class
subclass of: text file
definition: A file that has two or more columns of tabular data where each column is separated by a TAB character.
has_obo_namespace: NMR
id: NMR:1000914

Axiom
annotated source: tab delimited text file
annotated property: definition
annotated target: A file that has two or more columns of tabular data where each column is separated by a TAB character.
database_cross_reference: MSI:NMR

protein modification
type: Class
subclass of: protein attribute
definition: Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000933

Axiom
annotated source: protein modification
annotated property: definition
annotated target: Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein modification
annotated property: database_cross_reference
annotated target: value-type:xsd:string

gene name
type: Class
subclass of: protein attribute
definition: Name of the gene from which the protein is translated.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000934

Axiom
annotated source: gene name
annotated property: definition
annotated target: Name of the gene from which the protein is translated.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: gene name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

intermediate analysis format
type: Class
subclass of: data file format
definition: Type of the source file, the nmrIdentML was created from.
has_obo_namespace: NMR
id: NMR:1001040

Axiom
annotated source: intermediate analysis format
annotated property: definition
annotated target: Type of the source file, the nmrIdentML was created from.
database_cross_reference: MSI:MI

data stored in database
type: Class
subclass of: data file format
definition: Source file for this nmrIdentML was a data set in a database.
has_obo_namespace: NMR
id: NMR:1001107
editorial note: retire? Consider: "NMR database format" ?

Axiom
annotated source: data stored in database
annotated property: definition
annotated target: Source file for this nmrIdentML was a data set in a database.
database_cross_reference: MSI:MI

software vendor
type: Class
subclass of: vendor
has_obo_namespace: NMR
id: NMR:1001267

programmer
type: Class
subclass of: contact role
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001268

The allowed value-type for this CV term.
type: Axiom
annotated source: programmer
annotated property: database_cross_reference
annotated target: value-type:xsd:string

instrument vendor
type: Class
subclass of: vendor
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001269

The allowed value-type for this CV term.
type: Axiom
annotated source: instrument vendor
annotated property: database_cross_reference
annotated target: value-type:xsd:string

lab personnel
type: Class
subclass of: contact role
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001270

The allowed value-type for this CV term.
type: Axiom
annotated source: lab personnel
annotated property: database_cross_reference
annotated target: value-type:xsd:string

researcher
type: Class
subclass of: contact role
has_obo_namespace: NMR
id: NMR:1001271

analysis software
type: Class
subclass of: software
definition: Analysis software.
has_obo_namespace: NMR
id: NMR:1001456

Axiom
annotated source: analysis software
annotated property: definition
annotated target: Analysis software.
database_cross_reference: MSI:NMR

data processing software
type: Class
subclass of: software
definition: Conversion software.
has_obo_namespace: NMR
id: NMR:1001457

Axiom
annotated source: data processing software
annotated property: definition
annotated target: Conversion software.
database_cross_reference: MSI:NMR

data file format
type: Class
subclass of: data file attribute
definition: Format of data files.
has_obo_namespace: NMR
id: NMR:1001459

Axiom
annotated source: data file format
annotated property: definition
annotated target: Format of data files.
database_cross_reference: MSI:NMR

contact phone number
type: Class
subclass of: contact attribute
definition: Phone number of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001755

Axiom
annotated source: contact phone number
annotated property: definition
annotated target: Phone number of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact phone number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact fax number
type: Class
subclass of: contact attribute
definition: Fax number for the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001756

Axiom
annotated source: contact fax number
annotated property: definition
annotated target: Fax number for the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact fax number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact toll-free phone number
type: Class
subclass of: contact attribute
definition: Toll-free phone number of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001757

Axiom
annotated source: contact toll-free phone number
annotated property: definition
annotated target: Toll-free phone number of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact toll-free phone number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Digital Object Identifier (DOI)
type: Class
subclass of: external reference identifier
definition: DOI unique identifier.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001922

Axiom
annotated source: Digital Object Identifier (DOI)
annotated property: definition
annotated target: DOI unique identifier.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: Digital Object Identifier (DOI)
annotated property: database_cross_reference
annotated target: value-type:xsd:string

external reference keyword
type: Class
subclass of: keyword
definition: Free text attribute that can enrich the information about an entity.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001923

Axiom
annotated source: external reference keyword
annotated property: definition
annotated target: Free text attribute that can enrich the information about an entity.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: external reference keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

journal article keyword
type: Class
subclass of: keyword
definition: Keyword present in a scientific publication.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001924

Axiom
annotated source: journal article keyword
annotated property: definition
annotated target: Keyword present in a scientific publication.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: journal article keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

submitter keyword
type: Class
subclass of: keyword
definition: Keyword assigned by the data submitter.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001925

Axiom
annotated source: submitter keyword
annotated property: definition
annotated target: Keyword assigned by the data submitter.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: submitter keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

curator keyword
type: Class
subclass of: keyword
definition: Keyword assigned by a data curator.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001926

Axiom
annotated source: curator keyword
annotated property: definition
annotated target: Keyword assigned by a data curator.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: curator keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

NMR acquisition parameter
type: Class
subclass of: parameter
definition: Parameters used in the NMR spectrometry acquisition.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001954

Axiom
annotated source: NMR acquisition parameter
annotated property: definition
annotated target: Parameters used in the NMR spectrometry acquisition.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: NMR acquisition parameter
annotated property: database_cross_reference
annotated target: value-type:xsd:string

HMDB identifier
type: Class
subclass of: metabolomics database identifier
definition: A unique identifier for a metabolite in the HMDB database (HMDB00001).
database_cross_reference: value-type:xsd:integer
has_obo_namespace: NMR
id: NMR:1002000

Axiom
annotated source: HMDB identifier
annotated property: definition
annotated target: A unique identifier for a metabolite in the HMDB database (HMDB00001).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: HMDB identifier
annotated property: database_cross_reference
annotated target: value-type:xsd:integer

Chenomx software
type: Class
subclass of: commercial NMR software
definition: Chenomx software for data acquisition and analysis.
has_obo_namespace: NMR
id: NMR:1002001

Axiom
annotated source: Chenomx software
annotated property: definition
annotated target: Chenomx software for data acquisition and analysis.
database_cross_reference: MSI:NMR

Chenomx NMR Suite software
type: Class
subclass of: Chenomx software
definition: Chenomx software for data analysis.
Source: http://www.chenomx.com/software/
has_obo_namespace: NMR
id: NMR:1002002

Axiom
annotated source: Chenomx NMR Suite software
annotated property: definition
annotated target: Chenomx software for data analysis.
database_cross_reference: MSI:NMR

Varian FID format
type: Class
subclass of: FID format
definition: file=xsd:IDREF.
has_obo_namespace: NMR
id: NMR:1002003
comment: The nativeID must be the same as the source file ID.

Axiom
annotated source: Varian FID format
annotated property: definition
annotated target: file=xsd:IDREF.
database_cross_reference: MSI:NMR

NMR spectrometer file format
type: Class
subclass of: NMR software data format
definition: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
has_obo_namespace: NMR
id: NMR:1002004

Axiom
annotated source: NMR spectrometer file format
annotated property: definition
annotated target: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
database_cross_reference: MSI:NMR

text file
type: Class
subclass of: data file format
definition: Simple text file of peaks.
has_obo_namespace: NMR
id: NMR:1002005

Axiom
annotated source: text file
annotated property: definition
annotated target: Simple text file of peaks.
database_cross_reference: MSI:PI

acquisition parameter file
type: Class
subclass of: data file
definition: Parameter file used to configure the acquisition of raw data on the instrument.
has_obo_namespace: NMR
id: NMR:1002006

Axiom
annotated source: acquisition parameter file
annotated property: definition
annotated target: Parameter file used to configure the acquisition of raw data on the instrument.
database_cross_reference: MSI:NMR

NMR spectrum
type: Class
subclass of: data file content
definition: tempdef: A frequency sorted array of the NMR signal frequency components. Nuclei with different resonance frequencies will show up as peaks at different corresponding frequencies in the spectrum, or 'lines'. def: A NMR spectrum is a set of chemical shifts representing a chemical analysis. synonym: NMR spectrum
Source: as designated Experiment type on http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
has_obo_namespace: NMR
id: NMR:1002007

Conversion to nmrML
type: Class
subclass of: NMR data conversion
definition: Conversion of a file format to Metabolomics Standards Initiative nmrData file format.
has_obo_namespace: NMR
id: NMR:1002008

Axiom
annotated source: Conversion to nmrML
annotated property: definition
annotated target: Conversion of a file format to Metabolomics Standards Initiative nmrData file format.
database_cross_reference: MSI:NMR

Conversion to JCAMP-DX
type: Class
subclass of: NMR data conversion
definition: Conversion of a file format to JCAMP-DX file format.
has_obo_namespace: NMR
id: NMR:1002009

Axiom
annotated source: Conversion to JCAMP-DX
annotated property: definition
annotated target: Conversion of a file format to JCAMP-DX file format.
database_cross_reference: MSI:NMR

NMR solvent information
type: Class
subclass of: sample attribute
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002010

The allowed value-type for this CV term.
type: Axiom
annotated source: NMR solvent information
annotated property: database_cross_reference
annotated target: value-type:xsd:string

pH
type: Class
subclass of: sample attribute
definition: pH.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002011

Axiom
annotated source: pH
annotated property: definition
annotated target: pH.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: pH
annotated property: database_cross_reference
annotated target: value-type:xsd:string

chemical shift reference
type: Class
subclass of: quality check compound signal
definition: Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM.
bug-database: https://github.com/nmrML/nmrML/issues/29#issue
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002013

Axiom
annotated source: chemical shift reference
annotated property: definition
annotated target: Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: chemical shift reference
annotated property: database_cross_reference
annotated target: value-type:xsd:string

binned spectrum descriptor
type: Class
subclass of: NMR spectrum descriptor
definition: A bin for a spectrum.
database_cross_reference: value-type:xsd:string
has_exact_synonym: bucketed spectrum descriptor
has_obo_namespace: NMR
id: NMR:1002014

Axiom
annotated source: binned spectrum descriptor
annotated property: definition
annotated target: A bin for a spectrum.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: binned spectrum descriptor
annotated property: database_cross_reference
annotated target: value-type:xsd:string

bin label
type: Class
subclass of: binned spectrum descriptor
definition: Bin label.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002015

Axiom
annotated source: bin label
annotated property: definition
annotated target: Bin label.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin label
annotated property: database_cross_reference
annotated target: value-type:xsd:string

bin start
type: Class
subclass of: binned spectrum descriptor
definition: Bin start.
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002016

Axiom
annotated source: bin start
annotated property: definition
annotated target: Bin start.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin start
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

bin end
type: Class
subclass of: binned spectrum descriptor
definition: Bin end.
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002017

Axiom
annotated source: bin end
annotated property: definition
annotated target: Bin end.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin end
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

bin area
type: Class
subclass of: binned spectrum descriptor
definition: Bin area.
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002018

Axiom
annotated source: bin area
annotated property: definition
annotated target: Bin area.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin area
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

assigned chemical compound name
type: Class
subclass of: binned spectrum descriptor
definition: Name of metabolite.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002020

Axiom
annotated source: assigned chemical compound name
annotated property: definition
annotated target: Name of metabolite.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: assigned chemical compound name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

assigned chemical compound concentration
type: Class
subclass of: binned spectrum descriptor
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002021

The allowed value-type for this CV term.
type: Axiom
annotated source: assigned chemical compound concentration
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

Hilbert transformation based scaling
type: Class
subclass of: scaling

optional part of NMR instrument
type: Class
subclass of: instrument
comment: def: Part of an NMR instrument which is not cardinally important and hence optional / facultative for the proper intended function of the instrument. synonym: optional part of NMR instrument clsdel: ontologically there is no such universal which characteristic is a possible (!) state of being a part of something...
version info: TODO: Discuss "obligatory_part_of".

autosampler
type: Class
subclass of: optional part of NMR instrument
comment: def: An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. altdef: The autosampler is an automatic sample changer.

multiplicity feature
type: Class
subclass of: peak feature
definition source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
has_exact_synonym: multiplicity

projected spectrum
type: Class
subclass of: NMR spectrum by processing step
comment: tempdef: The data matrix a spectrum consists of can be projected from a higher dimension onto a lower dimension, e.g. a 3D NMR spectrum can be converted (projected) into a 2D NMR spectrum. defprov: Daniel Schober

bucketed spectrum
type: Class
subclass of: NMR spectrum by processing step
has_exact_synonym: binned spectrum
comment: def: A post-processed NMR spectrum in which the y-values of the datapoints have been summed based on periodic ranges of the x-axis values.
version info: TODO: has spectral post processing parameter

peak-picked spectrum
type: Class
subclass of: NMR spectrum by processing step
comment: defneed
version info: TODO: has spectral post processing parameter.

cardinal part of NMR instrument
type: Class
subclass of: instrument
comment: def: A part of an NMR instrument which is cardinally important and hence obligatory and compulsatory for the proper intended function of the instrument. synonym: cardinal part of NMR instrument

acquisition computer
type: Class
subclass of: cardinal part of NMR instrument
comment: def: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.

NMR probe
type: Class
subclass of: cardinal part of NMR instrument
comment: def: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile “single point of failure” that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency. altdef: The instrument that transmits and recieves radiofrequency to and from the NMR sample.

console
type: Class
subclass of: cardinal part of NMR instrument
comment: def: A component of an NMR instrument that controls the activities of the other components.
version info: TODO: same as or part of acquisition computer?

number of acquisition data points
type: Class
subclass of: NMR acquisition parameter
comment: tempdef: The number of data points in a data set.

hadamard frequency
type: Class
subclass of: NMR acquisition parameter
comment: def: A frequency used during Hadamard encoding.

projection axis
type: Class
subclass of: NMR acquisition parameter
comment: def: The axis onto which the spectrum was projected.

ninety degree pulse duration
type: Class
subclass of: pulse parameter
has_exact_synonym: 90 degree pulse duration
definition: The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees.

dwell time
type: Class
subclass of: NMR acquisition parameter
comment: def: A digital sampling interval. alsprcls: time interval

sample temperature in autosampler
type: Class
subclass of: sample temperature information
comment: def: The temperature of an item of analysis material whilst in an autosampler.

sample temperature in magnet
type: Class
subclass of: sample temperature information
comment: def: The temperature of an NMR sample whilst in the magnet of an NMR instrument.

irradiation frequency
type: Class
subclass of: NMR acquisition parameter
comment: def: The frequency of the RF radiation used to irradiate an NMR sample.

field strength
type: Class
subclass of: NMR acquisition parameter
comment: def: The intensity of an electric, magnetic, or other field.

spinning rate
type: Class
subclass of: NMR acquisition parameter
comment: def: The rate at which an item of analysis material is spun.

decoupled nucleus flag
type: Class
subclass of: NMR acquisition parameter
comment: def: An indication of whether the nucleus being studied is the acquitsition nucleus.

buffer information
type: Class
subclass of: sample attribute
comment: def: A compound added to a sample to alter its pH value.

calibration compound
type: Class
subclass of: chemical compound
has_exact_synonym: reference compound
has_exact_synonym: reference standard
comment: def: The compound that produced the peak used to reference a spectrum during data pre-processing.

chemical shift standard
type: Class
subclass of: calibration compound
Source: http://www.nmrnotes.org/NMRPages/refcomps.html
bug-database: https://github.com/nmrML/nmrML/issues/31
bug-database: https://github.com/nmrML/nmrML/issues/33
has_exact_synonym: chemical shift reference compound
comment: def: A compound that is added to an NMR sample to enable the alignment of spectra. The power of NMR is that for most nuclei the NMR frequency changes very slightly with different molecular environment or chemical bonding. These shifts are very small, on the order of 1 part in 10+9. This is referred to as "Chemical Shift." Tables of chemical shifts are tabulated and used to determine molecular structure. Combining NMR chemical shift information with other NMR information such as peak integration, coupling constants and Nuclear Overhauser Enhancement (NOE) can result in complete three-dimensional molecular structures of molecules in solution without using X-ray crystallography.

quality check compound signal
type: Class
subclass of: NMR quality check parameter set
comment: def: The compound that produced a peak that is measured to assess the quality of a data set.

NMR pulse sequence
type: Class
subclass of: pulse parameter
Source: http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
bug-database: https://github.com/nmrML/nmrML/issues/40
comment: def: A sequence of excitation pulses.
editorial note: May later import from http://purl.obolibrary.org/obo/CHMO_0001841
editorial note: See also http://www.jcamp-dx.org/protocols/NMR%20Pulse%20Sequences%20PAC%2079(11)%20pp1748-1764%202001.pdf

frequency domain data processing
type: Class
subclass of: NMR data processing
has_exact_synonym: nmr-spectrum data processing
has_exact_synonym: post-FT data processing
comment: def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values.

time domain data processing
type: Class
subclass of: NMR data processing
has_exact_synonym: pre-FT data processing
comment: def: The post acquisition process of producing or refining a spectrum from raw data. defprov: Daniel Schober

NMR data processing
type: Class
subclass of: data transformation
comment: def: A data transformation that converts an NMR input data set into an output data set in a tracable and useful manner.

non-fourier FID transformation
type: Class
subclass of: time domain data processing
comment: tempdef: A non FT based method for converting from the time to the frequency domain.
version info: TODO:Exclusion guided definition.

data encoding
type: Class
subclass of: NMR data processing
bug-database: https://github.com/nmrML/nmrML/issues/37
comment: tempdef: A data processing which alteres a data file for a specific purpose. defprov: Daniel Schober

G matrix fourier transform projection
type: Class
subclass of: spectral projection
comment: tempdef:GFT NMR allows for rapid multidimensional FT NMR spectral information gathering, avoiding sampling limitations without compromising on the precision of chemicalshift. defprov: ttp://www.nsm.buffalo.edu/Research/GFT/szyperski_publications_1st_page/Szyperski%2067.pdf synonym: GFT-projection

time proportional phase incrementation
type: Class
subclass of: data encoding
comment: defneed synonym: TPPI

states-time proportional phase incrementation
type: Class
subclass of: data encoding
comment: def: A method for quadrature detection. synonym: S-TPPI

Hadamard encoding
type: Class
subclass of: data encoding
comment: defneed

Frydman encoding
type: Class
subclass of: data encoding
Source: http://www.magnet.fsu.edu/library/publications/NHMFL_Publication-6859.pdf
comment: defneed

echo anti-echo coherence selection
type: Class
subclass of: quadrature detection
comment: defneed

NMR instrument
type: Class
subclass of: instrument
comment: def: An Instrument which is used to carry out a NMR analysis of some sample. synonym: NMR instrument

NMR instrument acquisition parameter set
type: Class
subclass of: NMR instrument parameter set
comment: def: The list of parameters that describe the instrument settings used for the acquisition of a spectrum. altdef: The set of variables dependent on a given pulse sequence that will be optimised in order to acquire a spectrum. synonym: NMR instrument acquisition parameter set

normalisation
type: Class
subclass of: scaling
term editor: Philippe Rocca Serra
definition source: http://pubs.acs.org/doi/pdf/10.1021/ac0519312 10.1021/ac0519312 Scaling and Normalization Effects in NMR Spectroscopic Metabonomic Data Sets Andrew Craig , Olivier Cloarec , Elaine Holmes , Jeremy K. Nicholson , and John C. Lindon * Biological Chemistry, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ U.K.
definition source: http://stats.stackexchange.com/questions/35591/normalization-vs-scaling
definition: normalization is a data transformation process which aims at making data seem roughly normally distributied by applying a mathematical function, which is most of time a continuous function. This is a row operation that is applied to the data from each sample and comprises methods to make the data from all samples directly comparable with each other. A common use is to remove or minimize the effects of variable dilution of the samples.

pre-acquisition water suppression
type: Class
subclass of: pre-acquisition solvent suppression
comment: tempdef: A technique used to suppress the water resonance peak in a spectrum. Suppression of the strong solvent signal is necessary in order to obtain high signal to noise for the peaks of the sample under investiogation, e.g. protein peaks. defprov: Daniel Schober

window function for apodization
type: Class
subclass of: parameter
definition: A function applied to a FID to increase the signal-to-noise ratio or the resolution.
Source: http://www.uwyo.edu/wheelernmr/nmr/window_functions.pdf
bug-database: https://github.com/nmrML/nmrML/issues/39
bug-database: https://github.com/nmrML/nmrML/issues/67
has_exact_synonym: apodization function

exponential multiplication window function
type: Class
subclass of: window function for apodization
definition: The exponential function used to multiply a FID by to produce a desitred amount of line broadening.
has_exact_synonym: exponential apodization
comment: Functional form: em(x_i) = exp(-pi*i*lb) Parameters: * data Array of spectral data. * lp Exponential line broadening. * inv Set True for inverse apodization.

Gaussian window function
type: Class
subclass of: window function for apodization
has_exact_synonym: gaussian broadening
comment: defneed

sine window function
type: Class
subclass of: window function for apodization
has_exact_synonym: sine
has_exact_synonym: sine bell window function
comment: defneed

sine squared window
type: Class
subclass of: sine window function
has_exact_synonym: QSINE
comment: defneed

spectral denoising
type: Class
subclass of: frequency domain data processing
comment: def: A method for eliminating or reducing the noise in a spectrum.

baseline correction
type: Class
subclass of: frequency domain data processing
comment: def: A method of flattening the baseline of a spectrum.

spectral projection
type: Class
subclass of: data encoding
comment: A method of spectral projection.

maximum intensity projection
type: Class
subclass of: spectral projection
comment: defneed

summation projection
type: Class
subclass of: spectral projection
comment: def: .A projection method that sums the intensities of a pre-processed 2D J-resolved NMR spectrum to obtain a projected spectrum. altdef: The adding of spectra together to produce a composite avergaed spectrum.

zero order phase correction
type: Class
subclass of: phase correction
comment: def: A parameter used to mix real and imaginary part of an NMR spectrum that the real part of the spectrum is in pure absorption mode. altdef: The number of degrees that a central peak must be moved in order to achieve an absorptive mode line width.

first order phase correction
type: Class
subclass of: phase correction
comment: defneed

symmetrisation
type: Class
subclass of: frequency domain data processing
comment: defneed

acquisition nucleus
type: Class
subclass of: object
comment: def: The nucleus of an element or isotope that is being studied during an NMR analysis. Common NMR requirements include direct 1D and 2D proton-only NMR, direct observation of 13C NMR with 1H decoupling, direct observation of other nuclei such as 19F, 31P, 29Si, 31P, 27Al, and 15N (with or without 1H decoupling), triple resonance NMR (especially inverse triple resonance such as 1H observe, 13C and 15N decouple), and inverse 2D and 3D experiments such as HMQC and HMBC.

quality check peak feature
type: Class
subclass of: NMR quality check parameter set
comment: def: A feature of a peak that is measured to assess the quality of a data set.

number of scans
type: Class
subclass of: NMR acquisition parameter
comment: def: The number of repeat scans performed and summed to create the data set for an NMR sample.

number of steady state scans
type: Class
subclass of: number of scans
comment: def: The number of scans whose data is not summed to create the data set for an NMR sample, but that are carried out to establish the steady-state of relaxation for the nuclei.

atom environment encoding
type: Class
subclass of: NMR acquisition parameter
comment: def: A scheme for producing a numerical representation of the environment of an atom.

relaxation delay
type: Class
subclass of: NMR acquisition parameter
comment: def: The delay between repeat scans to allow nuclei to relax back to their steady state.

x-axis unit
type: Class
subclass of: 1D spectrum coordinate system descriptor
comment: def: The units of measure for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. altdef: The units used to represent either time domain (for a FID) or the frequency domain (for a spectrum).

y-axis unit
type: Class
subclass of: 1D spectrum coordinate system descriptor
comment: defneed

additional axis unit
type: Class
subclass of: parameter
comment: def: The unit of measurement of the second dimension of a 2D NMR dataset.

x start value
type: Class
subclass of: 1D spectrum coordinate system descriptor
comment: def: The starting value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. altdef: The initial time or frequency a FID or spectrum is recorded from.

x end value
type: Class
subclass of: NMR data pre-processing parameter set
comment: tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.

window function parameter
type: Class
subclass of: parameter
comment: def: A parameter to a window function.

line broadening
type: Class
subclass of: apodization
term editor: Philippe Rocca-Serra
definition source: http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. Hans J. Reich 2015, University of Wisconsin
comment: defneed
definition: line broadening is a process resulting in spectral peak signal becoming hard to interpret and analysed. Line broadening is affected by spin-spin relaxation and/or spin-lattice relaxation processes. When relaxation is very fast, NMR lines are broad, J-coupling may not be resolved or the signal may even be difficult or impossible to detect. The maximum repetition rate during acquisition of an NMR signal is governed by T1 - short T1 means the magnetization recovers more rapidly, and a spectrum can be acquired in less time. Line broadening may be caused by: Sample inhomogeneity (poor mixing. solid particles), Temperature gradients across sample, Paramagnetic impurities.

line sharpening
type: Class
subclass of: apodization
term editor: Philippe Rocca-Serra
definition source: http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. Hans J. Reich 2015, University of Wisconsin
comment: defneed
definition: line sharpening is a data transformation process inverse to that of line broadening, which aims to improve the quality of the signal being acquired and being analyzed in order to obtain clear, sharp peaks, in turn making interpretation easier. Line sharpening can be optimized during data acquisition or performed during data analysis by applied digital processing and filtering.

parameter
type: Class
subclass of: generically dependent continuant
comment: defneed

NMR spectral projection parameter set
type: Class
subclass of: NMR data post-processing parameter set
comment: def: The data processing parameters that describe a method of translating a 2D NMR pre-processed spectrum into a 1D NMR spectrum. synonym: NMR spectral projection parameter set

NMR data post-processing parameter set
type: Class
subclass of: data processing parameter
comment: def: A description of the post-processing strategy used to convert a pre-processed NMR spectrum into a suitable data format for chemometric analysis. synonym: NMR spectrum post-processing parameter set
version info: TODO: altsprcls: process, not clear wether set is plural (list) or process.

NMR quality check parameter set
type: Class
subclass of: NMR data post-processing parameter set
comment: tempdef: A nuclear magnetic resonance spectroscopy quality check parameter set is a parameter set used for the quality check method for an NMR analysis synonym: NMR quality check parameter set

post-acquisition water suppression
type: Class
subclass of: post-acquisition solvent suppression
has_exact_synonym: excitation sculpting
comment: tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results. defprov: Daniel Schober

hankel singular value decomposition
type: Class
subclass of: post-acquisition water suppression
comment: def: This Method removes the residual water and its side lobes, thereby reducing the baseline for the metabolites of interest and allowing subsequent data analysis using more sophisticated nonlinear least squares algorithms. synonym: HSVD

convolution
type: Class
subclass of: post-acquisition water suppression
comment: defneed

polynomial fitting
type: Class
subclass of: post-acquisition water suppression
comment: defneed

WaveWat
type: Class
subclass of: post-acquisition water suppression
comment: def: A computational method that archieves water suppression via wavlet multi resolution analysis.

NMR data pre-processing parameter set
type: Class
subclass of: data processing parameter
comment: defneed synonym: NMR data pre-processing parameter set

NMR quality check
type: Class
subclass of: data transformation
comment: def: The process of ensuring the quality of the raw data that results from an NMR analysis. synonym: NMR quality check

reference
type: Class
subclass of: generically dependent continuant
comment: def: A reference is a label which refers to data elsewhere, as opposed to containing the data itself. Accessing the value that a reference refers to is called dereferencing it. References are fundamental in constructing many data structures and in exchanging information between different parts of programs and databases.

FID file
type: Class
subclass of: data file
has_exact_synonym: FID file reference
comment: def: A reference to a file containing the raw FID. synonym: FID file reference

pulse sequence literature reference
type: Class
subclass of: external reference identifier
comment: def: A reference to a description of a pulse sequence in the literature.

shaped pulse file
type: Class
subclass of: pulse sequence file
comment: def: A reference to a file containing a specfication of the shape of an excitation pulse.

pulse sequence file
type: Class
subclass of: data file
comment: def: A reference to a file containing a specification of a pulse sequence.

processing parameter file
type: Class
subclass of: data file
comment: def: A reference to a file of data pre-processing parameters produced by the machine.

NMR sample identifier
type: Class
subclass of: external reference identifier
comment: PRS: rename 'reference' to 'identifier'
comment: def: A reference to information on the provenance of the NMR sample. synonym: NMR sample reference

NMR quality check descriptor
type: Class
subclass of: NMR spectrum descriptor
comment: def: A result of an NMR quality check. synonym: NMR quality check result

NMR sample
type: Class
subclass of: sample
comment: def: A sample that has been prepared for chemical analysis by NMR. NMR samples are usually liquid solutions contained in glass tubes. NMR solution sample volume ranges from 50ul to 5ml depending on the NMR probe. Sample concentrations of solute for 1H NMR are usually in the range of 100ug to 5g, with 10 to 50mg being typical. NMR is not a chemical trace analysis technique. The NMR signal of solids and gases can be recorded but to measure solid-state NMR additional specialized hardware is required. synonym: NMR sample

sample introduction parameter
type: Class
subclass of: sample attribute
comment: tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the NMR instrument.

magic angle spinning rotor
type: Class
subclass of: sample introduction parameter
comment: defneed synonym: MAS rotor

flow probe
type: Class
subclass of: sample introduction parameter
comment: defneed

NMR sample tube
type: Class
subclass of: cardinal part of NMR instrument
definition: The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter.
Source: http://en.wikipedia.org/wiki/NMR_tube
bug-database: https://github.com/nmrML/nmrML/issues/54
has_exact_synonym: sample tube
comment: sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID

spectrum pre-processing software
type: Class
subclass of: NMR software
comment: def: A software artifact used during data pre-processing.

spectrum post-processing software
type: Class
subclass of: NMR software
comment: def: A software artifact used during spectral post-processing.

peak picking
type: Class
subclass of: peak processing
comment: defneed

bucketing
type: Class
subclass of: peak processing
has_exact_synonym: binning
comment: def: A post-processing method that divides a pre-processed NMR spectrum into a series of buckets (or bins) along the x-axis, and then integrates the spectral intensity within each bucket. altdef: A type of automated integration which occurs across pre-defined regions for a spectrum.
comment: for bucket parameters see 'binned spectrum descriptor'
definition: Taking advantage of the concentration variability of each compound in a series of samples, buckets are linked together into clusters based on significant correlations.This is done i.g. in ERVA-based bucketing

presat pulse sequence
type: Class
subclass of: NMR pulse sequence
has_exact_synonym: presaturation of the solvent resonance
comment: defneed synonym: presaturation

water suppression enhanced through T1 effects
type: Class
subclass of: NMR pulse sequence
comment: tempdef: An improved water-suppression technique called WET (water suppression enhanced through T1 effects), developed from a Bloch equation analysis of the longitudinal magnetization over the T1 and B1 ranges of interest, achieves T1- and B1-insensitive suppression with four RF pulses, each having a numerically optimized flip angle. Once flip angles have been optimized for a given sequence, time-consuming flip-angle adjustments during clinical examinations are eliminated. defprov: Daniel Schober synonym: WET
alternative label: WET

nuclear overhauser and exchange spectroscopy-presat
type: Class
subclass of: presat pulse sequence
has_exact_synonym: NOESY presat
comment: tempdef: The presat for an nuclear overhauser and exchange spectroscopy experiment. A 2D method used to map NOE correlations between protons within a molecule. The nuclear Overhauser effect (NOE) causes changes in peak areas, as a secondary effect of decoupling. defprov: Daniel Schober synonym: NOESY-presat

watergate
type: Class
subclass of: NMR pulse sequence
comment: defneed

coherence pathway rejection
type: Class
subclass of: pre-acquisition water suppression
comment: tempdef: A water suppression method which is used to suppress the natural water signal in a gradient selection experiment (e.g. echo/antiecho), where the water coherence is not "refocused" by the refocus gradient (therefore, is not selected). defprov: Daniel Schober

flip-back watergate
type: Class
subclass of: watergate
comment: defneed

jump and return pulse sequence
type: Class
subclass of: NMR pulse sequence
comment: tempdef: A jump and return pulse sequence method is a water suppression method that uses a defined pulse sequence to make fast exchanging protons visible.

jump and return 1-1
type: Class
subclass of: jump and return pulse sequence
comment: tempdef: A jump and return 1-1 pulse sequence method is a jump and return method that uses one 90 degree pulse and one 90 degree return puls to make fast exchanging protons visible, first described by Plateau,P. and Gueron,M. (1982) J. Am. Chem. Soc., 104, 7310–7311. Compared to the 1-3-3-1 method it has a lower receiver gain and the dispersive tail of water interferes with the signals of interest.

jump and return 1-3-3-1
type: Class
subclass of: jump and return pulse sequence
comment: tempdef:A jump and return 1-3-3-1 pulse sequence method is a jump and return method that uses a 1-3-3-1 pulse sequence to make fast exchanging protons visible. Compared to the 1-1 method it has better water suppression (higher receiver gain) capabilities, but with offset-dependent phase distortion (unsuitable for 2D).

1D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
comment: defneed synonym: 1D spectrum

2D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
comment: defneed synonym: 2D spectrum

1D NMR acquisition parameter set
type: Class
subclass of: NMR instrument acquisition parameter set
comment: defneed synonym: 1D NMR acquisition parameter set

2D NMR acquisition parameter set
type: Class
subclass of: NMR instrument acquisition parameter set
comment: defneed synonym: 2D NMR acquisition parameter set

carr purcell meiboom gill pulse sequence
type: Class
subclass of: 1D pulse sequence
comment: tempdef: A modification of Carr-Purcell RF pulse sequence with 90° phase shift in the rotating frame of reference between the 90° pulse and the subsequent 180° pulses to reduce accumulating effects of imperfections in the 180° pulses. Suppression of effects of pulse error accumulation can alternatively be achieved by alternating phases of the 180° pulses by 180°. defprov: Daniel Schober synonym: 1D CPMG
alternative label: CPMG

total correlation spectroscopy pulse sequence
type: Class
subclass of: 2D pulse sequence
has_exact_synonym: TCOSY pulse sequence
comment: tempdef: Total Correlation Spectroscopy. A 2D homonuclear correlation experiment used to analyse scalar (J) coupling networks between protons. TOCSY is able to relay magnetisation between spins, A-B-C-D.., and can therefore show correlations amongst spins that are not directly coupled (eg A-C and A-D) but exist within the same spin system. defprov: Daniel Schober synonym:2D TOCSY pulse sequence

1D pulse sequence
type: Class
subclass of: NMR pulse sequence
comment: def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum). synonym: 1D

J-resolved pulse sequence
type: Class
subclass of: 2D pulse sequence
comment: tempdef: In 1D NMR, as the multiplets from different chemically shifted nuclei overlap, spectral assignments become too difficult. In order to resolve the chemical shift and spin-spin coupling parameters along the different axis, 2D and 3D J-resolved NMR spectroscopies are used. defprov: Daniel Schober synonym: 2D J-resolved

hadamard total correlation spectroscopy pulse sequence
type: Class
subclass of: 2D pulse sequence
comment: defneed synonym: 2D hadamard TOCSY

diffusion edited pulse sequence
type: Class
subclass of: 1D pulse sequence
comment: defneed synonym: 1D diffusion edited

NMR magnet
type: Class
subclass of: cardinal part of NMR instrument
comment: def: A magnet which induces a certain frequency (MHz) and which has a certain bore diameter. altdef: The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.

Bruker NMR magnet
type: Class
subclass of: NMR magnet
comment: defneed

UltraShield
type: Class
subclass of: Bruker NMR magnet
comment: defneed

Ultrastabilized
type: Class
subclass of: Bruker NMR magnet

US 2
type: Class
subclass of: Bruker NMR magnet
version info: ??? How to model "hoch 2"?

UltraShield Plus
type: Class
subclass of: Bruker NMR magnet

Bruker CryoProbe
type: Class
subclass of: cryoprobe
subclass of: Bruker NMR probe
comment: def: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis: Significant S/N gains (with moderately salty samples also) Short pulse widths Short ring down times Linear behavior in power response Gradient capability CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher All high resolution probes have a lock circuit All high resolution probes have Z-gradient defprov: Bruker website

high resolution magic angle spin probe
type: Class
subclass of: high resolution probe
comment: def: Samples that are neither solid nor liquid, being of biological, chemical, and/or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Bruker’s high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject/insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g., 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. defprov: Bruker website altdef: High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples. synonyms: High resolution MAS, hr-MAS

solid magic angle spinning probe
type: Class
subclass of: Bruker NMR probe
comment: def: Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. defprov: Bruker website synonym: solid MAS probe

1mm MicroProbe
type: Class
subclass of: Bruker NMR probe
comment: def: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include: up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount) excellent solvent suppression properties virtually no salt effect discrete samples in tubes that can be sealed and stored automation accessory for sample preparation and handling available defprov: Bruker website

flow high resolution probe
type: Class
subclass of: high resolution probe
comment: def: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. defprov: Bruker website synonym: flow HR-probe

NMR instrument parameter set
type: Class
subclass of: parameter
comment: defneed

AVANCE II spectrometer
type: Class
subclass of: Bruker NMR instrument
comment: defneed
version info: TODO: May need no definition

Bruker NMR instrument
type: Class
subclass of: NMR instrument
comment: defneed

Metabolic Profiler instrument
type: Class
subclass of: Bruker NMR instrument
comment: For metabolism studies, and analysis of complex mixtures.

Hyphenated NMR instrument
type: Class
subclass of: NMR instrument type
comment: NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph.

Capillary LC-NMR
type: Class
subclass of: Bruker NMR instrument

NMR Case
type: Class
subclass of: Bruker autosampler
comment: def: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. defprov: Bruker website

NMR tube washing system
type: Class
subclass of: optional part of NMR instrument
comment: defneed

Bruker AutoClean
type: Class
subclass of: NMR tube washing system
comment: def: In today's fast-paced research environment, NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean™ system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. defprov: Bruker website

Bruker BEST NMR
type: Class
subclass of: Bruker autosampler
comment: def: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. defprov: Bruker website synonym: Bruker Efficient Sample Transfer NMR

SampleRail
type: Class
subclass of: autosampler
comment: def: This system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back defprov: website

SampleJet
type: Class
subclass of: Bruker autosampler
comment: def: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation. The SampleJet utilizes the modern-day industry standard for sample arrangements—the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. defprov: Bruker website

Bruker autosampler
type: Class
subclass of: autosampler
comment: defneed

B-ACS
type: Class
subclass of: Bruker autosampler
comment: def: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. defprov: Bruker website

Bruker MATCH
type: Class
subclass of: NMR sample holder
comment: def: The Bruker Multiple Adjustable Tube Clamp Holder MATCH™ system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications. The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. defprov: Bruker website synonym: Bruker Multiple Adjustable Tube Clamp Holder

NMR sample holder
type: Class
subclass of: cardinal part of NMR instrument
comment: def: A NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the NMR sample.

NMR software
type: Class
subclass of: software
comment: defneed

Bruker NMR software
type: Class
subclass of: commercial NMR software
comment: defneed
version info: TODO: May need no definition.

Bruker TopSpin software
type: Class
subclass of: Bruker NMR software

SampleTrack software
type: Class
subclass of: Bruker NMR software

Paravision software
type: Class
subclass of: Bruker NMR software

AURELIA software
type: Class
subclass of: Bruker NMR software

AUREMOL software
type: Class
subclass of: Bruker NMR software

AMIX VIEWER & AMIX-TOOLS
type: Class
subclass of: Bruker NMR software

high resolution probe
type: Class
subclass of: Bruker NMR probe
comment: def:BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. defprov: Bruker website synonym: HR Probe

high resolution probe with ATM
type: Class
subclass of: high resolution probe
comment: def: The ATM option for AVANCE spectrometers is available for: Double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90° pulsewidths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. defprov: Bruker website synonym: High Resolution Probes with Automatic Tuning and Matching, HR probe with ATM

micro imaging probe
type: Class
subclass of: Bruker NMR probe
comment: defneed

JEOL NMR instrument
type: Class
subclass of: NMR instrument

JNM-ECX Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: The JNM-ECX series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.

JNM-ECA Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: The JNM-ECA series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.

JEOL NMR software
type: Class
subclass of: commercial NMR software

Delta NMR software
type: Class
subclass of: JEOL NMR software

Bruker NMR probe
type: Class
subclass of: NMR probe
comment: https://www.bruker.com/products/mr/nmr/probes/probes.html

JEOL NMR probe
type: Class
subclass of: NMR probe
comment: defneed

CapNMR probe
type: Class
subclass of: JEOL NMR probe

Varian NMR instrument
type: Class
subclass of: NMR instrument

Varian MERCURY
type: Class
subclass of: Varian NMR instrument

Varian INOVA
type: Class
subclass of: Varian NMR instrument

Varian UNITY
type: Class
subclass of: Varian NMR instrument

Varian VXR
type: Class
subclass of: Varian NMR instrument

Varian GEMINI
type: Class
subclass of: Varian NMR instrument

AMX instrument
type: Class
subclass of: Bruker NMR instrument

AC instrument
type: Class
subclass of: Bruker NMR instrument

liquid NMR probe
type: Class
subclass of: NMR probe

solid NMR probe
type: Class
subclass of: NMR probe
comment: defneed

NMR imaging probe
type: Class
subclass of: NMR probe
comment: defneed

tecmag console
type: Class
subclass of: console

DISCOVERY console
type: Class
subclass of: tecmag console
comment: def: The Discovery™ is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network defprov: tecmag website

tecmag EAGLE probe
type: Class
subclass of: solid NMR probe
comment: def: The Eagle™ is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz widebore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. defprov: website

APOLLO console
type: Class
subclass of: tecmag console
comment: defneed

tecmag NMR instrument
type: Class
subclass of: NMR instrument

CAT
type: Class
subclass of: tecmag NMR instrument

magnetic field strength
type: Class
subclass of: field strength
comment: defneed

vendor
type: Class
subclass of: contact role
comment: defneed
version info: TODO: Belongs in Ref Ontol.

NMR instrument manufacturer
type: Class
subclass of: instrument attribute
comment: A manufacturer that produces (and eventually sells) NMR instruments.

Bruker
type: Class
subclass of: NMR instrument manufacturer
comment: defneed
version info: TODO: May not need definition due to its instance character.

Varian
type: Class
subclass of: NMR instrument manufacturer

JEOL
type: Class
subclass of: NMR instrument manufacturer

MR Resources
type: Class
subclass of: NMR instrument manufacturer

tecmag
type: Class
subclass of: NMR instrument manufacturer

sample temperature information
type: Class
subclass of: sample attribute
comment: def: In some cases, it is necessary or advisable to control the temperature of the sample at some value other than ambient. The sample may be only slightly solubility at room temperatures, or it may be desirable to control some aspect of the dynamics of the system. In such cases, a default temperature, or some means of selecting this parameter, can be built into the experiment.

Doty Scientific
type: Class
subclass of: NMR instrument manufacturer

Wilmad
type: Class
subclass of: NMR instrument manufacturer

JS Research
type: Class
subclass of: NMR instrument manufacturer

data file
type: Class
subclass of: generically dependent continuant
alternative label: file
definition: Any data file as generated by some acquisition computer or console.
editorial note: This is a class annotation exemplifying skos usage. We assume the rdfs:label to capture the skos:preferedLabel.
example: an FID raw data file
scope note: In the NMR case a file generated by an NMR acquisition computer, console or NMR processing software.

Acorn NMR Inc
type: Class
subclass of: NMR instrument manufacturer

liquid chromatography NMR
type: Class
subclass of: Hyphenated NMR instrument
has_exact_synonym: LC NMR

LC MS NMR
type: Class
subclass of: liquid chromatography NMR
comment: Includes the connection to a high-resolution TOF-LC-MS system.

solid phase extraction NMR
type: Class
subclass of: NMR instrument type
has_exact_synonym: SPE NMR
comment: A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE™ NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.

Capillary LC-NMR
type: Class
subclass of: liquid chromatography NMR
comment: Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume.

direct detection probe
type: Class
subclass of: NMR probe

indirect detection probe
type: Class
subclass of: NMR probe

continuous wave NMR
type: Class
subclass of: NMR instrument type
comment: Continuous wave NMR spectrometers are similar in principle to optical spectrometers. The sample is held in a strong magnetic field, and the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm

fourier transformation NMR instrument
type: Class
subclass of: NMR instrument type
comment: In FT-NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm

NMR software data format
type: Class
subclass of: data file format

ChemMagnetics format
type: Class
subclass of: NMR software data format

GE Omega format
type: Class
subclass of: NMR software data format

JEOL Lambda format
type: Class
subclass of: NMR software data format

JEOL Alpha format
type: Class
subclass of: NMR software data format

Jeol Delta format
type: Class
subclass of: NMR software data format

JEOL generic format
type: Class
subclass of: NMR software data format

JEOL AL95 format
type: Class
subclass of: NMR software data format

JEOL EX format
type: Class
subclass of: NMR software data format

TecMag format
type: Class
subclass of: NMR software data format

Varian VNMR format
type: Class
subclass of: NMR software data format

Galactic format
type: Class
subclass of: NMR software data format

Felix format
type: Class
subclass of: NMR software data format

JCAMP DX format
type: Class
subclass of: NMR software data format

Lybrics format
type: Class
subclass of: NMR software data format

Nuts format
type: Class
subclass of: NMR software data format

MACNMR format
type: Class
subclass of: NMR software data format

Nicolet GE/QE-300 format
type: Class
subclass of: NMR software data format

multiplet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: m
comment: J-coupler

ThermoMattson
type: Class
subclass of: NMR instrument manufacturer

FOSS
type: Class
subclass of: NMR instrument manufacturer

Jasco
type: Class
subclass of: NMR instrument manufacturer

Agilent Technologies
type: Class
subclass of: NMR instrument manufacturer

micromass
type: Class
subclass of: NMR instrument manufacturer

Waters
type: Class
subclass of: NMR instrument manufacturer

ThermoNicolet
type: Class
subclass of: NMR instrument manufacturer

Perkin Elmer
type: Class
subclass of: NMR instrument manufacturer

OceanOptics
type: Class
subclass of: NMR instrument manufacturer

ThermoFinnigan
type: Class
subclass of: NMR instrument manufacturer

Applied Biosystems
type: Class
subclass of: NMR instrument manufacturer

TX
type: Class
subclass of: NMR instrument manufacturer

Net CDF format
type: Class
subclass of: NMR software data format

Bruker DISNMR format
type: Class
subclass of: NMR software data format

Bruker UXNMR/XWIN-NMR format
type: Class
subclass of: NMR software data format

Bruker WIN NMR format
type: Class
subclass of: NMR software data format

acdlabs
type: Class
subclass of: NMR instrument manufacturer

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
imported from: Ontology for Biomedical Investigation
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
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: Ontology for Biomedical Investigation
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
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.
imported from: Ontology for Biomedical Investigation
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])
imported from: Ontology for Biomedical Investigation
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.
imported from: Ontology for Biomedical Investigation
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
imported from: Ontology for Biomedical Investigation
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)
imported from: chmo.owl
imported from: Ontology for Biomedical Investigation
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]
id: BFO:0000015

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.
imported from: Ontology for Biomedical Investigation
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.
imported from: Ontology for Biomedical Investigation
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
imported from: Ontology for Biomedical Investigation
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
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: Ontology for Biomedical Investigation
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
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: b is a 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: Ontology for Biomedical Investigation
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.
imported from: Ontology for Biomedical Investigation
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.
imported from: Ontology for Biomedical Investigation
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,
imported from: Ontology for Biomedical Investigation
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])
imported from: Ontology for Biomedical Investigation
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.
imported from: Ontology for Biomedical Investigation
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
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: Ontology for Biomedical Investigation
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
imported from: Ontology for Biomedical Investigation

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 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 term: 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

water
type: Class
subclass of: molecular entity
definition: An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.
imported from: chebi.owl
charge: 0
formula: H2O
inchi: InChI=1S/H2O/h1H2
inchikey: XLYOFNOQVPJJNP-UHFFFAOYSA-N
mass: 18.01530
monoisotopicmass: 18.011
smiles: [H]O[H]
has_alternative_id: CHEBI:10743
has_alternative_id: CHEBI:13352
has_alternative_id: CHEBI:27313
has_alternative_id: CHEBI:42043
has_alternative_id: CHEBI:42857
has_alternative_id: CHEBI:43228
has_alternative_id: CHEBI:44292
has_alternative_id: CHEBI:44701
has_alternative_id: CHEBI:44819
has_alternative_id: CHEBI:5585
database_cross_reference: Beilstein:3587155
database_cross_reference: CAS:7732-18-5
database_cross_reference: Gmelin:117
database_cross_reference: HMDB:HMDB0002111
database_cross_reference: KEGG:C00001
database_cross_reference: KEGG:D00001
database_cross_reference: MetaCyc:WATER
database_cross_reference: MolBase:1
database_cross_reference: PDBeChem:HOH
database_cross_reference: PDBeChem:MTO
database_cross_reference: Reaxys:3587155
database_cross_reference: Wikipedia:Water
has_exact_synonym: WATER
has_exact_synonym: Water
has_exact_synonym: oxidane
has_exact_synonym: water
has_obo_namespace: chebi_ontology
has_related_synonym: BOUND WATER
has_related_synonym: H2O
has_related_synonym: HOH
has_related_synonym: Wasser
has_related_synonym: [OH2]
has_related_synonym: acqua
has_related_synonym: agua
has_related_synonym: aqua
has_related_synonym: dihydridooxygen
has_related_synonym: dihydrogen oxide
has_related_synonym: eau
has_related_synonym: hydrogen hydroxide
id: CHEBI:15377
in_subset: 3 STAR

biotin
type: Class
subclass of: molecular entity
definition: An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.
imported from: chebi.owl
charge: 0
formula: C10H16N2O3S
inchi: InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1
inchikey: YBJHBAHKTGYVGT-ZKWXMUAHSA-N
mass: 244.31172
monoisotopicmass: 244.088
has_alternative_id: CHEBI:13905
has_alternative_id: CHEBI:22882
has_alternative_id: CHEBI:22884
has_alternative_id: CHEBI:3108
has_alternative_id: CHEBI:41236
database_cross_reference: Beilstein:86838
database_cross_reference: CAS:58-85-5
database_cross_reference: COMe:MOL000144
database_cross_reference: DrugBank:DB00121
database_cross_reference: Drug_Central:373
database_cross_reference: Gmelin:1918703
database_cross_reference: HMDB:HMDB0000030
database_cross_reference: KEGG:C00120
database_cross_reference: KEGG:D00029
database_cross_reference: KNApSAcK:C00000756
database_cross_reference: LINCS:LSM-3994
database_cross_reference: MetaCyc:BIOTIN
database_cross_reference: PDBeChem:BTN
database_cross_reference: PMID:11435506
database_cross_reference: PMID:11800048
database_cross_reference: PMID:12055344
database_cross_reference: PMID:12803839
database_cross_reference: PMID:15012185
database_cross_reference: PMID:15202718
database_cross_reference: PMID:15272000
database_cross_reference: PMID:15899401
database_cross_reference: PMID:16419467
database_cross_reference: PMID:16676358
database_cross_reference: PMID:16677798
database_cross_reference: PMID:16769720
database_cross_reference: PMID:17297119
database_cross_reference: PMID:18452485
database_cross_reference: PMID:18509457
database_cross_reference: PMID:19319844
database_cross_reference: PMID:19727438
database_cross_reference: PMID:19928962
database_cross_reference: PMID:20967359
database_cross_reference: PMID:20974274
database_cross_reference: PMID:21248194
database_cross_reference: PMID:21356565
database_cross_reference: PMID:21373679
database_cross_reference: PMID:21596550
database_cross_reference: PMID:21871906
database_cross_reference: PMID:25515858
database_cross_reference: Reaxys:86838
database_cross_reference: Wikipedia:Biotin
has_exact_synonym: 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
has_exact_synonym: BIOTIN
has_exact_synonym: Biotin
has_obo_namespace: chebi_ontology
has_related_synonym: (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid
has_related_synonym: (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid
has_related_synonym: 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid
has_related_synonym: Coenzyme R
has_related_synonym: D-(+)-biotin
has_related_synonym: D-Biotin
has_related_synonym: Vitamin H
has_related_synonym: biotina
has_related_synonym: biotine
has_related_synonym: biotinum
has_related_synonym: cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid
has_related_synonym: cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid
has_related_synonym: cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid
has_related_synonym: vitamin B7
id: CHEBI:15956
in_subset: 3 STAR

ammonia
type: Class
subclass of: molecular entity
definition: An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
imported from: chebi.owl
charge: 0
formula: H3N
inchi: InChI=1S/H3N/h1H3
inchikey: QGZKDVFQNNGYKY-UHFFFAOYSA-N
mass: 17.03056
monoisotopicmass: 17.027
smiles: [H]N([H])[H]
has_alternative_id: CHEBI:13405
has_alternative_id: CHEBI:13406
has_alternative_id: CHEBI:13407
has_alternative_id: CHEBI:13771
has_alternative_id: CHEBI:22533
has_alternative_id: CHEBI:44269
has_alternative_id: CHEBI:44284
has_alternative_id: CHEBI:44404
has_alternative_id: CHEBI:7434
database_cross_reference: Beilstein:3587154
database_cross_reference: CAS:7664-41-7
database_cross_reference: Drug_Central:4625
database_cross_reference: Gmelin:79
database_cross_reference: HMDB:HMDB0000051
database_cross_reference: KEGG:C00014
database_cross_reference: KEGG:D02916
database_cross_reference: KNApSAcK:C00007267
database_cross_reference: MetaCyc:AMMONIA
database_cross_reference: MolBase:930
database_cross_reference: PDBeChem:NH3
database_cross_reference: PMID:110589
database_cross_reference: PMID:11139349
database_cross_reference: PMID:11540049
database_cross_reference: PMID:11746427
database_cross_reference: PMID:11783653
database_cross_reference: PMID:13753780
database_cross_reference: PMID:14663195
database_cross_reference: PMID:15092448
database_cross_reference: PMID:15094021
database_cross_reference: PMID:15554424
database_cross_reference: PMID:15969015
database_cross_reference: PMID:16008360
database_cross_reference: PMID:16050680
database_cross_reference: PMID:16348008
database_cross_reference: PMID:16349403
database_cross_reference: PMID:16614889
database_cross_reference: PMID:16664306
database_cross_reference: PMID:16842901
database_cross_reference: PMID:17025297
database_cross_reference: PMID:17439666
database_cross_reference: PMID:17569513
database_cross_reference: PMID:17737668
database_cross_reference: PMID:18670398
database_cross_reference: PMID:22002069
database_cross_reference: PMID:22081570
database_cross_reference: PMID:22088435
database_cross_reference: PMID:22100291
database_cross_reference: PMID:22130175
database_cross_reference: PMID:22150211
database_cross_reference: PMID:22240068
database_cross_reference: PMID:22290316
database_cross_reference: PMID:22342082
database_cross_reference: PMID:22385337
database_cross_reference: PMID:22443779
database_cross_reference: PMID:22560242
database_cross_reference: Reaxys:3587154
database_cross_reference: Wikipedia:Ammonia
has_exact_synonym: AMMONIA
has_exact_synonym: Ammonia
has_exact_synonym: ammonia
has_exact_synonym: azane
has_obo_namespace: chebi_ontology
has_related_synonym: Ammoniak
has_related_synonym: NH3
has_related_synonym: R-717
has_related_synonym: [NH3]
has_related_synonym: ammoniac
has_related_synonym: amoniaco
has_related_synonym: spirit of hartshorn

pyridine
type: Class
subclass of: molecular entity
definition: An azaarene comprising a benzene core in which one -CH group is replaced by a nitrogen atom. It is the parent compound of the class pyridines.
imported from: chebi.owl
charge: 0
formula: C5H5N
inchi: InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H
inchikey: JUJWROOIHBZHMG-UHFFFAOYSA-N
mass: 79.09990
monoisotopicmass: 79.042
smiles: c1ccncc1
has_alternative_id: CHEBI:14974
has_alternative_id: CHEBI:26415
has_alternative_id: CHEBI:8662
database_cross_reference: Beilstein:103233
database_cross_reference: CAS:110-86-1
database_cross_reference: Gmelin:1996
database_cross_reference: HMDB:HMDB0000926
database_cross_reference: KEGG:C00747
database_cross_reference: PDBeChem:0PY
database_cross_reference: PMID:24364496
database_cross_reference: PMID:24425539
database_cross_reference: PMID:8070089
database_cross_reference: Reaxys:103233
database_cross_reference: Wikipedia:Pyridine
has_exact_synonym: Pyridine
has_exact_synonym: pyridine
has_obo_namespace: chebi_ontology
has_related_synonym: Azabenzene
has_related_synonym: py
id: CHEBI:16227
in_subset: 3 STAR

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: chebi.owl
imported from: Ontology for Biomedical Investigation

creatinine
type: Class
subclass of: molecular entity
definition: A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.
imported from: chebi.owl
charge: 0
formula: C4H7N3O
inchi: InChI=1S/C4H7N3O/c1-7-2-3(8)6-4(7)5/h2H2,1H3,(H2,5,6,8)
inchikey: DDRJAANPRJIHGJ-UHFFFAOYSA-N
mass: 113.11800
monoisotopicmass: 113.059
smiles: CN1CC(=O)NC1=N
has_alternative_id: CHEBI:14029
has_alternative_id: CHEBI:23406
has_alternative_id: CHEBI:3910
database_cross_reference: CAS:60-27-5
database_cross_reference: HMDB:HMDB0000562
database_cross_reference: KEGG:C00791
database_cross_reference: KEGG:D03600
database_cross_reference: MetaCyc:CREATININE
database_cross_reference: PMID:11256540
database_cross_reference: PMID:11981083
database_cross_reference: PMID:17190852
database_cross_reference: PMID:17422601
database_cross_reference: PMID:18182718
database_cross_reference: PMID:19236048
database_cross_reference: PMID:19715855
database_cross_reference: PMID:19968328
database_cross_reference: PMID:21775764
database_cross_reference: PMID:22047975
database_cross_reference: PMID:22121923
database_cross_reference: PMID:22166252
database_cross_reference: PMID:22207347
database_cross_reference: PMID:22212624
database_cross_reference: PMID:22223530
database_cross_reference: PMID:22331238
database_cross_reference: PMID:22338083
database_cross_reference: PMID:22349552
database_cross_reference: PMID:22390548
database_cross_reference: PMID:22432114
database_cross_reference: PMID:22441184
database_cross_reference: PMID:22459582
database_cross_reference: PMID:22498455
database_cross_reference: Reaxys:112064
database_cross_reference: Wikipedia:Creatinine
has_exact_synonym: 2-imino-1-methylimidazolidin-4-one
has_exact_synonym: Creatinine
has_exact_synonym: creatinine
has_obo_namespace: chebi_ontology
has_related_synonym: 1-Methylglycocyamidine
has_related_synonym: 1-Methylhydantoin-2-imide
has_related_synonym: 1-methylglycocyamidine
has_related_synonym: 2-Amino-1-methylimidazolin-4-one
has_related_synonym: 2-amino-1,5-dihydro-1-methyl-4H-Imidazol-4-one
has_related_synonym: Creatine anhydride
has_related_synonym: Kreatinin
has_related_synonym: creatinina
id: CHEBI:16737
in_subset: 3 STAR

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: deoxyribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl
imported from: Ontology for Biomedical Investigation
has_alternative_id: CHEBI:13302
has_alternative_id: CHEBI:21123
has_alternative_id: CHEBI:33698
has_alternative_id: CHEBI:4291
database_cross_reference: CAS:9007-49-2
database_cross_reference: KEGG:C00039
has_exact_synonym: Deoxyribonucleic acid
has_exact_synonym: deoxyribonucleic acids
has_obo_namespace: chebi_ontology
has_related_synonym: (Deoxyribonucleotide)m
has_related_synonym: (Deoxyribonucleotide)n
has_related_synonym: (Deoxyribonucleotide)n+m
has_related_synonym: DNA
has_related_synonym: DNAn
has_related_synonym: DNAn+1
has_related_synonym: DNS
has_related_synonym: Desoxyribonukleinsaeure
has_related_synonym: deoxyribonucleic acids
has_related_synonym: desoxyribose nucleic acid
has_related_synonym: thymus nucleic acid
id: CHEBI:16991
in_subset: 3 STAR

hydrogensulfite
type: Class
subclass of: molecular entity
imported from: chebi.owl
charge: -1
formula: HO3S
inchi: InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-1
inchikey: LSNNMFCWUKXFEE-UHFFFAOYSA-M
mass: 81.07214
monoisotopicmass: 80.965
smiles: OS([O-])=O
has_alternative_id: CHEBI:13367
has_alternative_id: CHEBI:5598
database_cross_reference: CAS:15181-46-1
database_cross_reference: Gmelin:1455
database_cross_reference: KEGG:C11481
database_cross_reference: PDBeChem:SO3
has_exact_synonym: hydrogen(trioxidosulfate)(1-)
has_exact_synonym: hydrogensulfite(1-)
has_exact_synonym: hydrogentrioxosulfate(1-)
has_exact_synonym: hydrogentrioxosulfate(IV)
has_exact_synonym: hydroxidodioxidosulfate(1-)
has_exact_synonym: monohydrogentrioxosulfate
has_obo_namespace: chebi_ontology
has_related_synonym: Bisulfite
has_related_synonym: HSO3(-)
has_related_synonym: HSO3-
has_related_synonym: Hydrogen sulfite
has_related_synonym: [SO2(OH)](-)
has_related_synonym: bisulfite
has_related_synonym: bisulphite
has_related_synonym: hydrogen sulfite(1-)
has_related_synonym: hydrosulfite anion
id: CHEBI:17137
in_subset: 3 STAR

lipid
type: Class
subclass of: molecular entity
definition: 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
imported from: chebi.owl
has_alternative_id: CHEBI:14517
has_alternative_id: CHEBI:25054
has_alternative_id: CHEBI:6486
database_cross_reference: KEGG:C01356
has_exact_synonym: Lipid
has_exact_synonym: lipids
has_obo_namespace: chebi_ontology
id: CHEBI:18059
in_subset: 3 STAR

chlorine atom
type: Class
subclass of: chemical entity
imported from: chebi.owl
charge: 0
formula: Cl
inchi: InChI=1S/Cl
inchikey: ZAMOUSCENKQFHK-UHFFFAOYSA-N
mass: 35.45270
monoisotopicmass: 34.969
smiles: [Cl]
database_cross_reference: WebElements:Cl
has_exact_synonym: chlorine
has_obo_namespace: chebi_ontology
has_related_synonym: 17Cl
has_related_synonym: Chlor
has_related_synonym: Cl
has_related_synonym: chlore
has_related_synonym: chlorine
has_related_synonym: chlorum
has_related_synonym: cloro
id: CHEBI:23116
in_subset: 3 STAR

molecular entity
type: Class
subclass of: chemical entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl
imported from: Ontology for Biomedical Investigation
has_exact_synonym: molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: entidad molecular
has_related_synonym: entidades moleculares
has_related_synonym: entite moleculaire
has_related_synonym: molecular entities
has_related_synonym: molekulare Entitaet
id: CHEBI:23367
in_subset: 3 STAR

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.
imported from: chebi.owl
has_exact_synonym: chemical entity
has_obo_namespace: chebi_ontology
id: CHEBI:24431
in_subset: 3 STAR

biological role
type: Class
subclass of: role
definition: A role played by the molecular entity or part thereof within a biological context.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: biological function
id: CHEBI:24432
in_subset: 3 STAR

isoprenoid
type: Class
subclass of: lipid
definition: Any lipid formally derived from isoprene (2-methylbuta-1,3-diene), the skeleton of which can generally be discerned in repeated occurrence in the molecule. The skeleton of isoprenoids may differ from strict additivity of isoprene units by loss or shift of a fragment, commonly a methyl group. The class includes both hydrocarbons and oxygenated derivatives.
imported from: chebi.owl
database_cross_reference: LIPID_MAPS_class:LMPR01
database_cross_reference: PMID:12769708
database_cross_reference: PMID:19219049
has_exact_synonym: isoprenoid
has_exact_synonym: isoprenoids
has_obo_namespace: chebi_ontology
has_related_synonym: isoprenoids
id: CHEBI:24913
in_subset: 3 STAR

metabolite
type: Class
subclass of: biochemical role
definition: Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
imported from: chebi.owl
has_alternative_id: CHEBI:26619
has_alternative_id: CHEBI:35220
has_exact_synonym: metabolite
has_obo_namespace: chebi_ontology
has_related_synonym: metabolites
has_related_synonym: primary metabolites
has_related_synonym: secondary metabolites
id: CHEBI:25212
in_subset: 3 STAR

phosphoric acid
type: Class
subclass of: molecular entity
definition: A phosphorus oxoacid that consits of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.
imported from: chebi.owl
charge: 0
formula: H3O4P
inchi: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
inchikey: NBIIXXVUZAFLBC-UHFFFAOYSA-N
mass: 97.99520
monoisotopicmass: 97.977
smiles: [H]OP(=O)(O[H])O[H]
database_cross_reference: Beilstein:1921286
database_cross_reference: CAS:7664-38-2
database_cross_reference: Drug_Central:4478
database_cross_reference: Gmelin:2000
database_cross_reference: HMDB:HMDB0002142
database_cross_reference: KEGG:C00009
database_cross_reference: KEGG:D05467
database_cross_reference: KNApSAcK:C00007408
database_cross_reference: PMID:11455380
database_cross_reference: PMID:15630224
database_cross_reference: PMID:17439666
database_cross_reference: PMID:17518491
database_cross_reference: PMID:22282755
database_cross_reference: PMID:22333268
database_cross_reference: PMID:22381614
database_cross_reference: PMID:22401268
database_cross_reference: Reaxys:1921286
database_cross_reference: Wikipedia:Phosphoric_Acid
has_exact_synonym: Phosphoric acid
has_exact_synonym: phosphoric acid
has_exact_synonym: tetraoxophosphoric acid
has_exact_synonym: trihydrogen tetraoxophosphate(3-)
has_exact_synonym: trihydroxidooxidophosphorus
has_obo_namespace: chebi_ontology
has_related_synonym: H3PO4
has_related_synonym: Orthophosphoric acid
has_related_synonym: Phosphate
has_related_synonym: Phosphorsaeure
has_related_synonym: Phosphorsaeureloesungen
has_related_synonym: [PO(OH)3]
has_related_synonym: acide phosphorique
has_related_synonym: acidum phosphoricum
has_related_synonym: orthophosphoric acid
id: CHEBI:26078
in_subset: 3 STAR

phosphorus atom
type: Class
subclass of: chemical entity
imported from: chebi.owl
charge: 0
formula: P
inchi: InChI=1S/P
inchikey: OAICVXFJPJFONN-UHFFFAOYSA-N
mass: 30.97376
monoisotopicmass: 30.974
smiles: [P]
has_alternative_id: CHEBI:26080
has_alternative_id: CHEBI:8168
database_cross_reference: CAS:7723-14-0
database_cross_reference: Gmelin:16235
database_cross_reference: KEGG:C06262
database_cross_reference: WebElements:P
has_exact_synonym: phosphorus
has_obo_namespace: chebi_ontology
has_related_synonym: 15P
has_related_synonym: P
has_related_synonym: Phosphor
has_related_synonym: Phosphorus
has_related_synonym: fosforo
has_related_synonym: phosphore
has_related_synonym: phosphorus
id: CHEBI:28659
in_subset: 3 STAR

protium atom
type: Class
subclass of: molecular entity
definition: The stable isotope of hydrogen with relative atomic mass 1.007825 and a natural abundance of 99.9885 atom percent (from Greek pirhoomegatauomicronsigma, first).
imported from: chebi.owl
charge: 0
formula: H
inchi: InChI=1S/H/i1+0
inchikey: YZCKVEUIGOORGS-IGMARMGPSA-N
mass: 1.00783
monoisotopicmass: 1.008
smiles: [1H]
has_exact_synonym: protium
has_obo_namespace: chebi_ontology
has_related_synonym: (1)1H
has_related_synonym: (1)H
has_related_synonym: hydrogen-1
has_related_synonym: protio
has_related_synonym: protium
id: CHEBI:29236
in_subset: 3 STAR

deuterium atom
type: Class
subclass of: molecular entity
definition: The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second).
imported from: chebi.owl
charge: 0
formula: D
inchi: InChI=1S/H2/h1H/i1+1
inchikey: UFHFLCQGNIYNRP-OUBTZVSYSA-N
mass: 2.01410
smiles: [2H]
has_exact_synonym: deuterium
has_obo_namespace: chebi_ontology
has_related_synonym: (2)1H
has_related_synonym: (2)H
has_related_synonym: D
has_related_synonym: Deuterium
has_related_synonym: deuterio
has_related_synonym: deuterium
has_related_synonym: heavy hydrogen
has_related_synonym: hidrogeno pesado
has_related_synonym: hydrogen-2
has_related_synonym: schwerer Wasserstoff
id: CHEBI:29237
in_subset: 3 STAR

sodium acetate
type: Class
subclass of: molecular entity
imported from: chebi.owl
charge: 0
formula: C2H3NaO2
inchi: InChI=1S/C2H4O2.Na/c1-2(3)4;/h1H3,(H,3,4);/q;+1/p-1
inchikey: VMHLLURERBWHNL-UHFFFAOYSA-M
mass: 82.03379
monoisotopicmass: 82.003
smiles: [Na+].CC([O-])=O
database_cross_reference: Beilstein:3595639
database_cross_reference: CAS:127-09-3
database_cross_reference: Gmelin:20502
database_cross_reference: Wikipedia:Sodium_Acetate
has_exact_synonym: sodium acetate
has_obo_namespace: chebi_ontology
has_related_synonym: Natriumazetat
has_related_synonym: acetic acid, sodium salt
has_related_synonym: anhydrous sodium acetate
has_related_synonym: sodium acetate anhydrous
id: CHEBI:32954
in_subset: 3 STAR

atom
type: Class
subclass of: material entity
editor preferred label: atom
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
imported from: chebi.owl
imported from: Ontology for Biomedical Investigation

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl
imported from: Ontology for Biomedical Investigation
has_exact_synonym: nucleic acids
has_obo_namespace: chebi_ontology
has_related_synonym: NA
has_related_synonym: Nukleinsaeure
has_related_synonym: Nukleinsaeuren
has_related_synonym: acide nucleique
has_related_synonym: acides nucleiques
has_related_synonym: acido nucleico
has_related_synonym: acidos nucleicos
id: CHEBI:33696
in_subset: 3 STAR

ribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: ribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
imported from: chebi.owl
imported from: Ontology for Biomedical Investigation

oxygen-17 atom
type: Class
subclass of: chemical entity
definition: The stable isotope of oxygen with relative atomic mass 16.999131. The least abundant (0.038 atom percent) isotope of naturally occurring oxygen.
imported from: chebi.owl
charge: 0
formula: O
inchi: InChI=1S/O/i1+1
inchikey: QVGXLLKOCUKJST-OUBTZVSYSA-N
mass: 16.99913
monoisotopicmass: 15.995
smiles: [17O]
database_cross_reference: CAS:13968-48-4
database_cross_reference: Gmelin:17561
has_exact_synonym: oxygen-17
has_obo_namespace: chebi_ontology
has_related_synonym: (17)8O
has_related_synonym: (17)O
has_related_synonym: oxygen, isotope of mass 17
has_related_synonym: oxygen-17
id: CHEBI:33819
in_subset: 3 STAR

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative term: polymer
imported from: chebi.owl
imported from: Ontology for Biomedical Investigation

morpholine
type: Class
subclass of: molecular entity
imported from: chebi.owl
charge: 0
formula: C4H9NO
inchi: InChI=1S/C4H9NO/c1-3-6-4-2-5-1/h5H,1-4H2
inchikey: YNAVUWVOSKDBBP-UHFFFAOYSA-N
mass: 87.12040
monoisotopicmass: 87.068
smiles: C1COCCN1
database_cross_reference: Beilstein:102549
database_cross_reference: CAS:110-91-8
database_cross_reference: Gmelin:1803
database_cross_reference: KEGG:C14452
has_exact_synonym: Morpholine
has_exact_synonym: morpholine
has_obo_namespace: chebi_ontology
has_related_synonym: Tetrahydro-1,4-oxazine
id: CHEBI:34856
in_subset: 3 STAR

chloroform
type: Class
subclass of: molecular entity
definition: A one-carbon compound that is methane in which three of the hydrogens are replaced by chlorines.
imported from: chebi.owl
charge: 0
formula: CHCl3
inchi: InChI=1S/CHCl3/c2-1(3)4/h1H
inchikey: HEDRZPFGACZZDS-UHFFFAOYSA-N
mass: 119.37674
monoisotopicmass: 117.914
smiles: [H]C(Cl)(Cl)Cl
has_alternative_id: CHEBI:23143
has_alternative_id: CHEBI:34628
database_cross_reference: Beilstein:1731042
database_cross_reference: CAS:67-66-3
database_cross_reference: Drug_Central:4363
database_cross_reference: Gmelin:1837
database_cross_reference: HMDB:HMDB0029596
database_cross_reference: KEGG:C13827
database_cross_reference: LINCS:LSM-37229
database_cross_reference: MetaCyc:CPD-843
database_cross_reference: PDBeChem:MCH
database_cross_reference: PMID:10379014
database_cross_reference: PMID:15583552
database_cross_reference: PMID:20051454
database_cross_reference: PMID:21850127
database_cross_reference: PMID:23093177
database_cross_reference: PMID:8476536
database_cross_reference: PMID:8625290
database_cross_reference: Reaxys:1731042
database_cross_reference: UM-BBD_compID:c0595
database_cross_reference: Wikipedia:Chloroform
has_exact_synonym: Chloroform
has_exact_synonym: chloroform
has_obo_namespace: chebi_ontology
has_related_synonym: 1,1,1-trichloromethane
has_related_synonym: CHCl3
has_related_synonym: Trichlormethan
has_related_synonym: chloroforme
has_related_synonym: chloroformium pro narcosi
has_related_synonym: trichloromethane
id: CHEBI:35255
in_subset: 3 STAR

tetraphosphorus
type: Class
subclass of: molecular entity
imported from: chebi.owl
charge: 0
formula: P4
inchi: InChI=1S/P4/c1-2-3(1)4(1)2
inchikey: OBSZRRSYVTXPNB-UHFFFAOYSA-N
mass: 123.89505
monoisotopicmass: 123.895
smiles: p12p3p1p23
database_cross_reference: CAS:12185-10-3
database_cross_reference: Gmelin:1856
database_cross_reference: Gmelin:25827
has_exact_synonym: [Td-(13)-Delta(4)-closo]tetraphosphorus
has_exact_synonym: tetrahedro-tetraphosphorus
has_exact_synonym: tetraphosphorus
has_obo_namespace: chebi_ontology
has_related_synonym: P4
has_related_synonym: molecular phosphorus
has_related_synonym: phosphorus
has_related_synonym: phosphorus tetraatomic molecule
has_related_synonym: phosphorus tetramer
has_related_synonym: tetraatomic phosphorus
has_related_synonym: tetrameric phosphorus
has_related_synonym: white phosphorus
id: CHEBI:35895
in_subset: 3 STAR

triphenylphosphane oxide
type: Class
subclass of: molecular entity
definition: A phosphine oxide in which the substituents on phosphorus are three phenyl groups.
imported from: chebi.owl
charge: 0
formula: C18H15OP
inchi: InChI=1S/C18H15OP/c19-20(16-10-4-1-5-11-16,17-12-6-2-7-13-17)18-14-8-3-9-15-18/h1-15H
inchikey: FIQMHBFVRAXMOP-UHFFFAOYSA-N
mass: 278.28486
monoisotopicmass: 278.086
smiles: O=P(c1ccccc1)(c1ccccc1)c1ccccc1
database_cross_reference: Beilstein:745854
database_cross_reference: CAS:791-28-6
database_cross_reference: Gmelin:6758
database_cross_reference: PMID:24280613
database_cross_reference: PMID:24285309
database_cross_reference: Reaxys:745854
database_cross_reference: Wikipedia:Triphenylphosphine_oxide
has_exact_synonym: triphenyl-lambda(5)-phosphanone
has_exact_synonym: triphenylphosphane oxide
has_obo_namespace: chebi_ontology
has_related_synonym: Triphenylphosphanoxid
has_related_synonym: triphenyl phosphine oxide
has_related_synonym: triphenyl phosphorus oxide
has_related_synonym: triphenylphosphanoxide
has_related_synonym: triphenylphosphine oxide
id: CHEBI:36601
in_subset: 3 STAR

carbon-13 atom
type: Class
subclass of: chemical entity
imported from: chebi.owl
charge: 0
formula: C
inchi: InChI=1S/C/i1+1
inchikey: OKTJSMMVPCPJKN-OUBTZVSYSA-N
mass: 13.00335
monoisotopicmass: 12.000
smiles: [13C]
database_cross_reference: CAS:14762-74-4
has_exact_synonym: carbon-13
has_exact_synonym: carbon-13 atom
has_obo_namespace: chebi_ontology
has_related_synonym: (13)6C
has_related_synonym: (13)C
has_related_synonym: carbon, isotope of mass 13
has_related_synonym: carbon-13
id: CHEBI:36928
in_subset: 3 STAR

carbon-12 atom
type: Class
subclass of: chemical entity
imported from: chebi.owl
charge: 0
formula: C
inchi: InChI=1S/C/i1+0
inchikey: OKTJSMMVPCPJKN-IGMARMGPSA-N
mass: 12.00000
monoisotopicmass: 12.000
smiles: [12C]
has_exact_synonym: carbon-12
has_obo_namespace: chebi_ontology
has_related_synonym: (12)6C
has_related_synonym: (12)C
has_related_synonym: carbon-12
id: CHEBI:36931
in_subset: 3 STAR

nitrogen-15 atom
type: Class
subclass of: chemical entity
definition: The stable isotope of nitrogen with relative atomic mass 15.000109. The least abundant (0.368 atom percent) isotope of naturally occurring nitrogen.
imported from: chebi.owl
formula: N
database_cross_reference: CAS:14390-96-6
has_exact_synonym: nitrogen-15
has_obo_namespace: chebi_ontology
has_related_synonym: (15)7N
has_related_synonym: (15)N
has_related_synonym: nitrogen, isotope of mass 15
has_related_synonym: nitrogen-15
id: CHEBI:36934
in_subset: 3 STAR

nitrogen-14 atom
type: Class
subclass of: chemical entity
definition: The stable isotope of nitrogen with relative atomic mass 14.003074. The most abundant (99.63 atom percent) isotope of naturally occurring nitrogen.
imported from: chebi.owl
formula: N
has_exact_synonym: nitrogen-14
has_obo_namespace: chebi_ontology
has_related_synonym: (14)7N
has_related_synonym: (14)N
has_related_synonym: nitrogen-14
id: CHEBI:36938
in_subset: 3 STAR

fluorine-19 atom
type: Class
subclass of: chemical entity
definition: The stable isotope of fluorine with relative atomic mass 18.998403 and nuclear spin (1)/2.
imported from: chebi.owl
charge: 0
formula: F
inchi: InChI=1S/F/i1+0
inchikey: YCKRFDGAMUMZLT-IGMARMGPSA-N
mass: 18.99840
monoisotopicmass: 18.998
smiles: [19F]
has_exact_synonym: fluorine-19
has_obo_namespace: chebi_ontology
has_related_synonym: (19)9F
has_related_synonym: (19)F
has_related_synonym: fluorine-19
id: CHEBI:36940
in_subset: 3 STAR

aluminium-27 atom
type: Class
subclass of: chemical entity
definition: The stable isotope of aluminium with relative atomic mass 26.98153 and nuclear spin (5)/2.
imported from: chebi.owl
charge: 0
formula: Al
inchi: InChI=1S/Al/i1+0
inchikey: XAGFODPZIPBFFR-IGMARMGPSA-N
mass: 26.98154
monoisotopicmass: 26.982
smiles: [27Al]
has_exact_synonym: aluminium-27
has_obo_namespace: chebi_ontology
has_related_synonym: (27)13Al
has_related_synonym: (27)Al
has_related_synonym: aluminium-27
has_related_synonym: aluminum, isotope of mass 27
has_related_synonym: aluminum-27
id: CHEBI:37968
in_subset: 3 STAR

phosphorus-31 atom
type: Class
subclass of: phosphorus atom
definition: The stable isotope of phosphorus with relative atomic mass 30.973762 and nuclear spin (1)/2.
imported from: chebi.owl
charge: 0
formula: P
inchi: InChI=1S/P/i1+0
inchikey: OAICVXFJPJFONN-IGMARMGPSA-N
mass: 30.97376
monoisotopicmass: 30.974
smiles: [31P]
has_exact_synonym: phosphorus-31
has_obo_namespace: chebi_ontology
has_related_synonym: (31)15P
has_related_synonym: (31)P
has_related_synonym: phosphorus-31
id: CHEBI:37971
in_subset: 3 STAR

silicon-29 atom
type: Class
subclass of: chemical entity
definition: The stable isotope of silicon with relative atomic mass 28.9764947, 4.683 atom percent natural abundancy, and nuclear spin (1)/2.
imported from: chebi.owl
charge: 0
formula: Si
inchi: InChI=1S/Si/i1+1
inchikey: XUIMIQQOPSSXEZ-OUBTZVSYSA-N
mass: 28.97649
monoisotopicmass: 27.977
smiles: [29Si]
has_exact_synonym: silicon-29
has_obo_namespace: chebi_ontology
has_related_synonym: (29)14Si
has_related_synonym: (29)Si
has_related_synonym: silicon-29
id: CHEBI:37974
in_subset: 3 STAR

acetonitrile
type: Class
subclass of: molecular entity
definition: A nitrile that is hydrogen cyanide in which the hydrogen has been replaced by a methyl group.
imported from: chebi.owl
charge: 0
formula: C2H3N
inchi: InChI=1S/C2H3N/c1-2-3/h1H3
inchikey: WEVYAHXRMPXWCK-UHFFFAOYSA-N
mass: 41.05196
monoisotopicmass: 41.027
smiles: CC#N
has_alternative_id: CHEBI:22185
has_alternative_id: CHEBI:30972
has_alternative_id: CHEBI:41432
database_cross_reference: Beilstein:741857
database_cross_reference: CAS:75-05-8
database_cross_reference: Gmelin:895
database_cross_reference: PDBeChem:CCN
database_cross_reference: PMID:17347819
database_cross_reference: PMID:19100763
database_cross_reference: PMID:20370615
database_cross_reference: PMID:985423
database_cross_reference: Reaxys:741857
database_cross_reference: Wikipedia:Acetonitrile
has_exact_synonym: ACETONITRILE
has_exact_synonym: acetonitrile
has_obo_namespace: chebi_ontology
has_related_synonym: CH3-C#N
has_related_synonym: MeCN
has_related_synonym: NCMe
has_related_synonym: cyanomethane
has_related_synonym: ethanenitrile
has_related_synonym: methyl cyanide
id: CHEBI:38472
in_subset: 3 STAR

hexafluorobenzene
type: Class
subclass of: molecular entity
definition: A member of the class of fluorobenzenes that is benzene in which all six hydrogen atom have been replaced by fluorine.
imported from: chebi.owl
charge: 0
formula: C6F6
inchi: InChI=1S/C6F6/c7-1-2(8)4(10)6(12)5(11)3(1)9
inchikey: ZQBFAOFFOQMSGJ-UHFFFAOYSA-N
mass: 186.05462
monoisotopicmass: 185.990
smiles: Fc1c(F)c(F)c(F)c(F)c1F
database_cross_reference: Beilstein:1683438
database_cross_reference: CAS:392-56-3
database_cross_reference: Gmelin:101976
has_exact_synonym: hexafluorobenzene
has_obo_namespace: chebi_ontology
has_related_synonym: 1,2,3,4,5,6-hexafluorobenzene
has_related_synonym: Hexafluorbenzol
has_related_synonym: perfluorobenzene
id: CHEBI:38589
in_subset: 3 STAR

dideuterium oxide
type: Class
subclass of: water
imported from: chebi.owl
charge: 0
formula: D2O
inchi: InChI=1S/H2O/h1H2/i/hD2
inchikey: XLYOFNOQVPJJNP-ZSJDYOACSA-N
mass: 20.02760
smiles: [2H]O[2H]
has_alternative_id: CHEBI:29373
has_alternative_id: CHEBI:41979
database_cross_reference: CAS:7789-20-0
database_cross_reference: Gmelin:97
database_cross_reference: MolBase:1647
database_cross_reference: PDBeChem:DOD
has_exact_synonym: dideuterium oxide
has_obo_namespace: chebi_ontology
has_related_synonym: ((2)H2)water
has_related_synonym: D2O
has_related_synonym: DEUTERATED WATER
has_related_synonym: Deuteriumoxid
has_related_synonym: [OD2]
has_related_synonym: deuterium oxide
has_related_synonym: heavy water
has_related_synonym: schweres Wasser
id: CHEBI:41981
in_subset: 3 STAR

trimethyl phosphate
type: Class
subclass of: molecular entity
definition: A trialkyl phosphate that is the trimethyl ester of phosphoric acid.
imported from: chebi.owl
charge: 0
formula: C3H9O4P
inchi: InChI=1S/C3H9O4P/c1-5-8(4,6-2)7-3/h1-3H3
inchikey: WVLBCYQITXONBZ-UHFFFAOYSA-N
mass: 140.07492
monoisotopicmass: 140.024
smiles: COP(=O)(OC)OC
database_cross_reference: Beilstein:1071731
database_cross_reference: CAS:512-56-1
database_cross_reference: Gmelin:49926
database_cross_reference: PDBeChem:TZZ
database_cross_reference: PMID:17083219
database_cross_reference: PMID:18409209
database_cross_reference: Reaxys:1071731
database_cross_reference: Wikipedia:Trimethyl_phosphate
has_exact_synonym: TRIMETHYL PHOSPHATE
has_exact_synonym: trimethyl phosphate
has_obo_namespace: chebi_ontology
has_related_synonym: O,O,O-Trimethyl phosphate
has_related_synonym: Phosphoric acid, trimethyl ester
has_related_synonym: TMP
has_related_synonym: TMPA
has_related_synonym: TMPO
has_related_synonym: Trimethoxyphosphine oxide
has_related_synonym: Trimethyl orthophosphate
id: CHEBI:46324
in_subset: 3 STAR

1,4-dioxane
type: Class
subclass of: molecular entity
definition: A dioxane with oxygen atoms at positions 1 and 4.
imported from: chebi.owl
charge: 0
formula: C4H8O2
inchi: InChI=1S/C4H8O2/c1-2-6-4-3-5-1/h1-4H2
inchikey: RYHBNJHYFVUHQT-UHFFFAOYSA-N
mass: 88.10512
monoisotopicmass: 88.052
smiles: C1COCCO1
has_alternative_id: CHEBI:34064
has_alternative_id: CHEBI:41951
has_alternative_id: CHEBI:46925
database_cross_reference: Beilstein:102551
database_cross_reference: CAS:123-91-1
database_cross_reference: DrugBank:DB03316
database_cross_reference: KEGG:C14440
database_cross_reference: LINCS:LSM-37087
database_cross_reference: PDBeChem:DIO
database_cross_reference: PMID:14550759
database_cross_reference: PMID:18044507
database_cross_reference: PMID:20598439
database_cross_reference: Reaxys:102551
database_cross_reference: Wikipedia:1,4-Dioxane
has_exact_synonym: 1,4-Dioxane
has_exact_synonym: 1,4-dioxane
has_obo_namespace: chebi_ontology
has_related_synonym: 1,4-DIETHYLENE DIOXIDE
has_related_synonym: 1,4-Dioxan
has_related_synonym: 1,4-dioxacyclohexane
has_related_synonym: Dioxan-1,4
has_related_synonym: di(ethylene oxide)
has_related_synonym: dioxane-1,4
has_related_synonym: glycol ethylene ether
has_related_synonym: p-Dioxane
has_related_synonym: tetrahydro-1,4-dioxin
has_related_synonym: tetrahydro-p-dioxin
has_related_synonym: tetrahydro-para-dioxin
id: CHEBI:47032
in_subset: 3 STAR

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acid
imported from: chebi.owl
formula: C10H17O8PR2(C5H8O5PR)n.C10H17O7PR2(C5H8O6PR)n
database_cross_reference: KEGG:C00434
has_exact_synonym: Double-stranded DNA
has_obo_namespace: chebi_ontology
id: CHEBI:4705
in_subset: 3 STAR

biochemical role
type: Class
subclass of: biological role
definition: A biological role played by the molecular entity or part thereof within a biochemical context.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:52206
in_subset: 3 STAR

boron-11
type: Class
subclass of: chemical entity
definition: The stable isotope of boron with relative atomic mass 11.009306, 80.1 atom percent natural abundance and nuclear spin 3/2.
imported from: chebi.owl
charge: 0
formula: B
inchi: InChI=1S/B/i1+0
inchikey: ZOXJGFHDIHLPTG-IGMARMGPSA-N
mass: 11.00931
monoisotopicmass: 11.009
smiles: [11B]
has_exact_synonym: boron-11
has_obo_namespace: chebi_ontology
has_related_synonym: (11)5B
has_related_synonym: (11)B
id: CHEBI:52451
in_subset: 3 STAR

sodium-23 atom
type: Class
subclass of: chemical entity
definition: The stable isotope of sodium with relative atomic mass 22.989770, 100 atom percent natural abundance and nuclear spin 3/2.
imported from: chebi.owl
charge: 0
formula: Na
inchi: InChI=1S/Na/i1+0
inchikey: KEAYESYHFKHZAL-IGMARMGPSA-N
mass: 22.98977
monoisotopicmass: 22.990
smiles: [23Na]
has_exact_synonym: sodium-23
has_obo_namespace: chebi_ontology
has_related_synonym: (23)11Na
has_related_synonym: (23)Na
has_related_synonym: sodium-23
id: CHEBI:52634
in_subset: 3 STAR

tetramethylammonium bromide
type: Class
subclass of: molecular entity
definition: The bromide salt of tetramethylammonium.
imported from: chebi.owl
charge: 0
formula: C4H12BrN
inchi: InChI=1S/C4H12N.BrH/c1-5(2,3)4;/h1-4H3;1H/q+1;/p-1
inchikey: DDFYFBUWEBINLX-UHFFFAOYSA-M
mass: 154.04900
monoisotopicmass: 153.015
smiles: [Br-].C[N+](C)(C)C
database_cross_reference: CAS:64-20-0
database_cross_reference: PMID:24804652
database_cross_reference: PMID:6196640
database_cross_reference: Reaxys:3620955
has_exact_synonym: N,N,N-trimethylmethanaminium bromide
has_obo_namespace: chebi_ontology
has_related_synonym: TMAB
id: CHEBI:55317
in_subset: 3 STAR

hexachlorobenzene
type: Class
subclass of: molecular entity
definition: A member of the class of chlorobenzenes that is benzene in which all of the hydrogens are replaced by chlorines. An agricultural fungicide introduced in the mid-1940s and formerly used as a seed treatment, its use has been banned since 1984 under the Stockholm Convention on Persistent Organic Pollutants.
imported from: chebi.owl
charge: 0
formula: C6Cl6
inchi: InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9
inchikey: CKAPSXZOOQJIBF-UHFFFAOYSA-N
mass: 284.78040
monoisotopicmass: 281.813
smiles: Clc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl
database_cross_reference: Beilstein:1912585
database_cross_reference: CAS:118-74-1
database_cross_reference: Gmelin:27278
database_cross_reference: HMDB:HMDB0032566
database_cross_reference: KEGG:C11042
database_cross_reference: PMID:10641019
database_cross_reference: PMID:12117784
database_cross_reference: PMID:17150971
database_cross_reference: PMID:23336922
database_cross_reference: PMID:23462309
database_cross_reference: PMID:23627767
database_cross_reference: PMID:23747559
database_cross_reference: PMID:23923419
database_cross_reference: PMID:23973543
database_cross_reference: PMID:24148401
database_cross_reference: PMID:24311623
database_cross_reference: PMID:24365113
database_cross_reference: Reaxys:1912585
database_cross_reference: Wikipedia:Hexachlorobenzene
has_exact_synonym: Hexachlorobenzene
has_exact_synonym: hexachlorobenzene
has_obo_namespace: chebi_ontology
has_related_synonym: 1,2,3,4,5,6-hexachlorobenzene
has_related_synonym: HCB
has_related_synonym: Hexachlorbenzol
has_related_synonym: perchlorobenzene
has_related_synonym: phenyl perchloryl
id: CHEBI:5692
in_subset: 3 STAR

sodium nitrate
type: Class
subclass of: molecular entity
definition: The inorganic nitrate salt of sodium.
imported from: chebi.owl
charge: 0
formula: NNaO3
inchi: InChI=1S/NO3.Na/c2-1(3)4;/q-1;+1
inchikey: VWDWKYIASSYTQR-UHFFFAOYSA-N
mass: 84.99470
monoisotopicmass: 84.978
smiles: [Na+].[O-][N+]([O-])=O
database_cross_reference: CAS:7631-99-4
database_cross_reference: Reaxys:11343077
database_cross_reference: Wikipedia:Sodium_nitrate
has_exact_synonym: sodium nitrate
has_exact_synonym: sodium trioxidonitrate(1-)
has_obo_namespace: chebi_ontology
has_related_synonym: Chile saltpeter
has_related_synonym: Cubic niter
has_related_synonym: Niter
has_related_synonym: Nitrate de sodium
has_related_synonym: Nitrate of soda
has_related_synonym: Nitric acid monosodium salt
has_related_synonym: Nitric acid sodium salt (1:1)
has_related_synonym: Nitric acid, sodium salt
has_related_synonym: Sodium saltpeter
has_related_synonym: Sodium(I) nitrate (1:1)
id: CHEBI:63005
in_subset: 3 STAR

flavonoids
type: Class
subclass of: molecular entity
definition: Any organic molecular entity whose stucture is based on derivatives of a phenyl-substituted 1-phenylpropane possessing a C15 or C16 skeleton, or such a structure which is condensed with a C6-C3 lignan precursors. The term is a 'superclass' comprising all members of the classes of flavonoid, isoflavonoid, neoflavonoid, chalcones, dihydrochalcones, aurones, pterocarpan, coumestans, rotenoid, flavonolignan, homoflavonoid and flavonoid oligomers. Originally restricted to natural products, the term is also applied to synthetic compounds related to them.
imported from: chebi.owl
database_cross_reference: Wikipedia:Flavonoids
has_obo_namespace: chebi_ontology
has_related_synonym: flavonoid
id: CHEBI:72544
in_subset: 3 STAR

nitromethane
type: Class
subclass of: molecular entity
definition: A primary nitroalkane that is methane in which one of the hydrogens is replace by a nitro group. A polar solvent (b.p. 101 degreeC), it is an important starting material in organic synthesis. It is also used as a fuel for rockets and radio-controlled models.
imported from: chebi.owl
charge: 0
formula: CH3NO2
inchi: InChI=1S/CH3NO2/c1-2(3)4/h1H3
inchikey: LYGJENNIWJXYER-UHFFFAOYSA-N
mass: 61.04000
monoisotopicmass: 61.016
smiles: C[N+]([O-])=O
database_cross_reference: CAS:75-52-5
database_cross_reference: KEGG:C19275
database_cross_reference: MetaCyc:CPD-8133
database_cross_reference: PMID:11100413
database_cross_reference: PMID:21860501
database_cross_reference: PMID:26735907
database_cross_reference: PMID:26800205
database_cross_reference: PMID:4207867
database_cross_reference: PMID:999282
database_cross_reference: Reaxys:1698205
database_cross_reference: Wikipedia:Nitromethane
has_exact_synonym: nitromethane
has_obo_namespace: chebi_ontology
has_related_synonym: CH3NO2
has_related_synonym: MeNO2
id: CHEBI:77701
in_subset: 3 STAR

N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide
type: Class
subclass of: derivatization agent
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: methylation
    union of: silylation
subclass of: Restriction
  on property: has role
  some values from: derivatization agent role
definition: An N-silyl compound that is N-methyltrifluoroacetamide in which the amide nitrogen is replaced by a tert-butyldimethylsilyl group.
imported from: chebi.owl
charge: 0
formula: C9H18F3NOSi
inchi: InChI=1S/C9H18F3NOSi/c1-8(2,3)15(5,6)13(4)7(14)9(10,11)12/h1-6H3
inchikey: QRKUHYFDBWGLHJ-UHFFFAOYSA-N
mass: 241.32600
monoisotopicmass: 241.111
smiles: CN(C(=O)C(F)(F)F)[Si](C)(C)C(C)(C)C
database_cross_reference: CAS:77377-52-7
database_cross_reference: Reaxys:3606546
has_exact_synonym: N-[tert-butyl(dimethyl)silyl]-2,2,2-trifluoro-N-methylacetamide
has_obo_namespace: chebi_ontology
has_related_synonym: N-(t-butyldimethylsilyl)-N-methyltrifluoroacetamide
has_related_synonym: N-methyl-N-(t-butyldimethylsilyl)trifluoroacetamide
has_related_synonym: N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide
id: CHEBI:85060
in_subset: 3 STAR

spectroscopy
type: Class
subclass of: assay
definition: The study of the interaction of a sample with radiation or particles for measurement or detection.
imported from: chmo.owl
has_exact_synonym: spectrometry
id: CHMO:0000228

mass spectrometry
type: Class
subclass of: spectroscopy
definition: Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.
imported from: chmo.owl
has_exact_synonym: MS
has_exact_synonym: mass spectroscopy
id: CHMO:0000470

gas chromatography-mass spectrometry
type: Class
subclass of: mass spectrometry
definition: Any method where a sample mixture is first separated by gas chromatography then ionised and characterised according to mass-to-charge ratio and relative abundance.
imported from: chmo.owl
has_alternative_id: FIX:0000921
has_exact_synonym: GC MS
has_exact_synonym: GC-MS
has_exact_synonym: GC/MS
has_exact_synonym: GCMS
has_exact_synonym: gas chromatography mass spectrometry
has_exact_synonym: gas chromatography mass spectroscopy
has_exact_synonym: gas chromatography with mass spectrometric detection
has_exact_synonym: gas chromatography-mass spectroscopy
has_exact_synonym: gas chromatography/mass spectrometry
id: CHMO:0000497

isotope ratio mass spectrometry
type: Class
subclass of: mass spectrometry
definition: Mass spectrometry where the relative abundance of isotopes in a sample is determined.
imported from: chmo.owl
has_exact_synonym: IR MS
has_exact_synonym: IR-MS
has_exact_synonym: IRMS
has_exact_synonym: isotope ratio mass spectroscopy
has_exact_synonym: isotope-ratio mass spectrometry
has_exact_synonym: isotopic ratios mass spectrometry
has_exact_synonym: isotopic ratios mass spectroscopy
id: CHMO:0000506

stable isotope ratio mass spectrometry
type: Class
subclass of: isotope ratio mass spectrometry
definition: Mass spectrometry where the relative abundance of non-radioactive isotopes in a sample is determined.
imported from: chmo.owl
has_exact_synonym: S-IRMS
has_exact_synonym: SIRMS
has_exact_synonym: stable isotope ratio mass spectroscopy
id: CHMO:0000514

liquid chromatography-mass spectrometry
type: Class
subclass of: mass spectrometry
definition: A method where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterised by their mass-to-charge ratio and relative abundance.
imported from: chmo.owl
has_alternative_id: FIX:0000924
has_exact_synonym: LC MS
has_exact_synonym: LC-MS
has_exact_synonym: LC/MS
has_exact_synonym: LCMS
has_exact_synonym: iquid chromatography/mass spectrometry
has_exact_synonym: liquid chromatography mass spectrometry
id: CHMO:0000524

selective ion monitoring
type: Class
subclass of: mass spectrometry
definition: Mass spectrometry where the intensities of one or more specific ion beams are recorded rather than the entire mass spectrum.
imported from: chmo.owl
has_exact_synonym: SIM
has_exact_synonym: selected ion monitoring
has_exact_synonym: selected-ion monitoring
has_exact_synonym: selective-ion monitoring
id: CHMO:0000571

tandem mass spectrometry
type: Class
subclass of: mass spectrometry
definition: Mass spectrometry involving multiple mass-selection steps, with some form of fragmentation occurring between each stage.
imported from: chmo.owl
has_exact_synonym: MS-MS
has_exact_synonym: MS/MS
has_exact_synonym: MS2
has_exact_synonym: double mass spectrometry
has_exact_synonym: tandem MS
has_exact_synonym: tandem mass spectroscopy
has_exact_synonym: tandem-MS
id: CHMO:0000575

nuclear magnetic resonance spectroscopy
type: Class
subclass of: nuclear magnetic resonance method
definition: Spectroscopy where the energy states of spin-active nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation.
imported from: chmo.owl
has_exact_synonym: NMR
has_exact_synonym: NMR spectrometry
has_exact_synonym: NMR spectroscopy
has_exact_synonym: nuclear magnetic resonance (NMR) spectroscopy
has_exact_synonym: nuclear magnetic resonance spectrometry
id: CHMO:0000591

one-dimensional nuclear magnetic resonance spectroscopy
type: Class
subclass of: pulsed nuclear magnetic resonance spectroscopy
definition: Spectroscopy where the energy states of spin-active nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them, and the spectrum is obtained by plotting chemical shift vs. frequency.
imported from: chmo.owl
has_exact_synonym: 1-D NMR
has_exact_synonym: 1D NMR
has_exact_synonym: 1D NMR spectrometry
has_exact_synonym: 1D NMR spectroscopy
has_exact_synonym: 1D nuclear magnetic resonance spectrometry
has_exact_synonym: 1D nuclear magnetic resonance spectroscopy
has_exact_synonym: one-dimensional nuclear magnetic resonance spectrometry
has_exact_synonym: one-dimensional nuclear magnetic resonance spectroscopy
id: CHMO:0000592

1H nuclear magnetic resonance spectroscopy
type: Class
subclass of: pulsed nuclear magnetic resonance spectroscopy
definition: Spectroscopy where the energy states of 1H nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them.
imported from: chmo.owl
has_exact_synonym: 1H NMR
has_exact_synonym: 1H NMR spectroscopy
has_exact_synonym: 1H nuclear magnetic resonance spectrometry
has_exact_synonym: 1H-NMR
has_exact_synonym: 1H-NMR spectrometry
has_exact_synonym: 1H-NMR spectroscopy
has_exact_synonym: proton NMR
has_exact_synonym: proton nuclear magnetic resonance spectroscopy
id: CHMO:0000593

13C nuclear magnetic resonance spectroscopy
type: Class
subclass of: pulsed nuclear magnetic resonance spectroscopy
definition: Spectroscopy where the energy states of 13C nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them.
imported from: chmo.owl
has_exact_synonym: 13C NMR
has_exact_synonym: 13C NMR spectroscopy
has_exact_synonym: 13C nuclear magnetic resonance spectrometry
has_exact_synonym: 13C-NMR spectrometry
has_exact_synonym: 13C-NMR spectroscopy
has_exact_synonym: C-NMR
has_exact_synonym: carbon NMR
id: CHMO:0000595

two-dimensional nuclear magnetic resonance spectroscopy
type: Class
subclass of: pulsed nuclear magnetic resonance spectroscopy
definition: An NMR experiment in which a second frequency dimension is employed to disperse the signals and reveal correlations between interacting nuclei.
imported from: chmo.owl
has_exact_synonym: 2-D NMR
has_exact_synonym: 2D NMR
has_exact_synonym: 2D NMR spectrometry
has_exact_synonym: 2D NMR spectroscopy
has_exact_synonym: 2D nuclear magnetic resonance
has_exact_synonym: 2D nuclear magnetic resonance spectrometry
has_exact_synonym: two-dimensional NMR
has_exact_synonym: two-dimensional nuclear magnetic resonance spectrometry
has_exact_synonym: two-dimensional nuclear magnetic resonance spectroscopy
id: CHMO:0000598

correlation spectroscopy
type: Class
subclass of: two-dimensional nuclear magnetic resonance spectroscopy
definition: A type of homonuclear NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between nuclei which are J-coupled (usually \leq 3 bonds apart).
imported from: chmo.owl
has_exact_synonym: COSY
has_exact_synonym: correlated spectrometry
has_exact_synonym: correlated spectroscopy
has_exact_synonym: correlation spectrometry
id: CHMO:0000599

heteronuclear correlation spectroscopy
type: Class
subclass of: heteronuclear two-dimensional nuclear magnetic resonance spectroscopy
definition: A type of NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between protons and heteronuclei.
imported from: chmo.owl
database_cross_reference: FIX:0001025
has_exact_synonym: 2D heteronuclear correlation spectroscopy
has_exact_synonym: HETCOR
has_exact_synonym: HETCORR
has_exact_synonym: HETCOSY
has_exact_synonym: HETEROCOR
has_exact_synonym: hetCOSY
has_exact_synonym: heteronuclear COSY
has_exact_synonym: two-dimensional heteronuclear correlation spectroscopy
id: CHMO:0000600

total correlation spectroscopy
type: Class
subclass of: pulsed nuclear magnetic resonance spectroscopy
definition: A type of homonuclear NMR spectroscopy which reveal correlations between all nuclei of a spin-system.
imported from: chmo.owl
has_exact_synonym: HOHAHA spectrometry
has_exact_synonym: HOHAHA spectroscopy
has_exact_synonym: TOCSY
has_exact_synonym: homonuclear Hartmann Hahn spectroscopy
has_exact_synonym: homonuclear Hartmann,Hahn spectroscopy
has_exact_synonym: homonuclear Hartmann-Hahn spectroscopy
has_exact_synonym: total correlated spectroscopy
has_exact_synonym: total correlation spectrometry
id: CHMO:0000605

J-spectroscopy
type: Class
subclass of: two-dimensional nuclear magnetic resonance spectroscopy
definition: A type of homonuclear proton--proton) NMR spectroscopy where chemical shift and J-coupling information are separated onto different frequency axes.
imported from: chmo.owl
has_exact_synonym: 2D J-resolved spectroscopy
has_exact_synonym: 2D J-spectroscopy
has_exact_synonym: 2DJ spectroscopy
has_exact_synonym: J-RES
has_exact_synonym: J-resolved NMR
has_exact_synonym: J-resolved NMR spectrometry
has_exact_synonym: J-resolved NMR spectroscopy
has_exact_synonym: J-resolved spectrometry
has_exact_synonym: J-resolved spectroscopy
has_exact_synonym: J-resolved spectroscopy NMR spectroscopy
has_exact_synonym: J-spectrometry
has_exact_synonym: JRES
has_exact_synonym: JRES NMR
has_exact_synonym: two-dimensional J-spectroscopy
id: CHMO:0000606

nuclear Overhauser enhancement spectroscopy
type: Class
subclass of: pulsed nuclear magnetic resonance spectroscopy
definition: A type of homonuclear NMR spectroscopy based on the nuclear Overhauser enhancement effect in which correlations are seen between nuclei that are spatially proximate within a molecule (\leq 6 \AA apart).
imported from: chmo.owl
has_exact_synonym: 2D EXSY
has_exact_synonym: 2D exchange spectroscopy
has_exact_synonym: EXSY
has_exact_synonym: NOE experiments
has_exact_synonym: NOESY
has_exact_synonym: NOESY NMR
has_exact_synonym: NOEsy
has_exact_synonym: exchange spectrometry
has_exact_synonym: exchange spectroscopy
has_exact_synonym: nOesy
has_exact_synonym: nuclear Overhauser effect spectrometry
has_exact_synonym: nuclear Overhauser effect spectroscopy
has_exact_synonym: nuclear Overhauser enhancement spectrometry
id: CHMO:0000607

pulsed nuclear magnetic resonance spectroscopy
type: Class
subclass of: nuclear magnetic resonance spectroscopy
definition: Spectroscopy where the energy states of spin-active nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them.
imported from: chmo.owl
has_exact_synonym: NMR
has_exact_synonym: NMR spectrometry
has_exact_synonym: NMR spectroscopy
has_exact_synonym: nuclear magnetic resonance spectrometry
has_exact_synonym: nuclear magnetic resonance spectroscopy
has_exact_synonym: pulsed nuclear magnetic resonance spectrometry
id: CHMO:0000613

Carr-Purcell-Meiboom-Gill pulse sequence
type: Class
subclass of: nuclear magnetic resonance pulse sequence
definition: A pulse sequence which is applied during nuclear magnetic resonance spectroscopy to measure spin--spin (T2) relaxation times. For the pulse sequence see Rev. Sci. Inst., (1958), 29, pg 688.
imported from: chmo.owl
has_alternative_id: FIX:0000215
has_exact_synonym: CPMG
has_exact_synonym: CPMG pulse sequence
has_exact_synonym: CPMG sequence
has_exact_synonym: Carr, Purcell,Meiboom,Gill pulse sequence
has_exact_synonym: Carr-Purcell Meiboom-Gill pulse sequence
has_exact_synonym: Carr-Purcell-Meiboom-Gill pulse sequence
id: CHMO:0000718

quadrupolar Carr-Purcell-Meiboom-Gill pulse sequence
type: Class
subclass of: Carr-Purcell-Meiboom-Gill pulse sequence
definition: A pulse sequence which is applied during nuclear magnetic resonance spectroscopy of quadrupolar nuclei, to measure spin--spin (T2) relaxation times. In the solid state, the sequence is used to achieve sensitivity enhancement for nuclei with low gyromagnetic ratios. For the pulse sequence see J. Phys. Chem. A, (1997), 101, pg 8597.
imported from: chmo.owl
has_exact_synonym: QCPMG
has_exact_synonym: QCPMG NMR
has_exact_synonym: QCPMG pulse sequence
has_exact_synonym: QCPMG sequence
has_exact_synonym: quadrupolar Carr, Purcell,Meiboom, Gill pulse sequence
has_exact_synonym: quadrupolar Carr-Purcell Meiboom-Gill pulse sequence
id: CHMO:0000719

heteronuclear two-dimensional nuclear magnetic resonance spectroscopy
type: Class
subclass of: two-dimensional nuclear magnetic resonance spectroscopy
definition: Any type of heteronuclear NMR spectroscopy where a second frequency dimension is employed.
imported from: chmo.owl
has_exact_synonym: heteronuclear 2D NMR
id: CHMO:0000931

1H--1H correlation spectroscopy
type: Class
subclass of: correlation spectroscopy
definition: A type of homonuclear NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between protons which are J-coupled (usually \leq 3 bonds apart).
imported from: chmo.owl
created by: burchh
creation date: 2009-03-11T05:11:37Z
has_exact_synonym: 1H--1H COSY
has_exact_synonym: 1H-1H COSY
has_exact_synonym: 1H-1H correlated spectroscopy
id: CHMO:0001150

Hadamard-encoded nuclear magnetic resonance spectroscopy
type: Class
subclass of: pulsed nuclear magnetic resonance spectroscopy
definition: An NMR experiment in which multiple frequencies in an NMR spectrum are excited simultaneously over a broad frequency rnage using polychromatic pulses.
imported from: chmo.owl
created by: burchh
creation date: 2009-03-19T05:34:21Z
has_exact_synonym: Hadamard NMR spectroscopy
has_exact_synonym: Hadamard encoded NMR
has_exact_synonym: Hadamard nuclear magnetic resonance spectroscopy
has_exact_synonym: Hadamard-encoded NMR
id: CHMO:0001195

magnetic resonance method
type: Class
subclass of: assay
definition: Any technique which detects the response of spins to a perturbing magnetic field.
imported from: chmo.owl
created by: burchh
creation date: 2009-03-25T11:36:57Z
has_alternative_id: FIX:0000012
id: CHMO:0001215

nuclear magnetic resonance method
type: Class
subclass of: magnetic resonance method
definition: A technique or procedure applied in nuclear magnetic resonance experiments.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-22T11:04:59Z
id: CHMO:0001806

nuclear magnetic resonance pulse sequence
type: Class
subclass of: planned process
definition: A series of short (microsecond) bursts (pulses) of rf radiation separated by delays (of defined duration) designed to interact with, and manipulate the magnetic moments of spin-active nuclei during NMR spectroscopy.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T01:41:59Z
has_exact_synonym: NMR pulse sequence
has_exact_synonym: pulse sequence
id: CHMO:0001841

decoupling pulse sequence
type: Class
subclass of: nuclear magnetic resonance pulse sequence
definition: An NMR pulse sequence that decouples nuclei i.e. removes the effects of (usually) J-coupling (line splitting) from the spectrum.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
id: CHMO:0001844

magic angle spinning decoupling pulse sequence
type: Class
subclass of: decoupling pulse sequence
definition: An NMR pulse sequence, used in magic angle spinning, that decouples nuclei i.e. removes the effects of (usually) J-coupling (line splitting) from the spectrum.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
id: CHMO:0001852

flip flop spectroscopy
type: Class
subclass of: nuclear magnetic resonance pulse sequence
definition: A sequence of composite pulses designed to allow isotropic mixing of magnetisation between nuclei. For the pulse sequence see J. Magn.Reson., (1988), 77, pg 274.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
has_exact_synonym: FLOPSY
has_exact_synonym: flip-flop spectroscopy
id: CHMO:0001862

heteronuclear Hartmann Hahn pulse sequence
type: Class
subclass of: nuclear magnetic resonance pulse sequence
definition: An NMR pulse sequence used to transfer magnetisation between protons and covalently bound (spin active) heteronuclei via isotropic mixing of their magnetisation. Used to e.g. enhance the NMR signal of heteronuclei or to correlate chemical shifts of protons with heteronuclei. For the pulse sequence see J. Magn. Reson., (1991), 91, pg 444.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
has_exact_synonym: HEHAHA
has_exact_synonym: HEHAHA pulse sequence
has_exact_synonym: HEHAHA sequence
has_exact_synonym: heteronuclear Hartman-Hahn pulse sequence
has_exact_synonym: heteronuclear Hartman-Hahn sequence
has_exact_synonym: heteronuclear Hartmann Hahn
id: CHMO:0001863

solvent suppression pulse sequence
type: Class
subclass of: nuclear magnetic resonance pulse sequence
definition: An NMR pulse sequence that is used to suppress or remove the solvent signal.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
id: CHMO:0001864

jump and return pulse sequence
type: Class
subclass of: solvent suppression pulse sequence
definition: A pulse cluster used for solvent suppression consisting of two rf pulses separated by a delay with conditions set such that the solvent signal alone is rendered unobservable by the second pulse. For the pulse sequence see J. Am. Chem. Soc., (1982), 104, pg 7310.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
has_exact_synonym: JR
has_exact_synonym: JR pulse sequence
has_exact_synonym: JR sequence
has_exact_synonym: jump and return
has_exact_synonym: jump-and-return
has_exact_synonym: jump-and-return pulse sequence
id: CHMO:0001865

water elimination Fourier transform
type: Class
subclass of: solvent suppression pulse sequence
definition: A pulse cluster used to suppress solvent (water) signals exploiting the differing relaxation properties of solvent and sample. Resonances are inverted and the subsequent recovery period is chosen such that the solvent signal is at a null point when the signal is detected. For the pulse sequence see J. Chem. Phys., (1972), 56, pg 3182.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
has_exact_synonym: WEFT
has_exact_synonym: WEFT pulse sequence
has_exact_synonym: WEFT sequence
has_exact_synonym: water-elimination Fourier transform
id: CHMO:0001866

water suppression through gradient tailored excitation
type: Class
subclass of: solvent suppression pulse sequence
definition: A pulse cluster used for solvent (water) suppression. The solvent resonances are selectively excited and pulsed field gradients used to destroy the signal. For the pulse sequence see J. Biomol. NMR, (1992), 2, pg 661.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
has_exact_synonym: WATERGATE
has_exact_synonym: WATERGATE pulse sequence
has_exact_synonym: WATERGATE sequence
id: CHMO:0001867

spin echo pulse sequence
type: Class
subclass of: nuclear magnetic resonance pulse sequence
definition: A pulse cluster used in NMR experiments which manipulates signals such that, at the end of the sequence, the effects of chemical shift differences have been compensated/removed. Used most simply to compensate for inhomogeneities in the magnetic field but delays in the sequence also permit various possible manipulations of the magnetisation. For the pulse sequence see Phys. Rev., (1950), 80, pg 580.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
has_exact_synonym: spin echo sequence
has_exact_synonym: spin-echo pulse sequence
has_exact_synonym: spin-echo sequence
id: CHMO:0001868

total suppression of sidebands pulse sequence
type: Class
subclass of: nuclear magnetic resonance pulse sequence
definition: A pulse sequence used in magic angle spinning NMR experiments to remove additional signals resulting from spinning the sample too slowly to obtain a response composed solely of isotropic chemical shifts.
imported from: chmo.owl
created by: burchh
creation date: 2009-05-29T12:00:00Z
has_exact_synonym: TOSS
has_exact_synonym: TOSS pulse sequence
has_exact_synonym: TOSS sequence
id: CHMO:0001869

two-dimensional heteronuclear single quantum coherence-nuclear Overhauser effect spectroscopy
type: Class
subclass of: heteronuclear two-dimensional nuclear magnetic resonance spectroscopy
definition: A 2D NMR experiment which correlates the chemical shifts of spatially proximate protons with the chemical shifts of all (of one type of) their covalently bound heteronuclei.
imported from: chmo.owl
created by: burchh
creation date: 2009-06-30T10:23:52Z
has_exact_synonym: 2D HSQC-NOESY
has_exact_synonym: 2D NOESY-HSQC
has_exact_synonym: two-dimensional heteronuclear single quantum coherence nuclear Overhauser effect spectroscopy
id: CHMO:0002060

13C--13C correlation spectroscopy
type: Class
subclass of: correlation spectroscopy
definition: A type of homonuclear NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between 13C nuclei that are J-coupled (usually \leq 3 bonds apart).
imported from: chmo.owl
created by: burchh
creation date: 2009-08-24T04:14:21Z
has_exact_synonym: 13C-13C COSY
has_exact_synonym: 13C-13C correlated spectroscopy
has_exact_synonym: CC-COSY
id: CHMO:0002301

1H--13C heteronuclear correlation spectroscopy
type: Class
subclass of: heteronuclear correlation spectroscopy
definition: A type of NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between protons and 13C nuclei.
imported from: chmo.owl
created by: burchh
creation date: 2009-09-15T05:40:49Z
has_exact_synonym: 1H--13C COSY
has_exact_synonym: 1H--13C HETCOR
has_exact_synonym: 1H--13C HETCORR
has_exact_synonym: 1H--13C HETCOSY
has_exact_synonym: 1H--13C HETEROCOR
has_exact_synonym: 1H-13C COSY
has_exact_synonym: 1H-13C HETCOR
has_exact_synonym: 1H-13C HETCORR
has_exact_synonym: 1H-13C HETCOSY
has_exact_synonym: 1H-13C HETEROCOR
has_exact_synonym: heteronuclear 13C-1H COSY
id: CHMO:0002380

one-dimensional 1H nuclear magnetic resonance spectroscopy
type: Class
subclass of: one-dimensional nuclear magnetic resonance spectroscopy
definition: Spectroscopy where the energy states of 1H nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them, and the spectrum is obtained by plotting chemical shift vs. frequency.
imported from: chmo.owl
created by: burchh
creation date: 2009-09-23T02:32:09Z
has_exact_synonym: 1D 1H NMR
has_exact_synonym: 1D proton NMR
id: CHMO:0002442

selected reaction monitoring
type: Class
subclass of: tandem mass spectrometry
imported from: chmo.owl
id: CHMO:0002867

cell
type: Class
subclass of: material entity
editor preferred label: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl
imported from: Ontology for Biomedical Investigation

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
editor preferred label: cultured cell
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl
imported from: Ontology for Biomedical Investigation

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: experimentally modified cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl
imported from: Ontology for Biomedical Investigation

disease
type: Class
subclass of: disposition
definition: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. [url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf ]
id: DOID:4

consent code
type: Class
subclass of: data item
definition: A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
id: DUO:0000001

consent code primary category
type: Class
subclass of: consent code
definition: A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016.
id: DUO:0000002

consent code secondary category
type: Class
subclass of: consent code
definition: A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016.
id: DUO:0000003

no restriction
type: Class
subclass of: consent code primary category
definition: This consent code primary category indicates there is no restriction on use.
id: DUO:0000004
comment: Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service

general research use and clinical care
type: Class
subclass of: consent code primary category
definition: This primary category consent code indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.
id: DUO:0000005

health/medical/biomedical research and clinical care
type: Class
subclass of: consent code primary category
definition: This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
id: DUO:0000006

disease-specific research and clinical care
type: Class
subclass of: consent code primary category
subclass of: Restriction
  on property: is restricted to
  some values from: disease
definition: This primary category consent code indicates that use is allowed provided it is related to the specified disease.
id: DUO:0000007

population origins or ancestry research
type: Class
subclass of: consent code primary category
definition: This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry.
alternative term: population origins/ancestry research
id: DUO:0000011

research-specific restrictions
type: Class
subclass of: consent code secondary category
subclass of: Restriction
  on property: is restricted to
  some values from: Topic
definition: This secondary category consent code indicates that use is limited to studies of a certain research type.
id: DUO:0000012

research use only
type: Class
subclass of: consent code secondary category
definition: This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care).
id: DUO:0000014

no general methods research
type: Class
subclass of: consent code secondary category
definition: This secondary category consent code indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations.
id: DUO:0000015

genetic studies only
type: Class
subclass of: consent code secondary category
definition: This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research)
id: DUO:0000016

data use requirements
type: Class
subclass of: data item
definition: Requirements indicate additional conditions set for use.
id: DUO:0000017

not-for-profit use only
type: Class
subclass of: data use requirements
definition: This requirement indicates that use is limited to not-for-profit organizations.
id: DUO:0000018

publication required
type: Class
subclass of: data use requirements
definition: This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
id: DUO:0000019

collaboration required
type: Class
subclass of: data use requirements
definition: This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s).
id: DUO:0000020

ethics approval required
type: Class
subclass of: data use requirements
definition: This requirement indicates that the requestor must provide documentation of local IRB/ERB approval.
id: DUO:0000021

geographical restriction
type: Class
subclass of: data use requirements
subclass of: Restriction
  on property: is restricted to
  some values from: geographic location
definition: This requirement indicates that use is limited to within a specific geographic region.
id: DUO:0000022

publication moratorium
type: Class
subclass of: data use requirements
definition: This requirement indicates that requestor agrees not to publish results of studies until a specific date
alternative term: publication embargo
id: DUO:0000024

time limit on use
type: Class
subclass of: data use requirements
definition: This requirement indicates that use is approved for a specific number of months.
id: DUO:0000025

user-specific restriction
type: Class
subclass of: data use requirements
definition: This requirement indicates that use is limited to use by approved users.
id: DUO:0000026

project-specific restriction
type: Class
subclass of: data use requirements
definition: This requirement indicates that use is limited to use within an approved project.
id: DUO:0000027

institution-specific restriction
type: Class
subclass of: data use requirements
definition: This requirement indicates that use is limited to use within an approved institution.
id: DUO:0000028

return to database/resource
type: Class
subclass of: data use requirements
definition: This requirement indicates that the requestor must return derived/enriched data to the database/resource.
id: DUO:0000029
shorthand: RTN

geographic location
type: Class
subclass of: site
editor preferred label: geographic location
definition: A reference to a place on the Earth, by its name or by its geographical location.
id: GAZ:00000448

molecular_function
type: Class
subclass of: function
editor preferred label: molecular_function
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
imported from: go.owl
imported from: Ontology for Biomedical Investigation

catalytic activity
type: Class
subclass of: molecular_function
editor preferred label: catalytic activity
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
imported from: go.owl
imported from: Ontology for Biomedical Investigation

biological_process
type: Class
subclass of: process
editor preferred label: biological_process
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
imported from: go.owl
imported from: Ontology for Biomedical Investigation

gene expression
type: Class
subclass of: biological_process
editor preferred label: gene expression
definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
imported from: go.owl
imported from: Ontology for Biomedical Investigation

protein complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: protein
editor preferred label: protein complex
example of usage: A ribosome is a protein complex
definition: Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
imported from: go.owl
imported from: Ontology for Biomedical Investigation

conditional specification
type: Class
subclass of: directive information entity
editor preferred label: conditional specification
has curation status: metadata complete
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000349
imported from: Ontology for Biomedical Investigation

unit
type: Class
subclass of: datum label
editor preferred label: 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.
definition: A unit of measurement is a standardized quantity of a physical quality.
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
imported from: Ontology for Biomedical Investigation
imported from: uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000000
label: measurement unit label

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: 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 term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: Ontology for Biomedical Investigation

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
imported from: Ontology for Biomedical Investigation

datum label
type: Class
subclass of: information content entity
editor preferred label: 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.
imported from: Ontology for Biomedical Investigation

software
type: Class
subclass of: plan specification
editor preferred label: software
has curation status: metadata complete
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
definition: Software related to the recording or transformation of spectra.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition source: GROUP: OBI
imported from: Ontology for Biomedical Investigation
has_obo_namespace: NMR
id: NMR:1000531

Axiom
annotated source: software
annotated property: definition
annotated target: Software related to the recording or transformation of spectra.
database_cross_reference: MSI:NMR

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

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
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
imported from: Ontology for Biomedical Investigation

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: 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: Ontology for Biomedical Investigation

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
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
imported from: Ontology for Biomedical Investigation

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
imported from: Ontology for Biomedical Investigation

graph
type: Class
subclass of: diagram
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

rule
type: Class
subclass of: conditional specification
editor preferred label: rule
example of usage: example to be added
has curation status: metadata incomplete
definition: a rule is an executable which guides, defines, restricts actions
editor note: MSI
term editor: PRS
definition source: OBI_0500021
definition source: PRS
imported from: Ontology for Biomedical Investigation

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: 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)
imported from: Ontology for Biomedical Investigation

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 label: 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
imported from: Ontology for Biomedical Investigation

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

image
type: Class
subclass of: figure
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

data about an ontology part
type: Class
subclass of: data item
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
imported from: Ontology for Biomedical Investigation

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 label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: 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.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: Ontology for Biomedical Investigation
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 label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
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
imported from: Ontology for Biomedical Investigation

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

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: conclusion based on data
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
term editor: Person:Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

textual entity
type: Class
subclass of: information content entity
editor preferred label: 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 term: text
imported from: Ontology for Biomedical Investigation

table
type: Class
subclass of: textual entity
editor preferred label: table
example of usage: | T F --+----- T | T F F | F F
has curation status: pending final vetting
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
term editor: PERSON: Lawrence Hunter
imported from: Ontology for Biomedical Investigation

figure
type: Class
subclass of: information content entity
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

diagram
type: Class
subclass of: figure
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
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
imported from: Ontology for Biomedical Investigation

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: zero-dimensional spatial region
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
has curation status: metadata complete
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
term editor: Alan Ruttenberg
curator note: AR notes: We need to discuss whether it should include site.
imported from: Ontology for Biomedical Investigation

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: one-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
has curation status: metadata incomplete
definition: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
term editor: Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: two-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
has curation status: metadata incomplete
definition: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
term editor: Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

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
imported from: Ontology for Biomedical Investigation

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: time unit
  intersection of: Restriction
    on property: is duration of
    all values from: process
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

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
imported from: Ontology for Biomedical Investigation

line graph
type: Class
subclass of: graph
editor preferred label: line graph
has curation status: ready for release
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:Melanie Courtot
alternative term: line chart
definition source: GROUP:OBI
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart
imported from: Ontology for Biomedical Investigation

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 term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: Ontology for Biomedical Investigation

centrally registered identifier
type: Class
subclass of: information content entity
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 term: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: Ontology for Biomedical Investigation

centrally registered identifier registry
type: Class
subclass of: data set
example of usage: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: Ontology for Biomedical Investigation

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
has curation status: metadata incomplete
imported from: Ontology for Biomedical Investigation

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: time stamped measurement datum
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: metadata complete
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
term editor: Alan Ruttenberg
alternative term: experimental time series
imported from: Ontology for Biomedical Investigation

openFlux2
type: Class
subclass of: software
has curation status: ready for release
definition: OpenFLUX2 is a MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Modern techniques like Elementary Metabolite Unit (EMU) framework, are implemented for efficient computing of fluxes. OpenFlux2 is an expanded version of OpenFLUX to support analysis of parallel labeling experiments (PLE) data, i.e. those experiments using several different tracers concomitantly.
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.1186/s12934-014-0152-x

chemical reaction
type: Class
subclass of: process
example of usage: 2H2O -> 2H2+ O2
definition: a process which uses or consumes chemical/molecular entities to generate other molecular entities
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Chemical_reaction last accessed: 2018-01-11

buffer role
type: Class
subclass of: role
has curation status: ready for release
definition: buffer role is a role played by a chemical solution to dampens pH variation
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

derivatization agent role
type: Class
subclass of: role
has curation status: ready for release
definition: derivatization agent role is a role played by a chemical entity involved in a chemical reaction known as derivatization whereby another chemical entity is augmented, but not altered otherwise, with groups specify to the chemical entity acting as a derivatization agent.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

external standard role
type: Class
subclass of: positive control role
has curation status: ready for release
definition: external standard role is a role played by a material entity used as a reference point for signal acquisition. this is a type of positive control role
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

internal standard role
type: Class
subclass of: positive control role
has curation status: ready for release
definition: internal standard role is a role played by a chemical entity added in known amount to an analytical sample
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

long term reference role
type: Class
subclass of: role
has curation status: ready for release
definition: long term reference role is a role played by a material entity known for its stability to provide the means to compare across sets of acquisitions
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

negative control role
type: Class
subclass of: role
has curation status: ready for release
definition: positive control role is a role played by a material entity in the context of analytical work to provide no signal or a signal as close to baseline as technically possible (within the limits of detection) thereby providing a reference point for the noise and indicative that the detectors and signal acquisition system operate nominally.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

positive control role
type: Class
subclass of: role
has curation status: ready for release
definition: positive control role is a role played by a material entity in the context of analytical work to provide a signal of known intensity indicative that the detectors and signal acquisition system operate nominally.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

solvent role
type: Class
subclass of: role
has curation status: ready for release
definition: solvent role is a role played by a chemical entity present in a solution and providing the solvatation activity to other compounds, the solutes.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

AbsoluteIDQ p150 Kit
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: targeted metabolite profiling
subclass of: Restriction
  on property: manufactured by
  has value: Biocrates AG
has curation status: ready for release
definition: AbsoluteIDQ p150 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 163 distinct molecular entities with quantitative accuracy on human plasma samples.
term editor: Philippe Rocca-Serra
definition source: http://www.biocrates.com/products/research-products/absoluteidq-p150-kit

AbsoluteIDQ p180 Kit
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: targeted metabolite profiling
subclass of: Restriction
  on property: manufactured by
  has value: Biocrates AG
has curation status: ready for release
definition: AbsoluteIDQ p180 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 188 distinct endogenous molecular entities with quantitative accuracy from 5 different compound classes (i.e. acylcarnitines, amino acids, hexoses, phospho- and sphingolipids and biogenic amines). The assay requires very small sample amounts (10 μL) and shows excellent reproducibility.
term editor: Philippe Rocca-Serra
definition source: http://www.biocrates.com/products/research-products/absoluteidq-p180-kit

AbsoluteIDQ Stero17 Kit
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: targeted metabolite profiling
subclass of: Restriction
  on property: manufactured by
  has value: Biocrates AG
has curation status: ready for release
definition: AbsoluteIDQ Stero17 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling (identification and quantification) of 17 steroid hormones (sex steroids, mineralocorticoids, glucocorticoids).
term editor: Philippe Rocca-Serra
definition source: http://www.biocrates.com/products/research-products/absoluteidq-p150-kit

AbsoluteIDQ p400 Kit
type: Class
subclass of: material entity
has curation status: ready for release
definition: AbsoluteIDQ p400 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 400 distinct molecular entities with quantitative accuracy on human plasma samples.
term editor: Philippe Rocca-Serra
definition source: http://www.biocrates.com/products/research-products/absoluteidq-p400-hr-kit

ammonium bicarbonate buffer
type: Class
subclass of: buffer
subclass of: Restriction
  on property: has role
  some values from: buffer role
has curation status: ready for release
definition: ammonium bicarbonate is kind of buffer solution where the weak base is ammonium and the weak acid carbonic acid.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

buffer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: buffer role
subclass of: material entity
example of usage: the bicarbonate buffering system is used to regulate the pH of blood.
has curation status: ready for release
definition: A buffer solution (more precisely, pH buffer or hydrogen ion buffer) is an aqueous solution consisting of a mixture of a weak acid and its conjugate base, or vice versa.
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Buffer_solution

dilution series reference
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: calibration
    union of: quality control
has curation status: ready for release
definition: a dilution series sample is a material entity which is part of a collection of such materials, each defined by its dilution factor with respect to a stock solution of reference sample. Dilution series samples are used to assess the linearity of the signal acquisition by providing a set of expected and known quantities.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

fetal bovine serum
type: Class
subclass of: material entity
has curation status: ready for release
definition: Fetal bovine serum (FBS) or fetal calf serum (spelled foetal in Commonwealth English) is a material entity which correspsonds to the blood fraction remaining after the natural coagulation of blood, followed by centrifugation to remove any remaining red blood cells.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group
definition source: https://en.wikipedia.org/wiki/Fetal_bovine_serum

HEPES buffer
type: Class
subclass of: buffer
subclass of: Restriction
  on property: has role
  some values from: buffer role
has curation status: ready for release
definition: HEPES buffer is a buffer which uses HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) as a zwitterionic organic chemical buffering agent .
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

long term reference
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: calibration
    union of: quality control
has curation status: ready for release
definition: a pooled sample made from fractions from samples collected from large, study independent collection of samples with the purpose of serving as a reference for quality control purpose. Long Term Reference Samples maybe used in ring trials to check cross facility data acquisition consistency but also to enable data integration, irrespective of data acquisition platform or study context but providing a single point of reference against which to normalize. purpose: Inter study variability(within a core facility)
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: LTR
alternative term: biological pool (inter) [CEA]
alternative term: biological pool [MASTR-MS]
alternative term: inter study QC
definition source: H2020 PhenoMenal

PBS buffer
type: Class
subclass of: buffer
subclass of: Restriction
  on property: has role
  some values from: buffer role
has curation status: ready for release
definition: Phosphated buffer saline (PBS) buffer is a buffer which is a water-based salt solution containing disodium hydrogen phosphate, sodium chloride and, in some formulations, potassium chloride and potassium dihydrogen phosphate.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group
definition source: https://en.wikipedia.org/wiki/Phosphate-buffered_saline

quality control material
type: Class
subclass of: material entity
has curation status: ready for release
definition: quality control material (qc material) is a material entity which is used for the purpose to quality control processes such as assessing unwanted source of variations during signal acquisitions. Typically, these materials are known compounds or mixture of compounds introduced in known quantities into test samples or run as is, diluted from stock to provide reference measurements at fixed temporal intervals.
term editor: Philippe Rocca-Serra
alternative term: QC material
definition source: EU H2020 PhenoMenAl

reference compound
type: Class
subclass of: material entity
has curation status: ready for release
definition: a reference compound is a chemical entity of know origin, formula and established spectral fingerprint added to a solution of unknown component in known quantities in order to provide a basis (hence the term reference) with which to establish a comparison, be used for calibration or quality control or quantitation estimate for unknown compound in spectral analysis such as NMR or mass spectrometry
term editor: Philippe Rocca-Serra
alternative term: pure standard
alternative term: reference material
definition source: cosmos tracer based metabolomics working group

reference compound mix
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: reference compound
example of usage: NIST reference material: https://www.nist.gov/publications/certification-standard-reference-materialr-968f-fat-soluble-vitamins-frozen-human-serum
has curation status: ready for release
definition: a reference compound mix is a material entity which consists of composite solution of several molecular entities acting as reference compound and present in known quantity in the mixture, with which to establish a comparison, be used for calibration or quality control or quantitation estimate for unknown compound in spectral analysis such as NMR or mass spectrometry
term editor: Philippe Rocca-Serra
alternative term: pure standard mix
alternative term: reference material mix
definition source: cosmos tracer based metabolomics working group

sample preparation blank
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: calibration
    union of: quality control
has curation status: ready for release
definition: a material entity corresponding to a sample containing no biological sample, which undergoes all laboratory process of preparation as used for test samples and used as a negative control to evaluate contamination effect and artefacts caused by reactions occurring during the sample preparation steps of test samples.
alternative term: method blank
alternative term: method reference

solvent blank
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: calibration
    union of: quality control
has curation status: ready for release
definition: a material entity corresponding to ‘solvent’ (mobile phase in chromatography context) only, containing no biological sample and used as a negative control to evaluate carry over effect between injections of test samples.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: normal blank [Leiden]
alternative term: solvent blank

study reference material
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: calibration
    union of: quality control
has curation status: ready for release
definition: a study reference sample is a pool made up of aliquots from all the sample collected in a given study. It is meant to be used to monitor intra study variability, also known as within study variability of the signal acquisition, for instance between batches of such data acquisition.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: SR
alternative term: iQC - internal quality control [Imperial College London]
alternative term: study reference

carrier gas
type: Class
subclass of: molecular entity
has curation status: ready for release
definition: a carrier gas is a chemical entity in gaseous phase with is used for eluting chemical compound in a gas chromatography process.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

derivatization agent
type: Class
equivalent class: Restriction
  on property: has role
  some values from: derivatization agent role
subclass of: molecular entity
example of usage: tert-Butyldimethylsilyl chloride is a derivatization agent
has curation status: ready for release
definition: a derivatization agent is a chemical entity which is used in a material combination process known as derivatization and which consists in adding chemical groups to a molecule in an attempt to make it more volatile and therefore amenable to gas-chromatography mass spectrometry.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

quaternary ammonium dodecyl aminooxy reagent
type: Class
subclass of: derivatization agent
has curation status: ready for release
term editor: Philippe Rocca-Serra
alternative term: QDA reagent

isotopic tracer
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: isotopic labeling
subclass of: molecular entity
subclass of: processed material
has curation status: ready for release
definition: an isotopic tracer is a molecular entity whose atoms may have entirely or partially replaced with isotopes of the normally occuring element and which can be distinguished from naturally occuring molecular entity through mass analysis or nucleic magnetic resonance analysis.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

positionally labeled isotopic tracer
type: Class
subclass of: isotopic tracer
has curation status: ready for release
definition: a specificly labeled isotopic tracer is an isotopic tracer where only specific positions on the backbone have been replaced with an isotopic atom. Such molecules are often used in Fluxomics analysis and metabolic path elucidation experiments.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

uniformly labeled isotopic tracer
type: Class
subclass of: isotopic tracer
has curation status: ready for release
definition: uniformly labeled isotopic tracer is an isotopic tracer where all atoms of the backbone are replaced with the same isotope. Such molecules are often used in Fluxomics analysis and metabolic path elucidation experiments.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

isotopologue
type: Class
subclass of: molecular entity
has curation status: requires discussion
definition: A single isotopologue represents a set of mass-equivalent isotopomers. It is therefore a set of chemicals representing molecules of the same chemical entity and same isotopic composition. Isotopologue can be monitored using mass spectrometry but only NMR spectroscopy can discriminate between positional isotopomer.
term editor: Philippe Rocca-Serra
definition source: adapted from IUPAC nomenclature
Contributor: cosmos tracer based metabolomics working group

openFlux
type: Class
subclass of: software
has curation status: ready for release
definition: OpenFLUX is a MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Modern techniques like Elementary Metabolite Unit (EMU) framework, are implemented for efficient computing of fluxes.
term editor: Philippe Rocca-Serra
definition source: https://www.ncbi.nlm.nih.gov/pubmed/19409084

isotopomer
type: Class
subclass of: molecular entity
has curation status: requires discussion
definition: a mass isotopomer (short for isotopic isomer) is a compound which differ from another one only by the position of an isotopic substitution in the molecular backbone. One in a collection of isomers with the same number of each isotope of each element but differing in their positions within the chemical structure.
term editor: Philippe Rocca-Serra
alternative term: isotopic isomer
alternative term: mass isotopomer
Contributor: cosmos tracer based metabolomics working group

solvent
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has role
    some values from: solvent role
subclass of: molecular entity
has curation status: ready for release
definition: a solvent is a chemical entity playing a solvent role in a solution.
term editor: Philippe Rocca-Serra
definition source: placeholder removed

uniformly-labeled [U-13C] glucose
type: Class
subclass of: isotopic tracer
subclass of: Restriction
  on property: is_specified_output_of
  some values from: isotopic labeling with uniformly labeled tracer
has curation status: placeholder removed
definition: A non-radioactive, glucose molecule in which all six carbons are substituted with stable carbon 13 (13C) isotope, with potential imaging application or fluxomics studies. CAS RN 110187-42-3
editor note: submit to CHEBI
term editor: Philippe Rocca-Serra

partial isotopomer
type: Class
subclass of: molecular entity
has curation status: requires discussion
definition: an isotopomer where the isotopic content of specific atoms is known for a part of the molecule
editor note: should it be a relation or a class?
term editor: Philippe Rocca-Serra

metabolic flux unit
type: Class
subclass of: unit
subclass of: Restriction
  on property: denotes
  some values from: metabolic flux
definition: metabolic flux unit is a measurement unit datum used to qualify a metabolic flux. It is therefore an amount of matter over a temporal interval.
term editor: Philippe Rocca-Serra
definition source: Philippe Rocca-Serra for the COSMOS-Fluxomics Ontology (CFO)

micromolar per milligram of protein per hour
type: Class
subclass of: metabolic flux unit
definition: micromolar per milligram of protein per hour is a unit used to report metabolic fluxes. it denotes a measurement indicative of an amount of material over a period of time and normalized to the amount of protein present in the cellular fraction under consideration
term editor: Philippe Rocca-Serra
alternative term: umol mg prot-1 hr-1

13cflux2
type: Class
subclass of: software
has curation status: ready for release
definition: c13Fluc2 is a software suite of applications for the detailed quantification of intracellular (quasi) steady-state fluxes as explored by 13C-based metabolic flux analysis. The tool is developed and maintained by W. Wiechert at the Institute of Bio- and Geosciences, IBG-1: Biotechnology and JARA High Performance Computing, Forschungszentrum, Julich GmbH, 52428 Julich, Germany.
term editor: Philippe Rocca-Serra
definition source: Weitzel M, Nöh K, Dalman T, Niedenführ S, Stute B, Wiechert W 13CFLUX2 - High-Performance Software Suite for 13C-Metabolic Flux Analysis Bioinformatics 2012 doi: 10.1093/bioinformatics/bts646
definition source: http://www.13cflux.net/13cflux2/

C13
type: Class
subclass of: software
has curation status: ready for release
definition: C13 is a tool for quantification of in vivo metabolic fluxes, from carbon labelling experiments. The underlying approach is metabolic flux analysis based on stationary carbon isotope labelling experiments, using fractional enrichment data. The mathematical framework adopted herein is the one developed by Wiechert and de Graaf (1997). It is developed and maintained at the Chalmers University of Technology, Department of Chemical and Biological Engineering, Systems Biology group , Kemivägen 10 412 96 Göteborg, Sweden.
term editor: Philippe Rocca-Serra
definition source: http://129.16.106.142/tools.php

fiatFlux
type: Class
subclass of: software
has curation status: ready for release
definition: An intuitive tool for quantitative investigations of intracellular metabolism by users that are not familiar with numerical methods or isotopic tracer experiments. The aim of this open source software is to enable non-specialists to adapt the software to their specific scientific interests, including other 13C-substrates, labeling mixtures, and organisms. FiatFlux is written in Matlab
term editor: Philippe Rocca-Serra
definition source: http://www.ncbi.nlm.nih.gov/pubmed/16122385

Fluxomer Iterative Algorithm
type: Class
subclass of: software
has curation status: ready for release
definition: FIA is a software written in python, implementing the FIA (Fluxomer Iterative Algorithm) - a new effective method for 13C metabolic fluxes (tracer) experiments analysis. It is developed by Orr Srour, Jamey D. Young and Yonina C. Eldar at the Technion, Israel Institute of Technology
term editor: Philippe Rocca-Serra
alternative term: FIA
definition source: https://doi.org/10.1186/1752-0509-5-129

iMAT
type: Class
subclass of: software
has curation status: ready for release
definition: iMAT is a software integrating transcriptomic and proteomic data with genome-scale metabolic network models to predict enzyme metabolic flux. The tool is developed by Tomer Shlomi at The Isreal Institute of Technology
term editor: Philippe Rocca-Serra
alternative term: Integrative Metabolic Analysis Tool
definition source: Bioinformatics (2010) 26 (24): 3140-3142. https://doi.org/10.1093/bioinformatics/btq602
definition source: http://www.cs.technion.ac.il/~tomersh/methods.html

INCA
type: Class
subclass of: software
subclass of: data item
subclass of: Restriction
  on property: is_specified_input_of
  some values from: 13C-constrained flux balance analysis
has curation status: ready for release
definition: INCA: a computational platform for isotopically non-stationary metabolic flux analysis, Jamey D. Young. Bioinformatics, first published online January 11, 2014. INCA is a software package that can perform both steady-state metabolic flux analysis and isotopically non-stationary metabolic flux analysis. The software provides a framework for comprehensive analysis of metabolic networks using mass balances and elementary metabolite unit balances. The generation of balance equations and their computational solution is completely automated and can be performed on networks of arbitrary complexity.
term editor: Philippe Rocca-Serra
alternative term: Isotopomer Network Compartmental Analysis
definition source: http://www.ncbi.nlm.nih.gov/pubmed/24413674

iso2flux
type: Class
subclass of: software
has curation status: ready for release
definition: Iso2Flux is a Python-based flux analysis software that allows to perform 13C Metabolic Flux Analysis on a sub-network of a large scale model. Iso2flux uses constraint-based modelling to compute steady state fluxes across a large metabolic network and uses such flxues to predict 13C distribution across a subser of the newtork. Then, given a set of 13C data Iso2flux can iteratively find the steady state flux distributions that are most consistent with such fluxes. the source code is available from: https://github.com/cfoguet/iso2flux
definition source: http://portal.phenomenal-h2020.eu/app-library/iso2flux
definition source: https://github.com/cfoguet/iso2flux
Contributor: Pedro de Atauri
Contributor: Vitaly Selivanov

isodyn
type: Class
subclass of: software
has curation status: ready for release
definition: “Isodyn” is a C++-program that performs an analysis of stable isotope tracer data to assess metabolic flux profiles in living cells. Isodyn simulates the dynamics of isotopic isomer (isotopomer) distribution in central metabolic pathways, and, by changing its parameters, which reflect the characteristics of corresponding biochemical reactions, fit the simulated dynamics of mass isotopomers to that observed experimentally. The simulated metabolic fluxes that correspond to the best fit are assumed to reproduce the real fluxes in the analyzed biological object and conditions. Isodyn contains tools that check the goodness of fit and perform a statistical analysis of obtained metabolic fluxes. the source code is available from: https://github.com/seliv55/isodyn
term editor: Philippe Rocca-Serra
definition source: http://portal.phenomenal-h2020.eu/app-library/isodyn
Contributor: Pedro de Atauri
Contributor: Vitaly Selivanov

isodesign
type: Class
subclass of: software
has curation status: ready for release
definition: IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to (13) C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, (1) H NMR, (13) C NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. The software is available from: http://metasys.insa-toulouse.fr/software/isodes/
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.1002/bit.24997

metran
type: Class
subclass of: software
has curation status: ready for release
definition: Metran is a software for Metabolic Flux Analysis implementing the Elementary Metabolite Units. Metabolic Flux Analysis (MFA) has emerged as a tool of great significance for metabolic engineering and quantitative cell physiology. An important limitation of MFA, as carried out via stable isotope labeling and GC-MS measurements, is the large number of isotopomer/cumomer equations that need to be solved, especially when multiple isotopic tracers are used for the labeling of the system. This restriction reduces the ability of MFA to fully utilize the power of multiple isotopic tracers in elucidating the physiology of realistic situations comprising complex bioreaction networks. To address this limitation, we have developed a novel framework for modeling of isotopic tracer distributions that significantly reduces the number of variables, without any loss of information. The EMU framework is based on a highly efficient decomposition method that identifies the minimum amount of information needed to simulate isotopic labeling within a reaction network using the knowledge of atomic transitions occurring in the network reactions. The functional units generated by the decomposition algorithm, called elementary metabolite units (EMUs), form the new basis for generating system equations that describe the relationship between fluxes and isotopomer abundances. The EMU decomposition algorithm is completely unsupervised and converges within seconds even for very genome-wide network models. Isotopomer abundances simulated using the EMU framework are identical to those obtained using the isotopomer and cumomer frameworks, however, requiring significantly less computation time. For a typical carbon labeling system the total number of equations that needs to be solved is reduced by one order-of-magnitude (100s EMUs vs. 1000s cumomers). As such, the EMU framework is most efficient for the analysis of labeling by multiple isotopic tracers. For example, the analysis of gluconeogenesis netw…
term editor: Philippe Rocca-Serra
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17088092

midcor
type: Class
subclass of: software
has curation status: ready for release
definition: “midcor.R” is an “R”-program that performs a primary analysis of isotopic isomers (isotopomers) distribution obtained by Gas Chromatography coupled with Mass Spectrometry (GCMS). The aim of this analysis is to have a correct distribution of isotopes originated from substrates that are artificially enriched with specific isotopes (usually 13C). To this end the program performs a correction for natural occurring isotopes and also correction for “impurities” of the assay media that give peaks overlapping with the spectra of analyzed labeled metabolites. This program offers two ways of corrections of “impurities” resulted from overlapping the assayed mass isotopomer distribution with peaks produced either by unknown metabolites in the media, or by different fragments produced by the assayed metabolite. The source code is available from https://github.com/seliv55/midcor
term editor: Philippe Rocca-Serra
definition source: http://portal.phenomenal-h2020.eu/app-library/midcor
Contributor: Pedra de Atauri
Contributor: Vitaly Selivanov

non-stationary isotopic labeling experiment
type: Class
subclass of: stable isotope resolved metabolomics study
subclass of: Restriction
  on property: has_specified_input
  some values from: isotopic tracer
disjoint with: steady state isotopic labeling experiment
has curation status: ready for release
definition: an isotopically non-stationary labeling experiment is a material processing used in fluxomics studies where cells cultures are grown in the presence of radiolabeled tracer compound for relatively short amount of time and samples collection before the system can reach an isotopic and metabolic steady state, and is therefore in a non-stationary phase. Such experiment are shorter to run that steady-state labeling experiment and usually allow to determine fluxes with increased precision.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

13C5-15N2-glutamine
type: Class
subclass of: isotopic tracer
subclass of: Restriction
  on property: is_specified_output_of
  some values from: isotopic labeling with uniformly labeled tracer
has curation status: placeholder removed
definition: A non-radioactive, glutamine molecule in which 5 carbons are substituted with stable carbon 13 (13C) isotope and both glutamin nitrogen atoms are substituted with 15N ones, with potential imaging application or fluxomics studies.
editor note: submit to CHEBI
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: 184161-19-1

openMoebius
type: Class
subclass of: software
has curation status: ready for release
definition: OpenMoebius is an integrated software for conventional 13C-Metabolic Flux Analysis and isotopically nonstationary 13C-Metabolic Flux Analysis (INST-13C-MFA). This work is partially supported by JST, Strategic International Collaborative Research Program, SICORP for JP-US Metabolomics.
term editor: Philippe Rocca-Serra
definition source: http://www-shimizu.ist.osaka-u.ac.jp/hp/en/software/OpenMebius.html

ramid
type: Class
subclass of: software
has curation status: ready for release
definition: RaMID is a computer program designed to read the machine-generated files saved in netCDF format containing registered time course of m/z chromatograms. It evaluates the peaks of mass isotopomer distribution (MID) making them ready for further correction for natural isotope occurrence. RaMID is written in “R”, uses library “ncdf4” (it should be installed before the first use of RaMID) and contains several functions, located in the files “ramid.R” and "libcdf.R," designed to read CDF files, and analyze and visualize the spectra that they contain. the source code is available from: https://github.com/seliv55/RaMID
term editor: Philippe Rocca-Serra
definition source: https://github.com/seliv55/RaMID
Contributor: Pedro de Atauri
Contributor: Vitaly Selivanov

sumoflux
type: Class
subclass of: software
has curation status: ready for release
definition: a software produced by Nicolas Zamboni and colleagues for flux ratio estimation based on a 5 step workflow known as SUMOFLUX and which relies on surrogate modeling. Matlab code available from: http://www.imsb.ethz.ch/research/zamboni/resources.html
term editor: Philippe Rocca-Serra
definition source: http://ncbi.nlm.nih.gov/pubmed/27626798

network
type: Class
subclass of: information content entity
has curation status: ready for release
definition: The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by enzymes. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called metabolic network. It is possible to use network analyses to infer how selection acts on metabolic pathways.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Biological_network

pathway
type: Class
subclass of: information content entity
has curation status: ready for release
definition: a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes.
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Metabolic_pathway

stoichiometric coefficient
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: denotes
  some values from: chemical reaction
example of usage: CH4 + 2 O2 → CO2 + 2 H2O, the stoichiometric coefficient of CH4 is -1, the stoichiometric coefficient of O2 is -2, for CO2 it would be +1 and for H2O it is +2
has curation status: ready for release
definition: a stoichiometric coefficient is an information object which is part of an equation describing a chemical reaction and which corresponds to the number of molecules of a reactant taking part in a reaction.
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Stoichiometry#Stoichiometric_coefficient

cell culture doubling time
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: Class
    union of: second
    union of: minute
subclass of: Restriction
  on property: is about
  some values from: cultured cell population
has curation status: ready for release
definition: the amount of time elapsed for a cell culture to growth twice its initial size, usually expressed in hour
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

cell seeding density
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: cultured cell population
has curation status: ready for release
definition: Cell seeding density is a measurement datum which denotes the number of cells per surface area in the case of adherent cells or number of cells per volume in the case of free cells deposited in the culture vessel to start a cell culture. The cell seeding density is therefore stated in number of cells per cm2 or number of cells per ml.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

cell volume
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: denotes
  some values from: cultured cell
has curation status: ready for release
definition: average cell volume is a measurement datum used to report over physcal occupancy of cells under study. This information is used for as input for kinetic modeling.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

confluence level
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: cultured cell population
example of usage: when cells reach 50% confluence level, replenish medium
has curation status: ready for release
definition: confluence level is a measurement datum denotes the status of a cell culture and how cells are occupying the space available in a plate. confluence levels are stated in %.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

dilution factor
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: dilution series reference
has curation status: ready for release
definition: dilution factor is a measurement data item which indicates in percentage the level of purity of a material in the context of dilution such as a dilution series.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

DNA content
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: denotes
  some values from: cultured cell
has curation status: ready for release
definition: the amount of dideoxyribonucleic acids present in a cell culture or tissue.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

interacellular metabolite average content
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: denotes
  some values from: cultured cell
has curation status: ready for release
definition: intracellular metabolite average content is a measurement provided of metabolite concentration normalized against cell average volume or DNA content or protein content or dry weight
term editor: Philippe Rocca-Serra
alternative term: metabolite content
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group Barcelona meeting, march 2015

metabolite concentration
type: Class
subclass of: measurement datum
has curation status: ready for release
definition: the concentration of a molecular entity acting as metabolite and stated in standard concentration units, such molar, micromolar and so on
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolite pool size estimate
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: pathway
    union of: Restriction
      on property: has role
      some values from: metabolite
has curation status: ready for release
definition: metabolite pool size estimate is an information entity used in fluxomics studies to estimate the amount of molecular entity available to a particular metabolic process. It is usually reported in umol per mg of protein.
editor note: can be also computed from simulation and be output of such simulation (then provide confidence indicator)
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: pool size
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

passage number
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: cultured cell population
has curation status: ready for release
definition: passage number is a measurement data item denoting how many times a cell culture has been split and transferred to a new culture vessel. It can also be considered to be equivalent to how many times a cell culture has reached 100% confluence
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

protein concentration
type: Class
subclass of: measurement datum
has curation status: ready for release
definition: ratio of protein content over a reference standard element (usually bovine serum albumin (BSA))
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

protein content
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has part
  some values from: mass measurement datum
subclass of: Restriction
  on property: denotes
  some values from: cultured cell
has curation status: ready for release
definition: the amount of (soluble) protein from cell culture or tissue. the quantity of total protein recovered from an extraction process varies depending on the solvent and buffers used during the extraction phase. the amount is usuall expressed in milligram (refer to Unit Ontology)
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

signal intensity
type: Class
subclass of: measurement datum
has curation status: ready for release
definition: signal intensity is a kind of measurement providing an estimate of the strength of a phenomena as it is recorded. For digital detector instrument, the signal intensity is usually a electric intensity or a field strength of the electromagnetic wave transmitting a signal.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

maximum m/z values signal intensity with baseline substraction
type: Class
subclass of: signal intensity
has curation status: ready for release
definition: Signal intensity of all m/z values at the maximum of the peak (also known as maximum signal intensity) and subtracting baseline.
term editor: Philippe Rocca-Serra
alternative term: peak height as signal intensity
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

total volume of cell culture
type: Class
subclass of: measurement datum
has curation status: ready for release
definition: total volume of cell culture is a measurement data item which denotes the volume occupied by a cell culture
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

isotopologue distribution matrix
type: Class
subclass of: table
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: chemical compound formula
    intersection of: signal intensity
    intersection of: corrected m/z
    intersection of: retention time
    intersection of: chemical entity assignment
example of usage: https://github.com/ISA-tools/isa-matrix-datapackages/tree/master/src/sirm_datapkg
has curation status: ready for release
definition: an isotopologue distribution matrix is an information object used in tracer based metabolomics experiments to report the amount of possible isotopologues (sets of isotopomers) derived from the tracer in a metabolic network. the matrix hold the mass isotopomer distributions (MIDs) of Elementary Metabolite Unit (EMU) which will be used as state variables. An EMU is defined as a distinct subset of a metabolite’s atoms. EMUs can exist in a variety of mass states depending on their isotopic compositions. An EMU in its lowest mass state is referred to as M+0, while an EMU that contains one additional atomic mass unit (e.g., due to the presence of a 13C atom in place of a 12C atom) is referred to as M+1, with higher mass states described accordingly. An MID is a vector that contains the fractional abundance of each mass state of an EMU.
term editor: Philippe Rocca-Serra
definition source: DOI 10.1002/bit.21632 An Elementary Metabolite Unit (EMU) BasedMethod of Isotopically Nonstationary Flux Analysis, Jamey D. Young, Jason L. Walther, Maciek R. Antoniewicz, Hyuntae Yoo,Gregory Stephanopoulos, Department of Chemical Engineering, Massachusetts Institute of Technology. http://onlinelibrary.wiley.com/doi/10.1002/bit.21632/epdf
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolic flux rate matrix
type: Class
subclass of: table
has curation status: ready for release
definition: a metabolic flux rate matrix is an information content entity which is defined as a 2 dimensional table associating chemical species with uptake and excretion rate in the cell
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

stoichiometry matrix
type: Class
subclass of: table
subclass of: Restriction
  on property: has part
  some values from: stoichiometric coefficient
subclass of: Restriction
  on property: is about
  min qualified cardinality: 1
  on class: chemical reaction
has curation status: ready for release
definition: a stoichiometry matrix is an information content entity holding arrays of stoichiometric coefficients, each associated to a specific chemical reactions
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolite identifier
type: Class
subclass of: centrally registered identifier
example of usage: a CHEBI identifier for chemical or an HMDB identifier
has curation status: ready for release
definition: a centrally registered identifier to denote a metabolite chemical entity
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

pathway identifier
type: Class
subclass of: centrally registered identifier
example of usage: a KEGG pathway identifier such as map00010 (http://www.genome.jp/dbget-bin/www_bget?map00010)
has curation status: ready for release
definition: a centrally registered identifier which denotes a pathway data item
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

protein identifier
type: Class
subclass of: centrally registered identifier
example of usage: a uniprot identifier such P20248 (http://www.uniprot.org/uniprot/P20248)
has curation status: ready for release
definition: a centrally registered identifier to denote a molecular entity of the type Protein.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

reaction identifier
type: Class
subclass of: centrally registered identifier
example of usage: a reactome identifier such as R-HSA-174054
has curation status: ready for release
definition: a centrally registered identifier which denotes a chemical reaction.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

calibration
type: Class
subclass of: planned process
has curation status: ready for release
definition: calibration is a process which relies on comparison between measurements in order to estimate the reliability of the measurements performed on a particular device or instrument configuration. a calibration process may be used to identify a systematic error in measurement and possibly include it into an error model. a calibration process may be used to detect degradation of parts of instruments when long data acquisition times are needed (e.g. degradation of a chromatography column in a GC-MS chain).
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

quality control
type: Class
subclass of: planned process
has curation status: ready for release
definition: quality control is a process which aims to ensure that procedures for producing a material or a measurement remain within established error tolerance margins. Quality control often relies on the use of references or standards against which readings are gauged. those standards can be 'negative control' which should produce in an absence of signal or 'positive control', which should result in the presence of a signal of known quality and intensity.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

assessing across studies variability
type: Class
subclass of: quality control
has curation status: ready for release
definition: assessing across studies variability is a quality control process which aims at monitoring the consistency of signal acquisitions between different studies (for instance in the context of meta-analysis and data integration) in order to detect unwanted causes of variation (i.e. variation that was not planned and that should be taken into account).
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

assessing instrument conditioning
type: Class
subclass of: quality control
has curation status: ready for release
definition: assessing instrument conditionning is a quality control process which aims at monitoring the stability of the analytical instrument prior to running data acquisition on specimen of interest by running a set of control runs.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

assessing within study variability
type: Class
subclass of: quality control
has curation status: ready for release
definition: assessing within study variability is a quality control process which aims at monitoring the consistency of signal acquisition throughout the course of a study in order to detect unwanted causes of variation (i.e. variation that was not planned and that should be taken into account).
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

assessing study batch to batch variation
type: Class
subclass of: assessing within study variability
has curation status: ready for release
definition: assessing study batch-to-batch variation is a within study variably quality control which specifically looks at how batching of data acquisition contributes to adding unwanted noice and how to account for it.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

detecting carry over event
type: Class
subclass of: quality control
subclass of: Restriction
  on property: has participant
  some values from: Class
    union of: sample preparation blank
    union of: solvent blank
has curation status: ready for release
definition: detecting carry over event is a quality control process which aims to determine if measurements in one sample are affected to earlier measurements made on different samples and indicative of insufficient matrix regeneration between 2 data acquisition events. this is usually assessed by running solvent blanks or sample preparation blank between analytical runs.
term editor: Philippe Rocca-Serra
alternative term: carry over detection
definition source: EU H2020 PhenoMenAl

detecting departure from linearity event
type: Class
subclass of: quality control
subclass of: Restriction
  on property: has participant
  some values from: dilution series reference
has curation status: ready for release
definition: detecting departure from linearity event is a quality control process which aims to determine if measurements respond in a linear fashion of a linear increase of concentration of analytes. this is usually assessed by running a dilution series between analytical runs.
term editor: Philippe Rocca-Serra
alternative term: linearity departure detection
definition source: EU H2020 PhenoMenAl

detecting sample degradation event
type: Class
subclass of: quality control
subclass of: Restriction
  on property: has participant
  some values from: sample preparation blank
has curation status: ready for release
definition: detecting sample degradation event is a quality control process which aims to determine if measurements in samples are affected by their run order or time of acquisition. This is usually assessed by running the same analytical samples at different points along the data acquistion plan (technical replication at the begining and end of runs).
term editor: Philippe Rocca-Serra
alternative term: sample degradatation detection
definition source: EU H2020 PhenoMenAl

metabolomics investigation
type: Class
equivalent class: Restriction
  on property: has part
  some values from: Class
    union of: targeted metabolite profiling
    union of: untargeted metabolite profiling
subclass of: investigation
has curation status: ready for release
definition: an investigation which focused on measuring small biological molecules known as metabolite with the goal of understanding biochemical process underlying normal or pathological biological processes
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

lipidomics investigation
type: Class
subclass of: metabolomics investigation
subclass of: Class
  intersection of: metabolomics investigation
  intersection of: Restriction
    on property: has_specified_input
    some values from: lipid
has curation status: ready for release
definition: lipidomics investigation is an investigation which aims at determining the lipid content of a biological system under given experimental conditions using data acquisition techniques such as mass spectrometry, nmr spectroscopy or chromatography techniques.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

stable isotope resolved metabolomics study
type: Class
subclass of: tracer analysis
subclass of: Restriction
  on property: has part
  some values from: isotope natural abundance correction
subclass of: Restriction
  on property: has part
  some values from: metabolic flux analysis
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: non-stationary isotopic labeling experiment
    union of: steady state isotopic labeling experiment
has curation status: ready for release
definition: stable isotope resolved metabolomics study is a kind of investigation which uses non-radioactive isotope for labeling compounds which are precursors in key metabolic reaction. These studies therefore allow deciphering reaction and understanding the fluxes in cells. Tracer based pathway discovery study is a specific type of fluxomics study which aims at discovery new metabolic routes and their associated signature metabolites by using isotopically labeled tracers
term editor: Philippe Rocca-Serra
alternative term: SIRMS
alternative term: tracer based metabolite profiling
definition source: cosmos tracer based metabolomics working group

metabolite quantitation using high performance liquid chromatography
type: Class
subclass of: assay
definition: A kind of assay which attempts to identify and measure relative concentration of all possible metabolites using the method high-performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography), is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group
definition source: https://en.wikipedia.org/wiki/High-performance_liquid_chromatography

targeted metabolite profiling
type: Class
subclass of: assay
has curation status: ready for release
definition: a kind of assay which attempts to identify and measure specific compound/ metabolites (known in advance) expressed as concentration or relative abundance ratio to a standard in a extract derived from a specimen using techniques such as gas chromatography mass spectrometry, liquid chromatography mass spectrometry, NMR spectroscopy or liquid chromatography DAD
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

untargeted metabolite profiling
type: Class
subclass of: assay
has curation status: ready for release
definition: a kind of assay which attempts to identify and measure relative concentration of all possible metabolites present in a extract derived from a specimen using techniques such as gas chromatography mass spectrometry, liquid chromatography mass spectrometry, NMR spectroscopy.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: global metabolite profiling
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

fresh culture medium
type: Class
subclass of: culture medium
has curation status: ready for release
definition: a fresh culture medium is a culture medium which presents its nominal characteristisc in terms of molecular concentration of its components, pH, and physical chemical expected properties.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

spent culture medium
type: Class
subclass of: culture medium
has curation status: ready for release
definition: spent culture medium is a culture medium which has been added to a cell culture and which has been depleted of its component as used by the growing cell and which has received the by products of cell metabolites excreted by the cells. Therefore, spent culture medium will different significantly in pH and physical chemical properties from the initial fresh culture medium added to the cell as the begining of the cell culture. Spent culture medium is usually recovered by aspiration or mild centrifugation (as not to distrupt cell membrane) of the cell culture.
term editor: Philippe Rocca-Serra
alternative term: cell culture supernatant
alternative term: spent medium
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolism quenching
type: Class
subclass of: material processing
has curation status: ready for release
definition: metabolism quenching is a planned processed whose objective is a quick extinction of all biochemical reactions occuring in a biological system in order to fix molecular entity concentrations for downstream quantitation and analysis. An array of physical or chemical agent may be used to achieve that goal.
term editor: Philippe Rocca-Serra
alternative term: metabolism immediate extinction
definition source: EU H2020 PhenoMenAl

direct metabolism quenching by solvent
type: Class
subclass of: metabolism quenching
has curation status: ready for release
definition: direct metabolism quenching by solvent is a kind biochemical reaction extinction process which relies on organic solvents to denature enzymatic machinery and inactivate it.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolism quenching by 13 CD3-QDA in cold CH3CN
type: Class
subclass of: direct metabolism quenching by solvent
has curation status: ready for release
definition: a type of metabolism immediate extinction using cold acetonitrile
term editor: Philippe Rocca-Serra
alternative term: metabolism quenching using QDA
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer
type: Class
subclass of: metabolism quenching
has curation status: ready for release
definition: a type of metabolism extinction which uses refrigerated buffer containing 60% of methanol ammonium bicarbonate solution
term editor: Philippe Rocca-Serra
alternative term: cooled 60% methanol NH4HCO3 metabolism quenching
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolism quenching using precooled 60 percent methanol HEPES buffer
type: Class
subclass of: metabolism quenching
has curation status: ready for release
definition: a type of metabolism extinction which uses refrigerated buffer containing 60% of methanol HEPES solution
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolism quenching using precooled PBS buffer
type: Class
subclass of: metabolism quenching
has curation status: ready for release
definition: a type of metabolism extinction which uses refrigerated PBS buffer
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

elution program
type: Class
subclass of: protocol
example of usage: acetonitrile 5%, isopropanol 95% for 15 minutes at flow rate 1 ml/min,
has curation status: ready for release
definition: an elution program is a set of recorded instructions which determine the mobile phase (gas or liquid) composition, pressure, temperature and flow rate during the chromatography separation.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

derivatization
type: Class
equivalent class: Restriction
  on property: has_specified_input
  some values from: derivatization agent
subclass of: material combination
has curation status: ready for release
definition: derivatization is a technique used in chemistry which transforms a chemical compound into a product (the reaction's derivate) of similar chemical structure, called a derivative. That compound has properties more amenable to a particular analytical method. Some samples analyzed by GC require derivatization in order to make them suitable for analysis. Compounds that have poor volatility, poor thermal stability, or that can be adsorbed in the injector will exhibit nonreproducible peak areas, heights, and shapes. Other compounds that respond poorly on a specific detector may need to be “tagged” with a different functional group to improve detection.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: adapted from https://en.wikipedia.org/wiki/Derivatization and https://www.restek.com/pdfs/CFTS1269.pdf. Last accessed: 2018-01-11

acetylation
type: Class
subclass of: derivatization
has curation status: ready for release
definition: a kind of derivatization which results in the addition of acetyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: EU cosmos tracer based metabolomics working group

trifluoroacetylation
type: Class
subclass of: acetylation
has curation status: ready for release
definition: a kind of derivatization which results in the addition of trifluoroacetyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenal

alkylation
type: Class
subclass of: derivatization
has curation status: ready for release
definition: a kind of derivatization which results in the addition of alkyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenal

methylation
type: Class
subclass of: derivatization
has curation status: ready for release
definition: a kind of derivatization which results in the addition of methyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenal

oximation
type: Class
subclass of: derivatization
has curation status: ready for release
definition: a kind of derivatization which results in the addition of oxime group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenal

silylation
type: Class
subclass of: derivatization
has curation status: ready for release
definition: a kind of derivatization which results in the addition of silyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenal

isotopic labeling
type: Class
subclass of: material combination
has curation status: ready for release
definition: Isotopic labeling (or isotopic labelling) is a technique used to track the passage of an isotope (an atom with a detectable variation) through a reaction, metabolic pathway, or cell. The reactant is 'labeled' by replacing specific atoms by their isotope.
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Isotopic_labeling

isotopic labeling with positional labeled tracer
type: Class
subclass of: isotopic labeling
subclass of: Restriction
  on property: has_specified_input
  some values from: isotopic tracer
subclass of: Restriction
  on property: has_specified_output
  some values from: positionally labeled isotopic tracer
has curation status: ready for release
definition: Specific isotopic labeling refers to the placement of a single label (e.g., 2H, 13C, or 15N) in a specified location in a molecule.
term editor: Philippe Rocca-Serra
alternative term: specific isotopic labeling
definition source: EU H2020 PhenoMenAl
definition source: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/stable-isotopes/biomolecular_nmr.pdf

isotopic labeling with uniformly labeled tracer
type: Class
subclass of: isotopic labeling
subclass of: Restriction
  on property: has_specified_input
  some values from: isotopic tracer
subclass of: Restriction
  on property: has_specified_output
  some values from: uniformly labeled isotopic tracer
has curation status: ready for release
definition: Uniform labeling refers to biosynthetic labeling of all carbon, nitrogen, or hydrogen sites with stable isotopes. Uniform labeling of proteins with 15N is particularly convenient because of the strategic locations of nitrogens in the backbone and the absence of homonuclear couplings due to the intervening carbons. It is also possible to replace all of the carbons with 13C, although in this case the spectroscopy has to deal with the network of couplings among bonded carbons. Similarly, all of the hydrogens can be replaced with deuterons in order to attenuate the dipolar couplings among the hydrogens that often present complications and difficulties in the experiments.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/stable-isotopes/biomolecular_nmr.pdf

collection at cell cycle phase
type: Class
subclass of: specimen collection process
has curation status: ready for release
definition: a process of collecting a sample when the cells of cell culture growth are collected at a specific phase of the cell division cycle (e.g collection at G2/G1). This often requires a cell synchronization step.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

collection at cytostatic phase
type: Class
subclass of: specimen collection process
has curation status: ready for release
definition: a process of collecting a sample when the cells of a cell culture growth are not dividing
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

collection at logarithmic phase
type: Class
subclass of: specimen collection process
has curation status: ready for release
definition: a process of collecting a sample when the cell culture growth can be approximated by a logarithm function.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

collection at specific cell culture passage
type: Class
subclass of: specimen collection process
has curation status: ready for release
definition: collection at specific cell culture passage is a kind of specimen collection which occurs after a strictly defined number of cell culture splitting, defined to control how many cell divisions have been performed.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

collection at stabilization phase before experiment
type: Class
subclass of: specimen collection process
has curation status: ready for release
definition: collection at stabilization phase before experiment is a kind of specimen collection process which takes places once cells have reached a stationary growth phase and prior the main experimental intervention is applied.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

collection at stationary phase
type: Class
subclass of: specimen collection process
has curation status: ready for release
definition: a process of collecting a sample when the cell culture growth has reached a plateau, indicative of a steady state
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: collection at steady state phase
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

flux balance analysis
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: isotopologue distribution matrix
    union of: metabolic flux rate matrix
has curation status: ready for release
definition: Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. Flux balance analysis calculates the flow of metabolites through a metabolic network, thereby making it possible to predict the growth rate of an organism or the rate of production of a biotechnologically important metabolite.
term editor: Philippe Rocca-Serra
definition source: What is flux balance analysis? Jeffrey D. Orth, Ines Thiele, and Bernhard Ø. Palsson Nat Biotechnol. 2010 Mar; 28(3): 245–248. doi: 10.1038/nbt.1614
definition source: cosmos tracer based metabolomics working group

13C-constrained flux balance analysis
type: Class
subclass of: flux balance analysis
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

isotopomer data matrix
type: Class
subclass of: table
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: chemical shift
    intersection of: chemical compound formula
    intersection of: multiplicity feature
    intersection of: centrally registered identifier
    intersection of: peak area
    intersection of: chemical entity assignment
definition: an isotopomer data matrix is a table resulting from the analysis of NMR data acquired in the context of tracer based studies and which contains information about chemical entity assignment
term editor: Philippe Rocca-Serra
definition source: MSIO

isotope natural abundance correction
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: part of
  some values from: stable isotope resolved metabolomics study
example of usage: Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. BMC Bioinformatics. 2010 Mar 17;11:139. doi: 10.1186/1471-2105-11-139.
has curation status: ready for release
definition: natural abundance correction is a data transformation which aims to take into account the contribution of natural random variation in isotopic composition in the environment and adjust for it during the calculation of mass isotopologue distribution in a tracer based metabolomics experiment
term editor: Hunter Moseley
term editor: Philippe Rocca-Serra
definition source: BMC Bioinformatics. 2010 Mar 17;11:139. doi: 10.1186/1471-2105-11-139. Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry.
definition source: cosmos tracer based metabolomics working group

metabolic flux analysis
type: Class
subclass of: tracer analysis
subclass of: Restriction
  on property: has_specified_input
  some values from: isotopic tracer
has curation status: ready for release
definition: metabolic flux analysis is a type of investigation which uses data from tracer based studies to provide insights into cellular metabolites creation and destruction.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

steady state 13C metabolic flux analysis
type: Class
subclass of: metabolic flux analysis
has curation status: ready for release
definition: steady-state 13C metabolic flux analysis is a metabolic flux analysis approach which relies on 13C tracer experiments and requires long incubation period necessary to meet methodological requirements that all reactions under study have reach steady state. By feeding cells a 13C-labeled substrate and subsequently measuring the patterns of isotope incorporation in downstream metabolic products, extensive information about the intracellular distribution of carbon flux can be obtained. This enables system-wide quantification of reversible, parallel, and cyclic metabolic pathways that would be otherwise unidentifiable based solely upon measurements of extracellular nutrient uptake and product excretion (Zamboni et al., 2009). While 13C MFA provides a rich source of phenotypic information, the application of this technique to mammalian systems presents unique challenges. In particular, the presence of subcellular compartmentation, complex media formulations, and slow labeling dynamics can lead to significant difficulties in experimental design and data interpretation (Zamboni, 2011).
term editor: Philippe Rocca-Serra
alternative term: conventional 13C metabolic flux analysis
alternative term: conventional 13C-MFA
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group
definition source: https://www.ncbi.nlm.nih.gov/pubmed/22140245

isotopically non-stationary 13C-metabolic flux analysis
type: Class
subclass of: metabolic flux analysis
has curation status: ready for release
definition: Isotopically non-stationary MFA (INST-MFA) is a metabolic flux analysis which provides an approach to circumvent limitations from other methods through computational analysis of metabolite labeling patterns obtained during the transient labeling period prior to isotopic steady state (Wiechert and Noh, 2005). This approach offers several advantages over steady-state MFA, including shorter experimental times and the ability to determine fluxes with increased precision (Nöh and Wiechert, 2011; Young and Walther, 2008).
term editor: Philippe Rocca-Serra
alternative term: INST-13C-MFA
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535509/

tracer analysis
type: Class
subclass of: fluxomics investigation
subclass of: Restriction
  on property: has_specified_input
  some values from: isotopic tracer
has curation status: ready for release
definition: a tracer analysis is a type of experimental procedure which relies on tracer molecules, usually non radioactive, to probe metabolic pathways and biochemical routes
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

normalization by optimal selection with multiple internal standards
type: Class
subclass of: normalization data transformation
has curation status: ready for release
definition: a normalization process which relies on the signal intensity measured for several reference compounds (internal standards) injected or added to the test samples in known quantities, thereby allowing sample comparison which have been placed on equal footing.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

normalization to a total sum
type: Class
subclass of: normalization data transformation
has curation status: ready for release
definition: a normalization process which relies on the computing to total signal intensity by simply summing up those signals and then for each sample measurements, dividing it by the total signal. The total sum is used as reference to which sample signals are then compared.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

normalization to multiple standard with cross contribution compensation
type: Class
subclass of: normalization data transformation
has curation status: ready for release
definition: a normalization process used in mass spectrometry signal processing which takes into account the fact that analytes can interact with internal standards and impair accurate estimatation of these. The interaction phenomenon is known as cross contribution and needs to be compensated for.
term editor: Philippe Rocca-Serra
definition source: Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data. Henning Redestig, Atsushi Fukushima, Hans Stenlund, Thomas Moritz, Masanori Arita, Kazuki Saito and Miyako Kusano. RIKEN Plant Science Center, Tsurumi-ku, Suehiro-cho, 1-7-22 Yokohama, Kanagawa, 230-0045, Japan, and Umea Plant Science Center, Umea University, 901 87 Umea, Sweden. Anal. Chem., 2009, 81 (19), pp 7974–7980 DOI: 10.1021/ac901143w
definition source: cosmos tracer based metabolomics working group

remove unwanted variation 2-step normalization
type: Class
subclass of: normalization data transformation
example of usage: ruv_starter_analysis(Y,X,ctl) http://www-personal.umich.edu/~johanngb/ruv/howto/howto.html
definition: the 2 step normalization is a normalization process which uses 2 complementary steps provided suitable quality controls have been supplied. The process attempts to remove overall unwanted variation given suitable controls and uses factors of interest in the normalization. It relies on linear mixed effects model which utilizes quality control metabolites to obtain normalized data in typical metabolomics experiments.
term editor: Philippe Rocca-Serra
alternative term: RUV
alternative term: RUV-2
definition source: Statistical Methods for Handling Unwanted Variation in Metabolomics Data. Alysha M. De Livera, Marko Sysi-Aho, Laurent Jacob, Johann A. Gagnon-Bartsch, Sandra Castillo, Julie A. Simpson, and Terence P. Speed Biostatistics Unit, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC 3800, Australia Zora Biosciences Oy, FIN-02150 Espoo, Finland VTT Technical Research Centre of Finland, P. O. Box 1000, FI-02044 VTT Espoo, Finland Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France Department of Statistics, University of California, Berkeley, California United States, 94720 Bioinformatics Division, Walter and Eliza Hall Institute, 1 G Royal Parade, Parkville, Victoria 3052, Australia Department of Mathematics and Statistics, University of Melbourne, VIC 3800, Melbourne, Australia Anal. Chem., 2015, 87 (7), pp 3606–3615 DOI: 10.1021/ac502439y
definition source: Using control genes to correct for unwanted variation in microarray data. Gagnon-Bartsch and Speed, 2012. Available at: http://biostatistics.oxfordjournals.org/content/13/3/539.full. Removing Unwanted Variation from High Dimensional Data with Negative Controls. GagnonBartsch, Jacob, and Speed, 2013. Available at: http://statistics.berkeley.edu/tech-reports/820.
definition source: cosmos tracer based metabolomics working group
definition source: http://www-personal.umich.edu/~johanngb/ruv/index.html

normalization to a single internal standard
type: Class
subclass of: normalization data transformation
has curation status: ready for release
definition: a normalization process which relies on the signal intensity measured for one reference compound (an internal standard) injected or added to the test samples in known quantity, thereby allowing sample comparison which have been placed on equal footing based on this reference.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

metabolite extraction
type: Class
subclass of: extraction
example of usage: ribose extraction
has curation status: ready for release
definition: metabolite extraction is an extraction process which aims to retrieve small molecules known as metabolites, from a specimen
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

lipid extraction
type: Class
subclass of: metabolite extraction
has curation status: ready for release
definition: lipid extraction is an extraction which aims to retrieve lipid (hydrophobic carbohydrate) from a specimen
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

polar metabolite extraction
type: Class
subclass of: metabolite extraction
has curation status: ready for release
definition: polar metabolite extraction is a metabolite extraction which aims to retrieve water soluble or metabolites with polar solvent solubility properties. This is usually exclusive of hydrophobique, lipophile and lipid like metabolites.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

cell layer enzymatic digestion
type: Class
subclass of: material component separation
has curation status: ready for release
definition: cell layer enzymatic digestion is a material component separation process which uses an enzyme, usually a protease, to lyse the bonds between cultured cells and their substrates (usually a microplate, which may be coated with anchoring material such as collagen). Once the digestion is complete, cell layers can be harvested with minimal damage to the cells themselves.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

cell scraping
type: Class
subclass of: material component separation
has curation status: ready for release
definition: cell scraping is a material component separation technique which uses mechanism means (as opposed to enzymatic ones) to detach cultured cells from the growth substrate. The technique is thought to be more aggressive and cause cellular breakage but has the benefit of avoiding use of enzymes, which may have their own side effects on cellular content.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

centrifugation
type: Class
subclass of: material component separation
has curation status: ready for release
definition: centrifugation is a material component separation process which relies on centrifugational forces applied by means of high velocity rotation to a sample placed in a vial or tube in a rotor, fixed to an centrifugation instrument.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

gas chromatography
type: Class
subclass of: material component separation
has curation status: ready for release
definition: gas chromatography is a material component separation process which use a mobile phase in gaseous form to force a mixture of chemical through chromatography columns and associated detecting equipment, which may be a mass spectrometry in GC-MS applications.
term editor: Philippe Rocca-Serra
alternative term: GC
definition source: EU H2020 PhenoMenAl

high performance liquid chromatography
type: Class
subclass of: material component separation
has curation status: ready for release
definition: high performance liquid chromatography is a kind of material component separation process which uses a mobile phase in liquid form to force a mixture of chemical through chromatography columns and associated detecting equipment, which may be a mass spectrometry in LC-MS applications. the notion of high performance comes from the fact that higher pressure is applied to the liquid phase to pass material with adsorbant properties. Those may vary depending on the composition of the mobile phase (gradients between 2 solutions may be used).
term editor: Philippe Rocca-Serra
alternative term: HPLC
definition source: EU H2020 PhenoMenAl
definition source: adapted from https://en.wikipedia.org/wiki/High-performance_liquid_chromatography

biomass
type: Class
subclass of: rate measurement datum
has curation status: ready for release
definition: biomass is a rate measurement datum of how much biochemical or biological material is produced over a period of time. it is usually reported in 'per hour'.
term editor: Philippe Rocca-Serra
definition source: COSMOS
definition source: EU H2020 PhenoMenAl

metabolic flux
type: Class
subclass of: rate measurement datum
has curation status: ready for release
definition: Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway. Within cells, regulation of flux is vital for all metabolic pathways to regulate the metabolic pathway's activity under different conditions. Flux is therefore of great interest in metabolic network modelling, where it is analysed via flux balance analysis. amount per unit of time maybe normalized by protein content
term editor: Philippe Rocca-Serra
alternative term: metabolic rate
definition source: http://en.wikipedia.org/wiki/Flux_%28metabolism%29

extracellular flux
type: Class
subclass of: information content entity
has curation status: ready for release
definition: An extracellular flux is a metabolic flux indicating the rate of absortion or release of a molecular entity by a cell system from or to its surroundings, respectively.
term editor: Philippe Rocca-Serra
definition source: https://www.microbialcellfactories.com/content/13/1/152
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolite excretion flux
type: Class
subclass of: extracellular flux
has curation status: ready for release
definition: an excretion flux is a metabolic flux indicating the rate of release of a metabolite by a cell system to its surroundings.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: excretion rate
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

metabolite uptake flux
type: Class
subclass of: extracellular flux
has curation status: ready for release
definition: an uptake flux is a metabolic flux indicating the rate of absorption of a molecular entity by a cell system from its surroundings
term editor: Philippe Rocca-Serra
alternative term: consumption rate
alternative term: uptake rate
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

reaction rate
type: Class
subclass of: rate measurement datum
has curation status: ready for release
definition: the reaction rate is a rate measurement datum denoting a biochemical reaction as measured according to standard experimental methods.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

continuous fermentation cell culture
type: Class
subclass of: cultured cell population
has curation status: requires discussion
definition: continuous fermentation cell culture is a type of processed material which involved a bacterial or yeast cell stock grown in conditions such as nutrients are added and product removed at a steady rate throughout the culture process. This is usually achieved using the specific type of fermenter known as a fed-batch culture reactor).
editor note: classes could be moved to become subclasses of 'cell culture process'
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: http://ib.bioninja.com.au/options/untitled/b1-microbiology-organisms/batch-versus-continuous.html

double layer cell culture
type: Class
subclass of: cultured cell population
has curation status: requires discussion
definition: a cell culture population where cells are grown on top of each other, producing two layers of cells on the surface of the growth substrate, usually a flask or a petri dish
editor note: classes could be moved to become subclasses of 'cell culture process'
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

monolayer cell culture
type: Class
subclass of: cultured cell population
has curation status: requires discussion
definition: a cell culture population where no cells are grown on top of each other, producing a single layer of cells on the surface of the growth substrate, usually a flask or a petri dish
editor note: classes could be moved to become subclasses of 'cell culture process'
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

sandwich cell culture
type: Class
subclass of: cultured cell population
example of usage: https://www.ncbi.nlm.nih.gov/pubmed/20109035
has curation status: requires discussion
definition: a sandwich cell culture is a type of cell culture population where the grown cells are in contact with a substratum at the bottom and the top, thereby providing a more defined boundary and level of interaction than in suspension grown cells or in classic monolayer cell cultures.
editor note: classes could be moved to become subclasses of 'cell culture process'
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

3D cell culture
type: Class
subclass of: cultured cell population
has curation status: requires discussion
definition: a 3D cell culture is a cultured cell population grown in conditions which better mimicks in-vivo growth environment (i.e. more effectively than a 2D culture) allowing more complex recapitulation of cellular processes. These cell cultures are achieved by used of scaffolding agents.
editor note: classes could be moved to become subclasses of 'cell culture process'
term editor: Philippe Rocca-Serra
alternative term: spheroid culture
definition source: EU H2020 PhenoMenAl
definition source: https://www.thermofisher.com/blog/cellculture/3d-culturing-leads-parkinsons-breakthrough/

chromatography column
type: Class
subclass of: device
has curation status: ready for release
definition: A Chromatography column is a device used in chromatography for the separation of chemical compounds. A chromatography column contains the stationary phase, allowing the mobile phase to pass through it. Chromatography columns of different types are used in both gas and liquid chromatography.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group
definition source: https://en.wikipedia.org/wiki/Chromatography_column

HPLC instrument
type: Class
subclass of: device
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: An Instrument which is used to carry out a high performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography) technique. HPLC is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. It relies on pumps to pass a pressurized liquid solvent containing the sample mixture through a column filled with a solid adsorbent material. The schematic of an HPLC instrument typically includes a degasser, sampler, pumps, and a detector. The sampler brings the sample mixture into the mobile phase stream which carries it into the column. The pumps deliver the desired flow and composition of the mobile phase through the column. The detector generates a signal proportional to the amount of sample component emerging from the column, hence allowing for quantitative analysis of the sample components. A digital microprocessor and user software control the HPLC instrument and provide data analysis.
definition source: EU H2020 PhenoMenAl
definition source: https://en.wikipedia.org/wiki/High-performance_liquid_chromatography

96-well microplate
type: Class
subclass of: container
definition: 96-well microplate is an array of wells usually arranged in 8 rows of 12 columns whose volume range from 0.2 ml to 1.5 ml and which are used to grow cell or perform biochemical, in-vitro reactions. The material making up the plate may vary and may be surface treated in many custom way.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

chemostat
type: Class
subclass of: container
definition: a chemostat is a device to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant. By changing the rate with which medium is added to the bioreactor the growth rate of the microorganism can be easily controlled. It allows culture to reach physiological steady state and chemostat is often used to gather steady state data about an organism in order to generate a mathematical model relating to its metabolic processes. The name chemostat stems from "Chemical environment is static". The most striking advantages of chemostats are two-fold: microorganisms can be kept at a constant environmental conditions until the cultivated microorganisms reach steady state, defined by their specific growth rate (μ) being in balance with the dilution rate (D). Once the system is equilibrated, the steady state data can be used for quantification of physiological parameters and metabolic rates of organisms, which are eventually required for the parameterization of mathematical models.
term editor: Philippe Rocca-Serra
definition source: 10.4319/lom.2014.12.432 http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group
definition source: http://en.wikipedia.org/wiki/Chemostat

coated microplate
type: Class
subclass of: container
definition: a coated microplate is a kind of microplate whom surface has been treated in some, for instance by covalently attaching protein such as antibodies and cell matrix molecules to favor cell growth or induce speficic cellular behavior.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

constantly fed-batch culture reactor
type: Class
subclass of: container
definition: a constantly fed-btach culture reactor is a device in which the feed rate of a growth-limiting substrate is constant, i.e. the feed rate is invariant during the culture.
term editor: Philippe Rocca-Serra
alternative term: CFBC
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group
definition source: http://en.wikipedia.org/wiki/Fed-batch_culture#Constantly-fed-batch_culture
definition source: http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf

exponentially fed-batch culture reactor
type: Class
subclass of: container
definition: an exponentially fed-batch culture reactor is a device which deliver the ability to grow cells in a way non too dissimilar to that of a chemostat based culture, meaning that the cells are in a quasi steady-state condition.
term editor: Philippe Rocca-Serra
alternative term: EFBC
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group
definition source: http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf

fermenter
type: Class
subclass of: container
definition: A container in which fermentation takes place.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: COSMOS tracer based metabolomics working group
definition source: EU H2020 PhenoMenAl

flask
type: Class
subclass of: container
definition: a flask is a kind of container used for cell culture, and which is available in an array of material (usually transparent plastic polymer) which may be surface treated.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

petri dish
type: Class
subclass of: container
definition: a petri dish is a container used to grow cells or perform biochemical reactions, which used to be made of glass, but which is now available in a variety of surface treated or non-treated plastic polymers. a petri dish is a thin cylinder with the upper part acting as a lid, resting on small peg, large enough to enable gaseaous exchanges but still preventing water evaporation.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

uncoated microplate
type: Class
subclass of: container
definition: a uncoated microplate is a kind of microplate whom surface has not received any treatment and is uniquely made of polymer.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

mass spectrometry instrument
type: Class
subclass of: material separation device
has curation status: to be replaced with external ontology term
definition source: EU H2020 PhenoMenAl

NMR instrument
type: Class
subclass of: measurement device
has curation status: to be replaced with external ontology term
term editor: import from NMRMLCV

high dose
type: Class
subclass of: dose
has curation status: ready for release
definition: high dose is a dose specifically set to trigger strong response in the system it is administered to, those effects may be toxic. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system).
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

low dose
type: Class
subclass of: dose
has curation status: ready for release
definition: low dose is a dose specifically set to trigger no or very limited response in the system it is administered to, those effects are not expected to be toxic. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system).
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

lethal dose
type: Class
subclass of: dose
has curation status: ready for release
definition: a "lethal dose" represents a dose (usually recorded as dose per kilogram of subject body weight) at which a given percentage of subjects will die.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl
definition source: https://en.wikipedia.org/wiki/Lethal_dose

lethal dose 50
type: Class
subclass of: lethal dose
has curation status: ready for release
definition: the "lethal dose 50" represents a dose (usually recorded as dose per kilogram of subject body weight) at which 50% of subjects will die.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: LD50
definition source: EU H2020 PhenoMenAl
definition source: https://en.wikipedia.org/wiki/Lethal_dose

medium dose
type: Class
subclass of: dose
has curation status: ready for release
definition: medium dose is a dose specifically set to trigger limited but clear response in the system it is administered to, those effects are not expected to be toxic but may be. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system).
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

NOAEL dose
type: Class
subclass of: dose
has curation status: ready for release
definition: noael dose is a dose defined as the highest experimental point that is without adverse effect.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: No Observed Adverse Effect Level dose
definition source: https://en.wikipedia.org/wiki/No-observed-adverse-effect_level

batch cell culture
type: Class
subclass of: cultured cell population
has curation status: ready for release
has curation status: requires discussion
definition: continuous fermentation cell culture is a type of processed material which involved a bacterial or yeast cell stock grown in conditions such as nutrients are added at the begining of the culture process and products removed at the end.
editor note: classes could be moved to become subclasses of 'cell culture process'
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

fluxomics investigation
type: Class
subclass of: metabolomics investigation
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: targeted metabolite profiling
    union of: untargeted metabolite profiling
definition: fluxomics is a kind of investigation which aims at identifying, quantifying the fluxes of molecules in cellular systems and understanding the cellular metabolism.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

mass isotopomer fractional abundance
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: part of
  some values from: isotopologue distribution matrix
has curation status: ready for release
definition: mass isotopomer fractional abundance is a measurement data item corresponding to the following: the most abundant species is given the value 100 and all other species are normalized relative to 100 and expressed as percent relative abundance. fractional abundance of Mx=Ax= (abundance Mx) / ∑(i=0..n) abundance Mi, where Mx represents mass isotopomer Mx.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: mass isotopomer distribution
definition source: https://www.ncbi.nlm.nih.gov/pubmed/10362629

steady state isotopic labeling experiment
type: Class
subclass of: stable isotope resolved metabolomics study
subclass of: Restriction
  on property: has_specified_input
  some values from: isotopic tracer
has curation status: ready for release
definition: steady state labeling experiment is a material processing used in fluxomics studies where cells cultures are grown continuously in the presence of radiolabeled tracer compound throughout multiple platings. The redistribution of the label into metabolic intermediates and end-products is analysed when the system has reached an isotopic and metabolic steady state.
term editor: Philippe Rocca-Serra
definition source: EU H2020 PhenoMenAl

m over z
type: Class
subclass of: measurement datum
has curation status: ready for release
definition: the m/z notation is used for the independent variable in a mass spectrum. The mass-to-charge ratio (m/Q) is a physical quantity that is most widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger electron spectroscopy, cosmology and mass spectrometry.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Mass-to-charge_ratio

corrected m/z
type: Class
subclass of: m over z
has curation status: ready for release
definition: a m over z ratio which underwent a correction data transformation to take into account variations caused by a specific aspects of the data acquisition process.
term editor: Philippe Rocca-Serra
definition source: MSIO

reference corrected m/z
type: Class
subclass of: corrected m/z
has curation status: ready for release
definition: a m over z ratio which underwent a correction data transformation that takes into account the signal obtained from a reference compound and its spectral characteristics.
term editor: Philippe Rocca-Serra
definition source: MSIO

reference and adduct corrected m/z
type: Class
subclass of: corrected m/z
has curation status: ready for release
definition: a m over z ratio which underwent a correction data transformation that takes into account the signal obtained from a reference compound, its spectral characteristics as well as the contributions caused by adducts generated during the ionization process.
term editor: Philippe Rocca-Serra
definition source: MSIO

retention time
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: Class
    union of: second
    union of: minute
has curation status: ready for release
definition: Retention time (RT) is a measure of the time taken for a solute to pass through a chromatography column. It is calculated as the time from injection to detection.
term editor: Philippe Rocca-Serra
definition source: https://www.chromatographytoday.com/news/autosamplers/36/breaking-news/understanding-the-difference-between-retention-time-and-relative-retention-time/31166

peak area
type: Class
subclass of: signal intensity
has curation status: ready for release
definition: The area of a peak is a kind of data derived from a spectrum which is proportional to the product of its height and its width of a spectrum peak, but the proportionality constant depends on the peak shape.
term editor: Philippe Rocca-Serra
definition source: adapted from: https://terpconnect.umd.edu/~toh/spectrum/Integration.html

normalized corrected peak area
type: Class
subclass of: peak area
has curation status: ready for release
definition: a normalized corrected peak area is a type of peak area which is produced followed a normalization data transformation and correction in order to make spectra comparable.
term editor: Philippe Rocca-Serra
definition source: MSIO

total m/z signal intensity integrating over the whole peak with baseline substraction
type: Class
subclass of: signal intensity
has curation status: ready for release
definition: Signal intensity of all m/z values after integrating the whole peak and subtracting baseline
term editor: Philippe Rocca-Serra
alternative term: peak area as signal intensity
definition source: EU H2020 PhenoMenAl
definition source: cosmos tracer based metabolomics working group

chemical entity assignment
type: Class
subclass of: information content entity
has curation status: ready for release
definition: chemical entity assignment is an annotation which uses spectral information to assign and identify and molecular entity/chemical compound. Various methods manual and computer assisted may be used.
term editor: Philippe Rocca-Serra

assignment by database search
type: Class
subclass of: chemical entity assignment
has curation status: ready for release
definition: assignment by database search is a type of chemical entity assignment which relies on probing chemical electronic libraries and chemical databases to determine matching structure and thereby attempt to assign a chemical identity. Searches may rely on InChi string or keys for instance.
term editor: Philippe Rocca-Serra
definition source: MSIO

direct assignment to standard
type: Class
subclass of: chemical entity assignment
has curation status: ready for release
definition: chemical entity assignment by direct assignment to standards is a data transformation process which uses spectral information from a known compound (ie. the standard) to match the signature and affirm identity based on the spectral features found in the sample.
term editor: Philippe Rocca-Serra
definition source: MSIO

indirect assignment to standard
type: Class
subclass of: chemical entity assignment
has curation status: ready for release
definition: chemical entity assignment by indirect assignment to standards is a data transformation process which uses spectral information from a known compound (ie. the standard) to infer chemical properties about another compound found in the sample.
term editor: Philippe Rocca-Serra
definition source: MSIO

standard
type: Class
subclass of: information content entity
definition: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
imported from: ms.owl
has_obo_namespace: MS
id: MS:1000898

de facto standard
type: Class
subclass of: standard
definition: A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
imported from: ms.owl
has_obo_namespace: MS
id: MS:1000899

minimum information standard
type: Class
subclass of: standard
definition: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
imported from: ms.owl
has_obo_namespace: MS
id: MS:1000900

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

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

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

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

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

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

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

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred label: Bilateria
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

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

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

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

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
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
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: chmo.owl
imported from: Ontology for Biomedical Investigation
has_alternative_id: CHMO:0001840
id: OBI:0000011

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
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
imported from: Ontology for Biomedical Investigation

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 label: 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: Ontology for Biomedical Investigation
ISA alternative term: study

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred label: 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.
imported from: Ontology for Biomedical Investigation

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: information content entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
term editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: chmo.owl
imported from: Ontology for Biomedical Investigation
ISA alternative term: study assay
IEDB alternative term: any method
has_alternative_id: CHMO:0000000
has_alternative_id: CHMO:0001133
has_exact_synonym: measurement method
id: OBI:0000070

quantitative confidence value
type: Class
subclass of: data item
editor preferred label: quantitative confidence value
has curation status: pending final vetting
definition: A data item which is used to indicate the degree of uncertainty about a measurement.
term editor: person:Chris Stoeckert
definition source: group:OBI
imported from: Ontology for Biomedical Investigation

culture medium
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: maintaining cell culture
    union of: establishing cell culture
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: ready for release
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
term editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI
imported from: Ontology for Biomedical Investigation

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
term editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
imported from: Ontology for Biomedical Investigation
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

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_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
subclass of: Restriction
  on property: has_specified_output
  all values from: material entity
editor preferred label: 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 term: material transformation
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigation

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
editor preferred label: study subject role
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has curation status: ready for release
definition: A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
editor note: A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
term editor: GROUP: Role Branch
definition source: OBI
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: Ontology for Biomedical Investigation

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  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 label: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: 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
imported from: Ontology for Biomedical Investigation

intervention design
type: Class
equivalent class: Class
  intersection of: study design
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: study design independent variable
      intersection of: Restriction
        on property: is about
        some values from: study intervention
subclass of: study design
editor preferred label: intervention design
example of usage: PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
has curation status: pending final vetting
definition: An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
term editor: Philppe Rocca-Serra
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigation

p-value
type: Class
subclass of: quantitative confidence value
editor preferred label: p-value
example of usage: PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
has curation status: organizational term
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
editor note: May be outside the scope of OBI long term, is needed so is retained
term editor: PERSON:Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/P-value
imported from: Ontology for Biomedical Investigation

population
type: Class
subclass of: material entity
editor preferred label: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: pending final vetting
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
term editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process
imported from: Ontology for Biomedical Investigation

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: image
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred label: imaging assay
has curation status: pending final vetting
definition: An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigation

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: ready for release
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: Ontology for Biomedical Investigation

dye role
type: Class
subclass of: molecular label role
editor preferred label: dye role
has curation status: metadata complete
definition: A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest.
term editor: Jennifer Fostel
alternative term: dye
definition source: A substance used to color materials www.answers.com/topic/dye 19feb09
imported from: Ontology for Biomedical Investigation

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: 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)
imported from: Ontology for Biomedical Investigation
ISA alternative term: study protocol

analyte role
type: Class
subclass of: role
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
subclass of: Restriction
  on property: realized in
  all values from: analyte assay
editor preferred label: analyte role
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
has curation status: ready for release
definition: A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
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.
imported from: Ontology for Biomedical Investigation

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
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
editor preferred label: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: 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
imported from: Ontology for Biomedical Investigation

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

contain function
type: Class
subclass of: function
editor preferred label: contain function
example of usage: A syringe, a beaker
has curation status: ready for release
definition: A contain function is a function to constrain a material entities location in space
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: Ontology for Biomedical Investigation

material separation function
type: Class
subclass of: function
editor preferred label: material separation function
has curation status: ready for release
definition: A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: Ontology for Biomedical Investigation

averaging objective
type: Class
subclass of: data transformation objective
editor preferred label: averaging objective
example of usage: A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
has curation status: ready for release
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
imported from: Ontology for Biomedical Investigation

enzyme
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Class
    union of: ribonucleic acid
    union of: protein complex
    union of: protein
    union of: Restriction
      on property: has part
      some values from: ribonucleic acid
    union of: Restriction
      on property: has part
      some values from: protein complex
    union of: Restriction
      on property: has part
      some values from: protein
  intersection of: Restriction
    on property: has function
    some values from: catalytic activity
subclass of: material entity
editor preferred label: enzyme
has curation status: pending final vetting
definition: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
editor note: MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
term editor: person: Melanie Courtot
definition source: GROUP:OBI
imported from: Ontology for Biomedical Investigation

analyte measurement objective
type: Class
subclass of: assay objective
editor preferred label: analyte measurement objective
example of usage: The objective to measure the concentration of glucose in a blood sample
has curation status: ready for release
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
term editor: PERSON: Bjoern Peters
definition source: PPPB branch
imported from: Ontology for Biomedical Investigation

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: 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
imported from: Ontology for Biomedical Investigation

analyte assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: assay
subclass of: Restriction
  on property: realizes
  some values from: analyte role
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
editor preferred label: analyte assay
example of usage: example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
has curation status: ready for release
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
editor note: 2013-09-23: simplify equivalent axiom
editor note: Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
editor note: logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
term editor: PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
definition source: PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
imported from: Ontology for Biomedical Investigation

normalized data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: normalization data transformation
subclass of: data set
editor preferred label: normalized data set
has curation status: pending final vetting
definition: A data set that is produced as the output of a normalization data transformation.
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
imported from: Ontology for Biomedical Investigation

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 label: 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
imported from: Ontology for Biomedical Investigation

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: 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 term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: Ontology for Biomedical Investigation

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
editor preferred label: 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: Ontology for Biomedical Investigation

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: ready for release
definition: is an objective to transform a material entity into spatially separated components.
term editor: PPPB branch
definition source: PPPB branch
imported from: Ontology for Biomedical Investigation

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material combination
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
has curation status: ready for release
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
term editor: bp
definition source: bp
imported from: Ontology for Biomedical Investigation

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
editor preferred label: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
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 term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
imported from: Ontology for Biomedical Investigation

error corrected data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: error correction data transformation
subclass of: data set
editor preferred label: error corrected data set
has curation status: pending final vetting
definition: A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
imported from: Ontology for Biomedical Investigation

error correction data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: error correction objective
subclass of: data transformation
editor preferred label: error correction data transformation
has curation status: ready for release
definition: An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
term editor: James Malone
term editor: Monnie McGee
definition source: EDITORS
imported from: Ontology for Biomedical Investigation

center value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: center calculation data transformation
subclass of: data item
editor preferred label: 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 term: median
imported from: Ontology for Biomedical Investigation

portioning objective
type: Class
subclass of: material separation objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: metadata incomplete
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
imported from: Ontology for Biomedical Investigation

average value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: averaging data transformation
subclass of: data item
editor preferred label: average value
has curation status: pending final vetting
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: arithmetic mean
imported from: Ontology for Biomedical Investigation

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: metadata complete
definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
imported from: Ontology for Biomedical Investigation

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: 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
imported from: Ontology for Biomedical Investigation

material combination objective
type: Class
subclass of: material transformation objective
editor preferred label: material combination objective
has curation status: ready for release
definition: is an objective to obtain an output material that contains several input materials.
term editor: PPPB branch
definition source: bp
imported from: Ontology for Biomedical Investigation

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: 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.
imported from: Ontology for Biomedical Investigation

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
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

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
editor preferred label: material sample
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: metadata incomplete
definition: A material entity that has the material sample role
term editor: OBI: workshop
alternative term: sample population
imported from: Ontology for Biomedical Investigation
ISA alternative term: sample

study design independent variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: study design
editor preferred label: independent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
has curation status: ready for release
definition: a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
editor note: 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative term: experimental factor
alternative term: independent variable
definition source: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
imported from: Ontology for Biomedical Investigation
ISA alternative term: study factor

study design dependent variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: study design
editor preferred label: dependent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
has curation status: ready for release
definition: dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
editor note: 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative term: dependent variable
definition source: WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
imported from: Ontology for Biomedical Investigation

survival rate
type: Class
subclass of: measurement datum
editor preferred label: survival rate
has curation status: metadata complete
definition: A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
term editor: Oliver He
definition source: adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
imported from: Ontology for Biomedical Investigation

multiple testing correction objective
type: Class
subclass of: error correction objective
editor preferred label: multiple testing correction objective
example of usage: Application of the Bonferroni correction
has curation status: metadata complete
definition: A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
alternative term: multiple comparison correction objective
definition source: http://en.wikipedia.org/wiki/Multiple_Testing_Correction
imported from: Ontology for Biomedical Investigation

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: ready for release
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters
imported from: Ontology for Biomedical Investigation

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
subclass of: region
editor preferred label: primary structure of DNA macromolecule
has curation status: metadata incomplete
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
term editor: BP et al
imported from: Ontology for Biomedical Investigation

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
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred label: material maintenance
has curation status: metadata incomplete
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
imported from: Ontology for Biomedical Investigation

study intervention
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: specimen
  intersection of: Restriction
    on property: has_specified_output
    some values from: specimen
subclass of: Restriction
  on property: part of
  some values from: Class
    intersection of: study design execution
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: intervention design
editor preferred label: study intervention
has curation status: metadata complete
definition: the part of the execution of an intervention design study which is varied between two or more subjects in the study
term editor: PERSON: Bjoern Peters
definition source: GROUP: OBI
imported from: Ontology for Biomedical Investigation

material separation device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: material separation function
subclass of: device
editor preferred label: material separation device
example of usage: flow cytometer
has curation status: metadata incomplete
definition: A device with a separation function realized in a planed process
imported from: Ontology for Biomedical Investigation

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: categorical value specification
editor preferred label: categorical measurement datum
has curation status: metadata complete
definition: A measurement datum that is reported on a categorical scale
term editor: Bjoern Peters
alternative term: nominal mesurement datum
definition source: Bjoern Peters
imported from: Ontology for Biomedical Investigation

categorical label
type: Class
subclass of: datum label
editor preferred label: categorical label
example of usage: The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
has curation status: metadata complete
definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
term editor: Bjoern Peters
definition source: Bjoern Peters
imported from: Ontology for Biomedical Investigation

container
type: Class
equivalent class: Restriction
  on property: has function
  some values from: contain function
subclass of: device
editor preferred label: container
has curation status: metadata incomplete
definition: A device that can be used to restrict the location of material entities over time
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
term editor: PERSON: Bjoern Peters
imported from: Ontology for Biomedical Investigation

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
subclass of: Restriction
  on property: manufactured by
  all values from: organization
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
term editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: Ontology for Biomedical Investigation

dose
type: Class
subclass of: measurement datum
editor preferred label: dose
example of usage: An organism has been injected 1ml of vaccine
has curation status: metadata incomplete
definition: A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
imported from: Ontology for Biomedical Investigation

dose response curve
type: Class
subclass of: line graph
editor preferred label: dose response curve
has curation status: metadata complete
definition: A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
term editor: Bjoern Peters; Randi Vita
imported from: Ontology for Biomedical Investigation

genetic population background information
type: Class
subclass of: genetic characteristics information
subclass of: Restriction
  on property: part of
  some values from: genotype information
editor preferred label: genetic population background information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
has curation status: metadata complete
definition: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
editor note: proposed and discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group
imported from: Ontology for Biomedical Investigation

genotype information
type: Class
subclass of: genetic characteristics information
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: genetic population background information
  intersection of: Restriction
    on property: has part
    some values from: genetic alteration information
editor preferred label: genotype information
example of usage: Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
has curation status: metadata complete
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor note: discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group
imported from: Ontology for Biomedical Investigation

allele information
type: Class
subclass of: genetic alteration information
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: genotype information
  intersection of: Restriction
    on property: is about
    some values from: region
editor preferred label: allele information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has curation status: metadata complete
definition: a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
editor note: discussed on San Diego OBI workshop, March 2011
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_58 Allele
imported from: Ontology for Biomedical Investigation

genetic alteration information
type: Class
subclass of: genetic characteristics information
editor preferred label: genetic alteration information
has curation status: metadata complete
definition: a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
editor note: proposed and discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group
imported from: Ontology for Biomedical Investigation

genetic characteristics information
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: region
    intersection of: Restriction
      on property: is concretized as
      some values from: Restriction
        on property: inheres in
        some values from: Class
editor preferred label: genetic characteristics information
has curation status: metadata complete
definition: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_66 IndividualGeneticCharacteristics
curator note: MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
imported from: Ontology for Biomedical Investigation

q-value
type: Class
subclass of: quantitative confidence value
editor preferred label: q-value
example of usage: PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
has curation status: ready for release
definition: A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
term editor: PERS:Philippe Rocca-Serra
alternative term: FDR adjusted p-value
definition source: Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
imported from: Ontology for Biomedical Investigation

rate measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred label: rate measurement datum
example of usage: The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
has curation status: metadata complete
definition: A scalar measurement datum that represents the number of events occuring over a time interval
term editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: Ontology for Biomedical Investigation

selection criterion
type: Class
subclass of: directive information entity
editor preferred label: selection criterion
example of usage: rats should be aged between 6 and 8 weeks and weight between 180-250grams
has curation status: ready for release
definition: A directive information entity which defines and states a principle of standard by which selection process may take place.
term editor: Person: Philippe Rocca-Serra
alternative term: selection rule
definition source: OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
imported from: Ontology for Biomedical Investigation

drawing a conclusion
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: conclusion textual entity
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
editor preferred label: drawing a conclusion
example of usage: Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. 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.
has curation status: metadata incomplete
definition: A planned process in which new information is inferred from existing information.
imported from: Ontology for Biomedical Investigation

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion based on data
example of usage: The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
has curation status: ready for release
definition: An information content entity that is inferred from data.
editor note: In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
term editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group
imported from: Ontology for Biomedical Investigation

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
has curation status: metadata complete
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
term editor: PERSON: Matthew Brush
imported from: Ontology for Biomedical Investigation

categorical value specification
type: Class
subclass of: value specification
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

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 label: 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
imported from: Ontology for Biomedical Investigation

value specification
type: Class
subclass of: information content entity
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: 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
imported from: Ontology for Biomedical Investigation

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
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: metadata complete
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
term editor: PERSON:Matthew Brush
alternative term: cell culture sample
definition source: PERSON:Matthew Brush
imported from: Ontology for Biomedical Investigation
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

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: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: data item
editor preferred label: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
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 term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: Ontology for Biomedical Investigation
has broad synonym: method
comment: defneed
version info: altspcls: process ???

Benjamini and Hochberg false discovery rate correction method
type: Class
subclass of: false discovery rate correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: p-value
subclass of: Restriction
  on property: has_specified_output
  some values from: error corrected data set
subclass of: Restriction
  on property: has_specified_output
  some values from: q-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: Benjamini and Hochberg false discovery rate correction method
example of usage: Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
has curation status: metadata complete
definition: A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
editor note: 2011-03-31: [PRS]. specified input and output of dt which were missing
term editor: Helen Parkinson
term editor: Philippe Rocca-Serra
definition source: Helen Parkinson
imported from: Ontology for Biomedical Investigation

Benjamini and Yekutieli false discovery rate correction method
type: Class
subclass of: false discovery rate correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: p-value
subclass of: Restriction
  on property: has_specified_output
  some values from: error corrected data set
subclass of: Restriction
  on property: has_specified_output
  some values from: q-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: Benjamini and Yekutieli false discovery rate correction method
example of usage: The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
has curation status: metadata complete
definition: A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
editor note: 2011-03-31: [PRS]. specified input and output of dt which were missing
term editor: Helen Parkinson
term editor: Philippe Rocca-Serra
definition source: Helen Parkinson
imported from: Ontology for Biomedical Investigation

multiple testing correction method
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
subclass of: error correction data transformation
editor preferred label: multiple testing correction method
has curation status: metadata incomplete
definition: A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
term editor: Monnie McGee
alternative term: multiple testing procedure
definition source: PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
imported from: Ontology for Biomedical Investigation

logarithmic transformation
type: Class
subclass of: normalization data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data normalization objective
editor preferred label: logarithmic transformation
has curation status: ready for release
definition: A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
term editor: Elisabetta Manduchi
definition source: WEB: http://en.wikipedia.org/wiki/Logarithm
imported from: Ontology for Biomedical Investigation

regression analysis method
type: Class
subclass of: data transformation
editor preferred label: regression analysis method
has curation status: pending final vetting
definition: Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
term editor: Tina Hernandez-Boussard
definition source: BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
imported from: Ontology for Biomedical Investigation

data visualization
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: graph
    union of: image
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: Class
    union of: graph
    union of: image
editor preferred label: data visualization
example of usage: Generation of a heatmap from a microarray dataset
has curation status: ready for release
definition: An planned process that creates images, diagrams or animations from the input data.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Tina Boussard
alternative term: data encoding as image
alternative term: visualization
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Tina Boussard
curator note: Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
imported from: Ontology for Biomedical Investigation

false discovery rate correction method
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: q-value
subclass of: multiple testing correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: false discovery rate correction method
has curation status: pending final vetting
definition: The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
editor note: 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt
term editor: Monnie McGee
term editor: Philippe Rocca-Serra
alternative term: FDR correction method
definition source: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
imported from: Ontology for Biomedical Investigation

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: 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
imported from: Ontology for Biomedical Investigation

data normalization objective
type: Class
subclass of: data transformation objective
editor preferred label: data normalization objective
example of usage: Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
has curation status: ready for release
definition: A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: Helen Parkinson
definition source: PERSON: James Malone
imported from: Ontology for Biomedical Investigation

correction objective
type: Class
subclass of: data transformation objective
editor preferred label: correction objective
example of usage: Type I error correction
has curation status: metadata incomplete
definition: A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
term editor: James Malone
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
imported from: Ontology for Biomedical Investigation

normalization data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: normalized data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: data normalization objective
subclass of: data transformation
editor preferred label: normalization data transformation
has curation status: metadata incomplete
definition: A normalization data transformation is a data transformation that has objective normalization.
term editor: James Malone
definition source: PERSON: James Malone
imported from: Ontology for Biomedical Investigation

averaging data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: average value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
subclass of: data transformation
editor preferred label: averaging data transformation
has curation status: metadata incomplete
definition: An averaging data transformation is a data transformation that has objective averaging.
term editor: James Malone
definition source: PERSON: James Malone
imported from: Ontology for Biomedical Investigation

center calculation objective
type: Class
subclass of: data transformation objective
editor preferred label: center calculation objective
example of usage: A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
has curation status: 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
imported from: Ontology for Biomedical Investigation

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 label: 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
imported from: Ontology for Biomedical Investigation

error correction objective
type: Class
subclass of: correction objective
editor preferred label: error correction objective
example of usage: Application of a multiple testing correction method
has curation status: pending final vetting
definition: An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
term editor: James Malone, Helen Parkinson
definition source: PERSON: James Malone
imported from: Ontology for Biomedical Investigation

observation design
type: Class
subclass of: study design
editor preferred label: observation design
example of usage: PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
has curation status: pending final vetting
definition: observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
term editor: Philippe Rocca-Serra
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigation

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred label: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: metadata incomplete
definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
imported from: Ontology for Biomedical Investigation

group randomization
type: Class
subclass of: group assignment
editor preferred label: group randomization
example of usage: PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
has curation status: metadata complete
definition: A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
imported from: Ontology for Biomedical Investigation

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred label: 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 term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: Ontology for Biomedical Investigation

repeated measure design
type: Class
subclass of: intervention design
editor preferred label: repeated measure design
example of usage: PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
has curation status: metadata complete
definition: a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
term editor: PlanAndPlannedProcess Branch
definition source: http://www.holah.karoo.net/experimentaldesigns.htm
imported from: Ontology for Biomedical Investigation

cross over design
type: Class
subclass of: repeated measure design
editor preferred label: cross over design
example of usage: PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
has curation status: metadata complete
definition: a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
term editor: Philippe Rocca-Serra
definition source: (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
imported from: Ontology for Biomedical Investigation

time series design
type: Class
subclass of: study design
editor preferred label: time series design
example of usage: PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limite…
has curation status: pending final vetting
definition: Groups of assays that are related as part of a time series.
term editor: Philippe Rocca-Serra on behalf of MO
definition source: MO_887
imported from: Ontology for Biomedical Investigation

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material component separation
example of usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
has curation status: ready for release
definition: a material processing in which components of an input material become segregated in space
term editor: Bjoern Peters
definition source: IEDB
imported from: Ontology for Biomedical Investigation

group assignment
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: role
    intersection of: Restriction
      on property: inheres in
      some values from: organism
editor preferred label: group assignment
example of usage: Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
has curation status: ready for release
definition: group assignment is a process which has an organism as specified input and during which a role is assigned
term editor: Philippe Rocca-Serra
alternative term: cohort assignment
alternative term: study assignment
definition source: OBI Plan
imported from: Ontology for Biomedical Investigation

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: maintaining cell culture
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has curation status: pending final vetting
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigation

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: 'establishing cell culture'
has curation status: metadata complete
definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
term editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: Ontology for Biomedical Investigation
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

phenotype
type: Class
subclass of: quality
editor preferred label: phenotype
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
imported from: Ontology for Biomedical Investigation
imported from: ogms.owl

mass
type: Class
subclass of: quality
editor preferred label: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: Ontology for Biomedical Investigation
imported from: pato.owl

protein
type: Class
subclass of: peptide
editor preferred label: protein
example of usage: antithrombin III is a protein
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
imported from: Ontology for Biomedical Investigation
imported from: pr.owl

molecular label role
type: Class
subclass of: role
editor preferred label: molecular label role
definition: a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
editor note: MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
alternative term: molecular tracer role
definition source: OBI developer call, 3-12-12
imported from: Ontology for Biomedical Investigation
imported from: reo.owl

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
alternative term: primary structure of sequence macromolecule
alternative term: sequence
imported from: Ontology for Biomedical Investigation
imported from: so.owl

length unit
type: Class
subclass of: unit
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: Ontology for Biomedical Investigation
imported from: uo.owl

mass unit
type: Class
subclass of: unit
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: Ontology for Biomedical Investigation
imported from: uo.owl

time unit
type: Class
subclass of: unit
editor preferred label: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: Ontology for Biomedical Investigation
imported from: uo.owl

kilogram
type: Class
subclass of: unit
definition: A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: kg
has_obo_namespace: unit.ontology
id: UO:0000009
in_subset: unit slim

second
type: Class
subclass of: unit
definition: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: s
has_obo_namespace: unit.ontology
id: UO:0000010
in_subset: unit slim

kelvin
type: Class
subclass of: unit
definition: A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: K
has_obo_namespace: unit.ontology
id: UO:0000012
in_subset: unit slim

gram
type: Class
subclass of: unit
definition: A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: g
has_obo_namespace: unit.ontology
id: UO:0000021
in_subset: unit slim

milligram
type: Class
subclass of: unit
definition: A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: mg
has_obo_namespace: unit.ontology
id: UO:0000022
in_subset: unit slim

microgram
type: Class
subclass of: unit
definition: A mass unit which is equal to one millionth of a gram or 10^[-6] g.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: ug
has_obo_namespace: unit.ontology
id: UO:0000023
in_subset: unit slim

degree Celsius
type: Class
subclass of: unit
definition: A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: C
has_obo_namespace: unit.ontology
id: UO:0000027
in_subset: unit slim

minute
type: Class
subclass of: unit
definition: A time unit which is equal to 60 seconds.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: min
has_obo_namespace: unit.ontology
id: UO:0000031
in_subset: unit slim

year
type: Class
subclass of: unit
definition: A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
imported from: uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000036
in_subset: unit slim

millimolar
type: Class
subclass of: unit
definition: A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: mM
has_obo_namespace: unit.ontology
id: UO:0000063
in_subset: unit slim

micromolar
type: Class
subclass of: unit
definition: A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: uM
has_obo_namespace: unit.ontology
id: UO:0000064
in_subset: unit slim

milliliter
type: Class
subclass of: unit
definition: A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: millilitre
has_exact_synonym: ml
has_obo_namespace: unit.ontology
id: UO:0000098
in_subset: unit slim

microliter
type: Class
subclass of: unit
definition: A volume unit which is equal to one millionth of a liter or 10^[-6] L.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: microlitre
has_exact_synonym: ul
has_obo_namespace: unit.ontology
id: UO:0000101
in_subset: unit slim

milligram per milliliter
type: Class
subclass of: unit
definition: A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: mg/ml
has_exact_synonym: milligram per millilitre
has_obo_namespace: unit.ontology
id: UO:0000176
in_subset: unit slim

percent
type: Class
subclass of: unit
definition: A dimensionless ratio unit which denotes numbers as fractions of 100.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: %
has_obo_namespace: unit.ontology
id: UO:0000187
in_subset: unit group slim

tesla
type: Class
subclass of: unit
definition: A magnetic flux density unit which is equal to one weber per square meter.
imported from: uo.owl
created by: george gkoutos
has_exact_synonym: T
has_exact_synonym: Wb/m2
has_obo_namespace: unit.ontology
id: UO:0000228
in_subset: unit slim

microgram per milliliter
type: Class
subclass of: unit
definition: A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters.
imported from: uo.owl
created by: George Gkoutos
creation date: 2011-03-21T10:40:21Z
has_exact_synonym: ug/ml
has_obo_namespace: unit.ontology
has_related_synonym: microgram per millilitre
id: UO:0000274
in_subset: unit slim

megaHertz
type: Class
subclass of: unit
definition: A frequency unit which is equal to one million hertz or 10^[6] V.
imported from: uo.owl
created by: gkoutos
creation date: 2013-12-06T12:17:48Z
has_obo_namespace: unit.ontology
has_related_synonym: mH
id: UO:0000325
in_subset: unit slim

Topic
type: Class
subclass of: information content entity
definition: A category denoting a rather broad domain or field of interest, study, application, work, data, or technology. Topics have no clearly defined borders between each other.
id: topic:0003

isotopomer analysis
type: Class
subclass of: assay
term editor: Philippe Rocca-Serra

isotopologue distribution analysis
type: Class
subclass of: assay
term editor: Philippe Rocca-Serra

metabolism quenching by snap freezing in liquid nitrogen
type: Class
subclass of: metabolism quenching
has curation status: ready for release
definition: metabolism quenching by snap freeing in liquid nitrogen is a kind biochemical reaction extinction process which relies on extremely low temperature afforded by nitrogen in liquid state to denature enzymatic machinery of live cells or live tissue and inactivate it.
term editor: Philippe Rocca-Serra
alternative term: LN2 snap freezing
definition source: EU H2020 PhenoMenAl

normalization to the mean
type: Class
subclass of: normalization data transformation
has curation status: ready for release
definition: a normalization process which relies on the computing to arithmetic mean signal intensity over all measurements (controls and samples) and then for each sample measurements, adjusting the signal with the mean (by substracting the mean, allowing to retain measurement unit, which is not the case with dividing with the mean). The arithmetic mean is used as reference to which sample signals are then compared.
term editor: Philippe Rocca-Serra
definition source: cosmos tracer based metabolomics working group

pH
type: Class
subclass of: measurement datum
has curation status: placeholder removed
editor note: import from PATO

example to be eventually removed
type: NamedIndividual
type: curation status specification

failed exploratory term
type: NamedIndividual
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: Thing
type: NamedIndividual
type: curation status specification
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: Thing
type: NamedIndividual
type: curation status specification
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: Thing
type: NamedIndividual
type: curation status specification
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: Thing
type: NamedIndividual
type: curation status specification
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

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

pending final vetting
type: Thing
type: NamedIndividual
type: curation status specification
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.

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

placeholder removed
type: NamedIndividual

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

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

term split
type: NamedIndividual
editor 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.

other
type: NamedIndividual
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.
deprecated: true

universal
type: NamedIndividual
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
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
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
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
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

Biocrates AG
type: NamedIndividual
type: organization
definition: Biocrates Life Sciences AG, a biotechnology company, develops and markets targeted metabolic phenotyping solutions that support the discovery and validation of biomarkers for complex multifactorial diseases in pre-clinical and clinical research. The company offers mass-spectrometry based reproducible and quantitative kits and services that analyze various endogenous metabolites; and tools for insight into pathways and metabolic signatures of diseases, such as cancer or neurodegenerative diseases. It also offers metabolic phenotyping, and biomarker discovery and development services.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: Biocrates Life Sciences AG
definition source: https://www.bloomberg.com/research/stocks/private/snapshot.asp

Agilent Technologies
type: NamedIndividual
type: organization
definition: Agilent Technologies is an American public research, development and manufacturing company established in 1999 as a spin-off from Hewlett-Packard. The resulting IPO of Agilent stock was the largest in the history of Silicon Valley at the time. The company provides analytical instruments, software, services and consumables for the entire laboratory workflow.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: Agilent
definition source: https://en.wikipedia.org/wiki/Agilent_Technologies

Bruker AG
type: NamedIndividual
type: organization
definition: Bruker Corporation is a manufacturer of scientific instruments for molecular and materials research, as well as for industrial and applied analysis. It is headquartered in Billerica, Massachusetts and is the publicly traded parent company of Bruker Scientific Instruments (Bruker AXS, Bruker BioSpin, Bruker Daltonics and Bruker Optics) and Bruker Energy & Supercon Technologies (BEST) divisions.
alternative term: Bruker
alternative term: Bruker Corporation
definition source: https://en.wikipedia.org/wiki/Bruker

Thermo Fisher Scientific
type: NamedIndividual
type: organization
definition: Thermo Fisher Scientific is an American multinational biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific

axiom holds for all times
type: NamedIndividual
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

Ontology for Biomedical Investigation
type: NamedIndividual
default language: en
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Alan Ruttenberg
creator: Allyson Lister
creator: Barry Smith
creator: Bill Bug
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Mungall
creator: Chris Stoeckert
creator: Chris Taylor
creator: Christian Bolling
creator: Cristian Cocos
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Elisabetta Manduchi
creator: Eric Deutsch
creator: Frank Gibson
creator: Gilberto Fragoso
creator: Helen C. Causton
creator: Helen Parkinson
creator: Holger Stenzhorn
creator: James A. Overton
creator: James Malone
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jessica Turner
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Brush
creator: Matthew Pocock
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
creator: Philip Lord
creator: Philippe Rocca-Serra
creator: Pierre Grenon
creator: Richard Bruskiewich
creator: Richard Scheuermann
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
date: 2009-07-31
description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
Format: OWL-DL
license: http://creativecommons.org/licenses/by/3.0/
subject: An ontology for the annotation of biomedical and functional genomics experiments.
comment: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
version info: 2017-09-03

IAO Release 2015-02-23
type: NamedIndividual
file-release: iao.owl
revision: SVN $Revision: 717 $

bfo-spec-label
definition source: Person:Alan Ruttenberg

BFO_0000134
elucidation: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
elucidation: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/080-003

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/081-003