PROCO: PROcess Chemistry Ontology
type: Ontology
versionIRI: proco.owl
creator: Anna Dunn
creator: Wes A. Schafer
creator: Yongqun "Oliver" He (YH)
creator: Zachary Dance
description: PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.
Format: OWL-DL
subject: PROCO: a formal ontology in the domain of process chemistry.
license: http://creativecommons.org/licenses/by/4.0/
creation date: 04-14-2022
comment: This work is licensed under a Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/. THESE MATERIALS ARE PROVIDED "AS IS" AND WITHOUT ANY WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, TITLE, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
version info: PROCO release 20220414

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

example of usage
type: AnnotationProperty
editor preferred label: example of usage
has curation status: ready for release
textual 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

textual definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
textual 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.
textual 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: definition

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

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

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

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

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

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: pending final vetting
textual 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>

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: pending final vetting
textual definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

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

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: ready for release
textual 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
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
textual 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
textual definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.

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.

license
type: AnnotationProperty
term editor: Mark Miller
date: 2018-05-11T13:47:29Z

has_alternative_id
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

label
type: AnnotationProperty
editor preferred label: label

versionIRI
type: AnnotationProperty
comment: The property that identifies the version IRI of an ontology.
range: Ontology
domain: Ontology

contains
type: ObjectProperty
sub property of: RO_0001015
inverse of: contained in
domain: container
range: material entity
definition: The relation between a container and its physical content. A material entity a contains a material entity b if b is located in some cavity of a. [Allotrope]

contained in
type: ObjectProperty
sub property of: RO_0001025
domain: material entity
range: container
definition: Inverse of contains. [Allotrope]

quality influenced by
type: ObjectProperty
sub property of: RO_0002502
type: TransitiveProperty
alternative label: influenced by
definition: Inverse of quality influences. [Allotrope]

has proper part
type: ObjectProperty
sub property of: has part
inverse of: proper part of
type: TransitiveProperty
AFX_0002809: SIO_000053
definition: Has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part. [SIO]
example: An atom has subatomic particles as its proper parts.

facet of
type: ObjectProperty
sub property of: proper part of
inverse of: has facet
type: TransitiveProperty
alternative label: is facet of
definition: Facet of relates two information content entities where one information content entity is an aspect of the other one. [Allotrope]

has facet
type: ObjectProperty
sub property of: has proper part
type: TransitiveProperty
domain: information content entity
range: facet
definition: Relation between an information content entity and some part of it called a facet that is covers some general aspect of information context. [Allotrope]
example: a timestamp
example: a title
example: an ordering

proper part of
type: ObjectProperty
sub property of: part of
alternative label: is proper part of
definition: Inverse of has proper part. [Allotrope]

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
temporal interpretation: axiom holds for all times

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
textual 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: chebi.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
temporal interpretation: axiom holds for all times
database_cross_reference: BFO:0000051
has_obo_namespace: chebi_ontology
id: has_part
is cyclic: false
shorthand: has_part

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

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

has participant
type: ObjectProperty
equivalent property: has participant
imported from: chmo.owl
id: BFO:0000057

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: measurement unit label
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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

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

denoted by
type: ObjectProperty
domain: entity
range: information content entity
textual definition: inverse of the relation 'denotes'
term editor: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/206
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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 Investigations

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
textual 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 Investigations

is_specified_input_of
type: ObjectProperty
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
textual 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 Investigations

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
textual 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 Investigations

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
textual 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 Investigations

obsolete_has_role
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred label: has_role
has curation status: ready for release
textual definition: A relation between a continuant C and a role R. The reciprocal relation of role_of.
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000087
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON:Chris Mungal
has obsolescence reason: term imported
imported from: Ontology for Biomedical Investigations
deprecated: true

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
textual 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: chmo.owl
imported from: Ontology for Biomedical Investigations
id: OBI:0000417

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

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

monotropically related to
type: ObjectProperty
textual definition: is thermodynically preferred at all temperatures
definition source: [PROCO]

profile of
type: ObjectProperty
domain: process profile
textual definition: a relationship indicating that the process profile quantitates some aspect of the process (e.g. a quality of a material participant)
definition source: [PROCO]

enantiotropically related to
type: ObjectProperty
textual definition: a relationship between polymorphs that has a cross-over temperature at which one form becomes more thermodynamically favored than the other.
definition source: [PROCO]

is solvate of
type: ObjectProperty
textual definition: an object property that represents a relation between a chemical moiety and a physical form that incorporates solvent molecules either in the crystal lattice or by adsorption on the surface or in channels within the particles.
definition source: https://en.wikipedia.org/wiki/Solvation
definition source: https://en.wikipedia.org/wiki/Solvent

is polymorph of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
textual definition: an object property that represents a relation between polymorphs, i.e. different physical forms of the same chemical moiety.
term editor: Wes Schafer, Oliver He
definition source: https://en.wikipedia.org/wiki/Polymorphism_(materials_science)

inheres in
type: ObjectProperty
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
textual 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 Investigations
temporal interpretation: axiom holds for all times

bearer of
type: ObjectProperty
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
textual 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 Investigations
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
textual 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 Investigations

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
textual 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 Investigations
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

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

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
textual 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 Investigations

has role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
textual 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: chebi.owl
imported from: Ontology for Biomedical Investigations
database_cross_reference: RO:0000087
has_obo_namespace: chebi_ontology
id: has_role
is cyclic: false
is transitive: false
shorthand: has_role

has functional parent
type: ObjectProperty
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: has_functional_parent
is cyclic: false
is transitive: false

has parent hydride
type: ObjectProperty
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: has_parent_hydride
is cyclic: false
is transitive: false

is conjugate acid of
type: ObjectProperty
inverse of: is conjugate base of
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: is_conjugate_acid_of
is cyclic: true
is transitive: false

is conjugate base of
type: ObjectProperty
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: is_conjugate_base_of
is cyclic: true
is transitive: false

is substituent group from
type: ObjectProperty
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: is_substituent_group_from
is cyclic: false
is transitive: false

is tautomer of
type: ObjectProperty
type: TransitiveProperty
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: is_tautomer_of
is cyclic: true

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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 Investigations

has specified value
type: DatatypeProperty
domain: value specification
editor preferred label: has specified value
has curation status: metadata incomplete
textual 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 Investigations

quantitative systems description parameter
type: Class
subclass of: information content entity
imported from: sbo.owl
comment: A numerical value that defines certain characteristics of systems or system functions. It may be part of a calculation, but its value is not determined by the form of the equation itself, and may be arbitrarily assigned.

kinetic constant
type: Class
subclass of: quantitative systems description parameter
textual definition: Numerical parameter that quantifies the velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants.
term editor: Anna Dunn
imported from: sbo.owl
comment: Synonym: reaction rate constant

half-life
type: Class
subclass of: kinetic constant
subclass of: temporal measure
imported from: sbo.owl
comment: Time interval over which a quantified entity is reduced to half its original value.

half-life of an exponential decay
type: Class
subclass of: half-life
imported from: sbo.owl
comment: Time taken by a quantity decreasing according to a mono-exponential decay to be divided by two. Sometimes called t1/2.
see also: <n0:math xmlns:n0="http://www.w3.org/1998/Math/MathML"> <n2:lambda xmlns:n2="http://biomodels.net/SBO/"> <n2:bvar><n2:ci definitionURL="http://biomodels.net/SBO/#SBO:0000356">l</n2:ci></n2:bvar> <n2:apply> <n2:divide /> <n2:apply> <n2:ln /> <n2:cn type="integer">2</n2:cn> </n2:apply> <n2:ci>l</n2:ci> </n2:apply> </n2:lambda> </n0:math>

temporal measure
type: Class
subclass of: quantitative systems description parameter
imported from: sbo.owl
comment: Fundamental quantity of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions or the transformation of entities. The SI base unit for time is the SI second. The second is 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.

exponential time constant
type: Class
subclass of: kinetic constant
subclass of: temporal measure
imported from: sbo.owl
comment: Synonym: mean lifetime
see also: <n0:math xmlns:n0="http://www.w3.org/1998/Math/MathML"> <n2:lambda xmlns:n2="http://biomodels.net/SBO/"> <n2:bvar><n2:ci definitionURL="http://biomodels.net/SBO/#SBO:0000356">l</n2:ci></n2:bvar> <n2:apply> <n2:divide /> <n2:cn type="integer">1</n2:cn> <n2:ci>l</n2:ci> </n2:apply> </n2:lambda> </n0:math>

diffusion coefficient
type: Class
subclass of: kinetic constant
textual definition: A proportionality constant between the molar flux due to molecular diffusion and the gradient in the concentration of the species (or the driving force for diffusion). Diffusivity is encountered in Fick's law and numerous other equations of physical chemistry.
alternative term: mass diffusivity
definition source: [Wikipedia]
imported from: sbo.owl
comment: Synonym: diffusivity

effective catalytic rate
type: Class
subclass of: kinetic constant
imported from: sbo.owl
comment: Under nutrient limited conditions, it may be assumed that enzymes are operating below their maximal capacity (Kcat). Keff represents the lumped turnover rate of a reaction, expressed in units per time.

device
type: Class
subclass of: material entity
AFX_0002818: true
AFX_0002865: aft
alternative label: engineered artifact
definition: A device is an artifact that is designed to perform a function primarily by means of its mechanical or electrical nature. [Allotrope]
note: A device has a designed form or physical structure. This distinguishes a device from a chemical and a biological artifact, that are typical bulk or portions of materials without a designed form. [Allotrope]

container
type: Class
subclass of: device
subclass of: Class
  intersection of: Restriction
    on property: has function
    some values from: to contain
  intersection of: Restriction
    on property: contains
    all values from: material entity
AFX_0002808: OBI_0000967
AFX_0002818: true
alternative label: vessel
definition: A device that has the function to contain material. [Allotrope]
example: box, can, plate, rack
example: tray, flask, vial

heating device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: to heat
AFX_0002818: true
alternative label: heater
alternative label: heating equipment
definition: A device used for heating something. [Allotrope]

transferring device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: to transfer
AFX_0002818: true
definition: A transferring device is a device that is designed to transfer material. [Allotrope]

to control
type: Class
equivalent class: Class
  intersection of: function
  intersection of: Restriction
    on property: realized in
    some values from: controlling
subclass of: function
AFX_0002818: true
alternative label: controlling function
definition: To alter or govern the size or amplitude of a flow (material, energy, signal). [NIST]

to heat
type: Class
subclass of: to increment
alternative label: heating function
definition: A function that gives thermal energy to a recipient. [Allotrope]

to store
type: Class
equivalent class: Class
  intersection of: to provision
  intersection of: Restriction
    on property: realized in
    some values from: storing state
subclass of: to provision
alternative label: storing function
definition: To accumulate a flow. [NIST]
example: A DC electrical battery stores the energy in a flashlight. [NIST]

to localize
type: Class
equivalent class: Class
  intersection of: function
  intersection of: Restriction
    on property: realized in
    some values from: localizing
subclass of: function
AFX_0002818: true
alternative label: channeling function
alternative label: localizing function
alternative label: to channel
definition: To cause a flow (material, energy, signal) to move from one location to another location. [NIST]

to change
type: Class
equivalent class: Class
  intersection of: to localize
  intersection of: Restriction
    on property: realized in
    some values from: changing
subclass of: to control
subclass of: to localize
AFX_0002818: true
alternative label: adjusting function
alternative label: changing function
alternative label: to adjust
definition: To adjust the flow of energy, signal, or material in a predetermined and fixed manner. [NIST]

to increment
type: Class
subclass of: to change
alternative label: enlarging function
alternative label: incrementing function
alternative label: to enlarge
definition: To enlarge a flow in a predetermined and fixed manner. [NIST]

to provision
type: Class
equivalent class: Class
  intersection of: function
  intersection of: Restriction
    on property: realized in
    some values from: providing state
subclass of: function
alternative label: provisioning function
definition: To accumulate or provide a material or energy flow. [NIST]

to contain
type: Class
equivalent class: Class
  intersection of: to store
  intersection of: Restriction
    on property: realized in
    some values from: containing state
subclass of: to store
alternative label: containing function
definition: To keep a flow within limits. [NIST]
example: A vacuum bag contains debris vacuumed from a house. [NIST]

to transfer
type: Class
equivalent class: Class
  intersection of: to localize
  intersection of: Restriction
    on property: realized in
    some values from: transferring
subclass of: to localize
alternative label: conveying function
alternative label: shifting function
alternative label: to convey
alternative label: to shift
alternative label: transferring function
definition: To shift, or convey, a flow (material, energy, signal) from one place to another. [NIST]

heterogeneous mixture
type: Class
subclass of: portion of mixed material
definition: A heterogeneous mixture is a portion of mixed material that is not uniform in composition, but proportions of its components vary throughout the sample. [Wikipedia]
example: sea water with sand

homogeneous mixture
type: Class
subclass of: portion of mixed material
definition: A homogeneous mixture is a portion of mixed material that has the same proportions of its components throughout a given sample. Homogeneous mixture can have a variable composition. [Wikipedia]
example: air
example: sea water

portion of mixed material
type: Class
subclass of: portion of material
alternative label: blend
alternative label: mixture
alternative label: portion of mixture
definition: An portion of mixed material is a material entity that consists of different kinds of grains if you inspect it at a higher level of granularity. [Allotrope]
example: portion of milk
example: sand
example: sea water
example: sea water with sand

chemical substance
type: Class
subclass of: portion of material
license: iupac-license
rights: iupac-copyright
source: IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997).
definition: A chemical substance is a portion of material that is matter of constant composition best characterized by the entities (molecules, formula units, atoms) it is composed of. [IUPAC]

containing state
type: Class
subclass of: storing state
alternative label: being contained
definition: The state of keeping a flow within spatial limits. [Allotrope]
example: A vacuum bag contains debris vacuumed from a house. [NIST]

transferring
type: Class
subclass of: localizing
subclass of: Class
  intersection of: localizing
  intersection of: Restriction
    on property: RO_0002344
    some values from: continuant
AFX_0002818: true
alternative label: deliver
alternative label: transmitting
definition: Transferring is channeling a flow (material, energy, signal) from one place to another. [NIST]

localizing
type: Class
subclass of: activity
subclass of: Restriction
  on property: RO_0002337
  some values from: continuant
AFX_0002798: true
AFX_0002818: true
alternative label: channeling
alternative label: localization
alternative label: spatial process
definition: A processing that affects the spatial location or orientation of some participants. [Allotrope]

controlling
type: Class
subclass of: activity
AFX_0002818: true
definition: Controlling is changing or regulating a flow in its magnitude. [NIST, Allotrope]

state
type: Class
subclass of: process
AFX_0002818: true
source: http://www.loa.istc.cnr.it/old/Papers/D18.pdf
definition: A state is a homomeric, cumulative process in which all the temporal parts are described by the same expression used for the whole. [Allotrope]
example: corroding

changing
type: Class
subclass of: controlling
AFX_0002818: true
alternative label: modifying
definition: Changing is a processing by which an entity gains or looses parts, qualities, roles, dispositions, functions etc in a predetermined and fixed manner but maintains its identity. [Allotrope]

storing state
type: Class
subclass of: providing state
alternative label: storing
definition: Storing is containing or collecting flows to accumulate. [NIST]

providing state
type: Class
subclass of: state
alternative label: providing
definition: Providing is the state of accumulating or supplying a material or energy flow. [NIST]

activity
type: Class
subclass of: process
AFX_0002818: true
definition: An activity is a process that is cumulative but not homomeric. [Allotrope, DOLCE]
editorial note: Same as process in DOLCE. [Allotrope]

state of matter
type: Class
subclass of: morphology
AFX_0002818: true
alternative label: material state
definition: A state of matter is a quality of material that is one of the distinct forms in which matter can exist. Four states of matter are observable in everyday life: solid, liquid, gas, and plasma. Many other states are known to exist only in extreme situations, such as Bose-Einstein condensates, neutron-degenerate matter, and quark-gluon plasma, which only occur in situations of extreme cold, extreme density, and extremely high-energy color-charged matter respectively. [Wikipedia]

solid
type: Class
subclass of: state of matter
AFX_0002818: true
alternative label: solid state of matter
definition: A state of matter, in which particles are closely packed together. The forces between particles are strong so that the particles cannot move freely but can only vibrate. As a result, a solid has a stable, definite shape, and a definite volume. Solids can only change their shape by force, as when broken or cut. [Wikipedia]

liquid
type: Class
subclass of: state of matter
AFX_0002818: true
alternative label: liquid state of matter
definition: A state of matter that is a nearly incompressible fluid that conforms to the shape of its container but retains a (nearly) constant volume independent of pressure. [Wikipedia]

gas
type: Class
subclass of: state of matter
AFX_0002818: true
alternative label: gaseous
alternative label: gaseous state of matter
definition: A state of matter that is a compressible fluid. Not only will a gas conform to the shape of its container but it will also expand to fill the container. In a gas, the molecules have enough kinetic energy so that the effect of intermolecular forces is small (or zero for an ideal gas), and the typical distance between neighboring molecules is much greater than the molecular size. A gas has no definite shape or volume, but occupies the entire container in which it is confined. [Wikipedia]

plasma
type: Class
subclass of: state of matter
AFX_0002818: true
alternative label: plasma state of matter
definition: A physical quality that inheres in a bearer by virtue of its plasma is a state of matter, that is, it does not have definite shape or volume. Unlike gases, plasmas are electrically conductive, produce magnetic fields and electric currents, and respond strongly to electromagnetic forces. Positively charged nuclei swim in a "sea" of freely-moving disassociated electrons, similar to the way such charges exist in conductive metal. [Wikipedia]

molar concentration (quality)
type: Class
subclass of: concentration of
AFX_0002818: true
source: Green Book, 2nd ed.: IUPAC Quantities, Units and Symbols in Physical Chemistry. Second Edition, Blackwell Scientific Publications, Oxford, 1993.
alternative label: amount concentration
alternative label: amount concentration (quality)
alternative label: amount of substance concentration
alternative label: molar concentration
alternative label: molarity
alternative label: molarity (quality)
alternative label: substance concentration
alternative label: substance concentration (quality)
change note: 2019-08-19 Changed pref label. [Allotrope]
change note: 2020-05-11 Changed pref label to molar concentration. [Allotrope]
change note: 2020-06-18 Added alt labels. [Allotrope]
definition: Molar concentration is the ratio of molar amount of a substance divided by volume of mixture containing the amount of substance. [Allotrope]

chemical substance quality
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: chemical substance
definition: A chemical substance quality is a quality that inheres in some portion of chemical substance. [Allotrope]

molecular mass (molecular quality)
type: Class
subclass of: mass
subclass of: molecular quality
alternative label: atomic mass
alternative label: molecular mass
change note: 2020-03-16 Changed pref label. [Allotrope]
change note: 2020-03-16 Subclassed under pato:mass. [Allotrope]
definition: Molecular mass is a molecular quality inhered in a molecular entity that expresses its mass relative to 1/12 of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at rest. [Allotrope]

hygroscopicity
type: Class
subclass of: chemical substance quality
source: Hygroscopy
definition: Hygroscopicity is a quality inhered in a compound by virtue of its ability to readily take up and retain water, especially from the atmosphere. [Wikipedia]

classification
type: Class
subclass of: information content entity
AFX_0002818: true
definition: A classification is a proposition that categorizes things into classes or collections of things differentiated by some criteria. [Allotrope]

facet
type: Class
subclass of: information content entity
AFX_0002818: true
definition: A facet is a partial information that contains an aspect of some information content entity or parts of it when participating in some process. The facet abstracts of the concrete representation of this aspect of information. [Allotrope]

representation form
type: Class
subclass of: information content entity
AFX_0002818: true
source: Part3V3.pdf
definition: A representation form is a type of information content entity that represents an entity in a certain way. [Allotrope]
example: plot as representation form of a temperature profile

material cleaned role
type: Class
subclass of: operand role
subclass of: cleaning role
alternative label: material cleaned
alternative label: part cleaned
alternative label: part cleaned role
change note: 2019-10-02 Changed pref label. [Allotrope]
definition: Material that is undergoing a cleaning process. [Allotrope]

support role
type: Class
subclass of: role
definition: A support role is a type of role whose bearer participates in a process in order to support the process so that it proceeds towards a secondary objective. [Allotrope]
editorial note: 2018-12-05 Moved to AFO to maintain single inheritence [Allotrope]

operand role
type: Class
subclass of: role
source: Hubka, Eder, Ernst, Design Science, Springer, 1996
alternative label: operand
definition: The role of a participant that is being changed in the process (passive participant) from an input state to an output state. [Allotrope]

additive role
type: Class
subclass of: support role
subclass of: synthesis role
alternative label: additive
definition: Additive is a role of material that is added to a mixture in order to achieve a supportive purpose. [Allotrope]

catalyst role
type: Class
subclass of: reagent role
license: iupac-license
rights: iupac-copyright
source: PAC, 1996, 68, 155 (Glossary of terms used in chemical kinetics, including reaction dynamics.)
alternative label: catalyst
definition: A catalyst role is a reagent role of a substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction; the process is called catalysis. The catalyst is both a reactant and product of the reaction. [IUPAC]

debris role
type: Class
subclass of: role
alternative label: debris
definition: Debris is a role of material to be waste. [Allotrope]

detergent role
type: Class
subclass of: cleaning role
license: iupac-license
rights: iupac-copyright
source: PAC, 1972, 31, 577 (Manual of Symbols and Terminology for Physicochemical Quantities and Units, Appendix II: Definitions, Terminology and Symbols in Colloid and Surface Chemistry) on page 612
alternative label: detergent
definition: A detergent role is a cleaning role of a surface active agent (or a mixture containing one of more surface active agents) having cleaning properties in dilute solution. [IUPAC]

reaction intermediate role
type: Class
subclass of: reagent role
alternative label: intermedate reagent role
alternative label: intermediate
alternative label: intermediate reagent role
alternative label: intermediate role
alternative label: reaction intermediate
definition: Intermediate role is a role of material that is formed from reactants (or preceding intermediates) and reacts further to give the directly observed products of a chemical reaction. [Wikipedia]

reactant role
type: Class
subclass of: reagent role
alternative label: reactant
alternative label: starting material
definition: Reactant role is a role of a chemical entity that is present at the start of a reaction. [Allotrope]

cleaning agent role
type: Class
subclass of: cleaning role
alternative label: detergent
alternative label: detergent role
alternative label: washing agent
alternative label: washing agent role
definition: Cleaning agent role is a role of material used for cleaning something. [Allotrope]

ingredient role
type: Class
subclass of: synthesis role
alternative label: ingredient
definition: Ingredient is a role of material that is used in a material combining process to produce a new material. [Allotrope]

cleaning role
type: Class
subclass of: role
definition: The role of a participant of a cleaning process. [Allotrope]

synthesis role
type: Class
subclass of: role
definition: A synthesis role is a role of a material that is participating in a synthesis (material conversion) process. [Allotrope]

formulation role
type: Class
subclass of: synthesis role
definition: A formulation role is a role of a material that is participating in a formulation process. [Allotrope]

active pharmaceutical ingredient role
type: Class
subclass of: formulation role
alternative label: API
alternative label: active pharmaceutical ingredient
alternative label: drug substance
alternative label: drug substance role
change note: 2020-06-22 Add alt labels. [Allotrope]
definition: The role of a material in a drug product that is biologically active when interacting with other components of the drug product, other potential drug products, or the chemistry of the body into which the drug will be applied. [Allotrope]

by-product role
type: Class
subclass of: synthesis role
alternative label: by-product
definition: A material role of an expected but not desired product of a synthesis. [Allotrope]
example: the leaving group in a de-protection step.

product role
type: Class
subclass of: synthesis role
alternative label: chemical product
alternative label: product
definition: A role of a material that is intended and desired to be produced in a synthesis. [Allotrope]

batch role
type: Class
subclass of: product role
alternative label: batch
alternative label: lot
alternative label: lot role
definition: Batch role is a product role of a portion of material that is intended to have uniform character and quality, within specified limits, and is produced according to a single manufacturing order during the same cycle of manufacture. [Allotrope, CFR21]

filtration role
type: Class
subclass of: role
change note: 2019-08-27 Fixed OWL definition, bug #694. [Allotrope]
definition: A filtration role is a role of a material in a filtration process. [Allotrope]

rinse solution role
type: Class
subclass of: cleaning agent role
alternative label: flush
alternative label: rinse
alternative label: rinse solution
alternative label: rinsing agent
alternative label: rinsing role
alternative label: rinsing solution
change note: 2019-09-20 Changed definition. [Allotrope]
definition: The rinse solution role is a cleaning agent role of a fluid used to flush something in order to remove contaminants. [Allotrope]

impurity role
type: Class
subclass of: synthesis role
alternative label: impurity
definition: A material role for any component of material that is not part of the defined product at the particular stage of manufacture or storage. [Allotrope]
example: For example a starting material is not an impurity at the start of a reaction but it is an impurity after the final purification step.

degradation product role
type: Class
subclass of: impurity role
alternative label: degradation product
definition: A degradation product is an impurity resulting from a chemical change in the drug substance brought about during manufacture and/or storage of the new drug product by the effect of, for example, light, temperature, pH, water, or by reaction with an excipient and/or the immediate container closure system. [ICH-Q3B]

unidentified degradation product role
type: Class
subclass of: degradation product role
subclass of: unidentified impurity role
alternative label: unidentified degradation product
definition: A degradation product role for which a structural characterization has not been achieved and that is defined solely by qualitative analytical properties (e.g., chromatographic retention time). [ICH-Q3A]

unspecified degradation product role
type: Class
subclass of: degradation product role
subclass of: unspecified impurity role
alternative label: unspecified degradation product
definition: A degradation product role that is limited by a general acceptance criterion, but not individually listed with its own specific acceptance criterion, in the new drug product specification. [ICH-Q3A]

starting material role
type: Class
subclass of: reactant role
definition: A role for a material used in the synthesis of a new drug substance that is incorporated as an element into the structure of an intermediate and/or of the new drug substance. [ICH-Q3A]
note: Starting materials are normally commercially available and of defined chemical and physical properties and structure. [ICH-Q3A]

limiting reagent role
type: Class
subclass of: reagent role
definition: A reagent role of the material with the least mole quantity in a chemical process and as such limits the amount of product that can be formed. [Allotrope]

enantiomeric impurity role
type: Class
subclass of: impurity role
alternative label: enantiomere
alternative label: enantiomeric impurity
definition: An enantiomeric impurity is the impurity role of a compound with the same molecular formula as the drug substance that differs in the spatial arrangement of atoms within the molecule and is a non-superimposable mirror image. [ICH-Q3A]

extraneous contaminant role
type: Class
subclass of: impurity role
alternative label: contaminant
alternative label: contaminant role
alternative label: extraneous contaminant
definition: An extraneous contaminant role is an impurity role arising from any source extraneous to the manufacturing process. [ICH-Q3A]

identified impurity role
type: Class
subclass of: impurity role
alternative label: identified impurity
definition: An impurity for which a structural characterization has been achieved. [ICH-Q3A]

potential impurity role
type: Class
subclass of: impurity role
alternative label: potential impurity
definition: An impurity role for a material that theoretically can arise during manufacture or storage. It may or may not actually appear in the new drug substance. [ICH-Q3A]

specified impurity role
type: Class
subclass of: impurity role
alternative label: specified impurity
definition: An impurity that is individually listed and limited with aspecific acceptance criterion in the new drug substance specification. A specified impurity can be either identified or unidentified. [ICH-Q3A]

unidentified impurity role
type: Class
subclass of: impurity role
alternative label: unidentified impurity
definition: An impurity for which a structural characterization has not been achieved and that is defined solely by qualitative analytical properties (e.g., chromatographic retention time). [ICH-Q3A]

unspecified impurity role
type: Class
subclass of: impurity role
alternative label: unspecified impurity
definition: An impurity role that is limited by a general acceptance criterion, but not individually listed with its own specific acceptance criterion, in the new drug substance specification. [ICH-Q3A]

identified degradation product role
type: Class
subclass of: degradation product role
alternative label: identified degradation product
definition: A degradation product role for which a structural characterization has been achieved. [ICH-Q3A]

specified degradation product role
type: Class
subclass of: degradation product role
alternative label: specified degradation product
definition: A degradation product role that is individually listed and limited with a specific acceptance criterion in the new drug product specification. A specified degradation product can be either identified or unidentified. [ICH-Q3A]

sample role (preparation)
type: Class
subclass of: role
alternative label: sample
alternative label: sample (preparation)
alternative label: sample role
definition: A sample role (preparation) is a role of a material that is prepared for a bearing the sample role in an experiment. [Allotrope]

drying additive role
type: Class
subclass of: additive role
subclass of: drying role
alternative label: drying additive
definition: A drying additive role is the role of a material in a drying process that supports the drying process. [Allotrope]

drying role
type: Class
subclass of: role
definition: A drying role role is a role realized in some drying process. [Allotrope]

drying medium role
type: Class
subclass of: drying role
alternative label: drying agent
alternative label: drying agent role
alternative label: drying medium
definition: A drying medium role is a drying role of a material that takes or transports the solvent from the material being dried. [Allotrope]

material dried role
type: Class
subclass of: drying role
alternative label: dried material
alternative label: dried material role
alternative label: material dried
definition: Material dried role is the drying role of the material being dried. [Allotrope]

reaction mixture role
type: Class
subclass of: reactant role
alternative label: reaction mixture
definition: A reaction mixture role is a role of a chemical mixture undergoing some chemical reaction. [Allotrope]

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: bfo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

continuant
type: Class
subclass of: entity
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
editor preferred label: continuant
textual 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: bfo.owl
imported from: chmo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
imported from: pato.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
id: BFO:0000002

occurrent
type: Class
subclass of: entity
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
textual 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: bfo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
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]

independent continuant
type: Class
subclass of: 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
textual 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.
textual 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: bfo.owl
imported from: Ontology for Biomedical Investigations
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]

temporal region
type: Class
subclass of: occurrent
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
imported from: bfo.owl
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]

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.
textual definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
textual 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: bfo.owl
imported from: chmo.owl
imported from: Ontology for Biomedical Investigations
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

disposition
type: Class
subclass of: realizable entity
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
imported from: bfo.owl
imported from: Ontology for Biomedical Investigations
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]

realizable entity
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
textual 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: bfo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
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]

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: bfo.owl
imported from: pato.owl
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
editor preferred label: specifically dependent continuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
textual 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.
textual 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])
textual 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: bfo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
imported from: pato.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

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
textual 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: bfo.owl
imported from: Ontology for Biomedical Investigations
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]

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
imported from: bfo.owl
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]

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.
imported from: bfo.owl
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]

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.
textual 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.
textual 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: chmo.owl
imported from: Ontology for Biomedical Investigations
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
id: BFO:0000031

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: bfo.owl
imported from: Ontology for Biomedical Investigations
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]

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.
textual 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])
imported from: bfo.owl
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]

material entity
type: Class
subclass of: independent continuant
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
textual 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: bfo.owl
imported from: chmo.owl
imported from: Ontology for Biomedical Investigations
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]
id: BFO:0000040

process profile
type: Class
subclass of: process
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.
textual 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])
imported from: bfo.owl
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]

electron
type: Class
subclass of: lepton
textual definition: Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
imported from: chebi.owl
charge: -1
mass: 0.000548579903
monoisotopicmass: 0.0
database_cross_reference: KEGG:C05359
database_cross_reference: PMID:21614077
database_cross_reference: Wikipedia:Electron
has_exact_synonym: electron
has_obo_namespace: chebi_ontology
has_related_synonym: Elektron
has_related_synonym: beta
has_related_synonym: beta(-)
has_related_synonym: beta-particle
has_related_synonym: e
has_related_synonym: e(-)
has_related_synonym: e-
has_related_synonym: negatron
id: CHEBI:10545
in_subset: 3 STAR

Mycoplasma genitalium metabolite
type: Class
subclass of: bacterial metabolite
textual definition: Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: Mycoplasma genitalium metabolites
id: CHEBI:131604
in_subset: 3 STAR

hydrogen acceptor
type: Class
subclass of: electron acceptor
textual definition: A molecular entity that can undergo reduction by the gain of hydrogen atom(s).
imported from: chebi.owl
formula: R
smiles: *
has_obo_namespace: chebi_ontology
has_related_synonym: A
id: CHEBI:13193
in_subset: 3 STAR

volatile organic compound
type: Class
subclass of: organic molecule
textual definition: Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa.
imported from: chebi.owl
database_cross_reference: Wikipedia:Volatile_organic_compound
has_obo_namespace: chebi_ontology
has_related_synonym: VOC
has_related_synonym: VOCs
has_related_synonym: volatile organic compounds
id: CHEBI:134179
in_subset: 3 STAR

inorganic acid
type: Class
subclass of: Bronsted acid
textual definition: A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.
imported from: chebi.owl
database_cross_reference: Wikipedia:Mineral_acid
has_obo_namespace: chebi_ontology
has_related_synonym: inorganic acids
has_related_synonym: mineral acid
has_related_synonym: mineral acids
id: CHEBI:138103
in_subset: 3 STAR

gas molecular entity
type: Class
subclass of: main group molecular entity
textual definition: Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
imported from: chebi.owl
database_cross_reference: Wikipedia:https://en.wikipedia.org/wiki/Gas
has_obo_namespace: chebi_ontology
has_related_synonym: gas molecular entities
has_related_synonym: gaseous molecular entities
has_related_synonym: gaseous molecular entity
id: CHEBI:138675
in_subset: 3 STAR

carbamate
type: Class
subclass of: amino-acid anion
subclass of: Restriction
  on property: is conjugate base of
  some values from: carbamic acid
imported from: chebi.owl
charge: -1
formula: CH2NO2
inchi: InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1
inchikey: KXDHJXZQYSOELW-UHFFFAOYSA-M
mass: 60.03212
monoisotopicmass: 60.00910
smiles: NC([O-])=O
database_cross_reference: Beilstein:3903503
database_cross_reference: CAS:302-11-4
database_cross_reference: Gmelin:239604
has_exact_synonym: carbamate
has_obo_namespace: chebi_ontology
has_related_synonym: Carbamat
has_related_synonym: Karbamat
has_related_synonym: carbamate ion
has_related_synonym: carbamic acid, ion(1-)
id: CHEBI:13941
in_subset: 3 STAR

impurity
type: Class
subclass of: chemical role
textual definition: A chemical role played by any unwanted chemical substance inside a confined amount of liquid, gas, or solid, which differs from the chemical composition of the material or compound. For example, an impurity can be an undesired by-product of a chemical reaction or manufacturing process, a drug contaminant, or can be created upon degradation during storage.
imported from: chebi.owl
database_cross_reference: Wikipedia:Impurity
has_exact_synonym: impurity
has_obo_namespace: chebi_ontology
has_related_synonym: contaminant
has_related_synonym: contaminants
has_related_synonym: impurities
id: CHEBI:143130
in_subset: 3 STAR

electron donor
type: Class
subclass of: donor
textual definition: A molecular entity that can transfer an electron to another molecular entity.
imported from: chebi.owl
has_exact_synonym: electron donor
has_obo_namespace: chebi_ontology
has_related_synonym: Elektronendonator
has_related_synonym: donneur d'electron
id: CHEBI:15022
in_subset: 3 STAR

acceptor
type: Class
subclass of: chemical role
textual definition: A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
imported from: chebi.owl
has_alternative_id: CHEBI:13699
has_alternative_id: CHEBI:2377
database_cross_reference: KEGG:C00028
database_cross_reference: KEGG:C16722
has_exact_synonym: Acceptor
has_obo_namespace: chebi_ontology
has_related_synonym: A
has_related_synonym: Akzeptor
has_related_synonym: Hydrogen-acceptor
has_related_synonym: Oxidized donor
has_related_synonym: accepteur
id: CHEBI:15339
in_subset: 3 STAR

acetone
type: Class
subclass of: volatile organic compound
subclass of: propanones
subclass of: methyl ketone
subclass of: ketone body
subclass of: Restriction
  on property: has role
  some values from: polar aprotic solvent
subclass of: Restriction
  on property: has role
  some values from: human metabolite
subclass of: Restriction
  on property: has role
  some values from: EC 3.5.1.4 (amidase) inhibitor
textual definition: A methyl ketone that consists of propane bearing an oxo group at C2.
imported from: chebi.owl
charge: 0
formula: C3H6O
inchi: InChI=1S/C3H6O/c1-3(2)4/h1-2H3
inchikey: CSCPPACGZOOCGX-UHFFFAOYSA-N
mass: 58.07914
monoisotopicmass: 58.04186
smiles: CC(C)=O
has_alternative_id: CHEBI:13708
has_alternative_id: CHEBI:22182
has_alternative_id: CHEBI:2398
has_alternative_id: CHEBI:40571
database_cross_reference: Beilstein:635680
database_cross_reference: CAS:67-64-1
database_cross_reference: Gmelin:1466
database_cross_reference: HMDB:HMDB0001659
database_cross_reference: KEGG:C00207
database_cross_reference: KEGG:D02311
database_cross_reference: LIPID_MAPS_instance:LMFA12000057
database_cross_reference: MetaCyc:ACETONE
database_cross_reference: PDBeChem:ACN
database_cross_reference: PMID:17190852
database_cross_reference: PMID:17347819
database_cross_reference: Reaxys:635680
database_cross_reference: UM-BBD_compID:c0556
database_cross_reference: Wikipedia:Acetone
has_exact_synonym: ACETONE
has_exact_synonym: Acetone
has_exact_synonym: acetone
has_exact_synonym: propan-2-one
has_obo_namespace: chebi_ontology
has_related_synonym: 2-Propanone
has_related_synonym: Aceton
has_related_synonym: Azeton
has_related_synonym: Dimethyl ketone
has_related_synonym: Dimethylketon
has_related_synonym: Propanon
has_related_synonym: Pyroacetic ether
has_related_synonym: beta-Ketopropane
has_related_synonym: dimethylcetone
has_related_synonym: dimethylketone
has_related_synonym: methyl ketone
has_related_synonym: propanone
id: CHEBI:15347
in_subset: 3 STAR

primary alcohol
type: Class
subclass of: alcohol
textual definition: A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
imported from: chebi.owl
charge: 0
formula: CH3OR
mass: 31.034
monoisotopicmass: 31.01839
smiles: *C(O)([H])[H]
has_alternative_id: CHEBI:13676
has_alternative_id: CHEBI:14887
has_alternative_id: CHEBI:26262
has_alternative_id: CHEBI:57489
has_alternative_id: CHEBI:8406
database_cross_reference: KEGG:C00226
has_exact_synonym: Primary alcohol
has_obo_namespace: chebi_ontology
has_related_synonym: 1-Alcohol
has_related_synonym: a primary alcohol
has_related_synonym: primary alcohols
id: CHEBI:15734
in_subset: 3 STAR

formate
type: Class
subclass of: monocarboxylic acid anion
subclass of: Restriction
  on property: has role
  some values from: Saccharomyces cerevisiae metabolite
subclass of: Restriction
  on property: has role
  some values from: human metabolite
subclass of: Restriction
  on property: is conjugate base of
  some values from: formic acid
textual definition: A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects.
imported from: chebi.owl
charge: -1
formula: CHO2
inchi: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)/p-1
inchikey: BDAGIHXWWSANSR-UHFFFAOYSA-M
mass: 45.01744
monoisotopicmass: 44.99820
smiles: [H]C([O-])=O
has_alternative_id: CHEBI:14276
has_alternative_id: CHEBI:24081
database_cross_reference: Beilstein:1901205
database_cross_reference: CAS:71-47-6
database_cross_reference: Gmelin:1006
database_cross_reference: HMDB:HMDB0000142
database_cross_reference: KEGG:C00058
database_cross_reference: MetaCyc:FORMATE
database_cross_reference: PMID:17190852
database_cross_reference: PMID:3946945
database_cross_reference: Reaxys:1901205
database_cross_reference: UM-BBD_compID:c0106
database_cross_reference: Wikipedia:Formate
has_exact_synonym: formate
has_obo_namespace: chebi_ontology
has_related_synonym: HCO2 anion
has_related_synonym: aminate
has_related_synonym: formiate
has_related_synonym: formic acid, ion(1-)
has_related_synonym: formylate
has_related_synonym: hydrogen carboxylate
has_related_synonym: methanoate
id: CHEBI:15740
in_subset: 3 STAR

ammonia
type: Class
subclass of: gas molecular entity
subclass of: azane
subclass of: mononuclear parent hydride
textual 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: 17.02655
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

formamide
type: Class
subclass of: formamides
subclass of: monocarboxylic acid amide
subclass of: one-carbon compound
subclass of: Restriction
  on property: has role
  some values from: solvent
subclass of: Restriction
  on property: has functional parent
  some values from: formic acid
subclass of: Restriction
  on property: is tautomer of
  some values from: formimidic acid
textual definition: The simplest monocarboxylic acid amide, obtained by formal condensation of formic acid with ammonia. The parent of the class of formaldehydes.
imported from: chebi.owl
charge: 0
formula: CH3NO
inchi: InChI=1S/CH3NO/c2-1-3/h1H,(H2,2,3)
inchikey: ZHNUHDYFZUAESO-UHFFFAOYSA-N
mass: 45.04066
monoisotopicmass: 45.02146
smiles: [H]C(N)=O
has_alternative_id: CHEBI:14275
has_alternative_id: CHEBI:24078
has_alternative_id: CHEBI:40895
has_alternative_id: CHEBI:5143
database_cross_reference: Beilstein:505995
database_cross_reference: CAS:75-12-7
database_cross_reference: Gmelin:824
database_cross_reference: HMDB:HMDB0001536
database_cross_reference: KEGG:C00488
database_cross_reference: MetaCyc:FORMAMIDE
database_cross_reference: PDBeChem:ARF
database_cross_reference: PMID:11282235
database_cross_reference: PMID:11545392
database_cross_reference: PMID:12115814
database_cross_reference: PMID:14750843
database_cross_reference: PMID:15082074
database_cross_reference: PMID:17184725
database_cross_reference: PMID:19334838
database_cross_reference: PMID:21215846
database_cross_reference: PMID:21229996
database_cross_reference: PMID:21573300
database_cross_reference: PMID:21647491
database_cross_reference: PMID:21647492
database_cross_reference: PMID:21769603
database_cross_reference: PMID:21932847
database_cross_reference: Reaxys:505995
database_cross_reference: UM-BBD_compID:c0796
database_cross_reference: Wikipedia:Formamide
has_exact_synonym: FORMAMIDE
has_exact_synonym: Formamide
has_exact_synonym: formamide
has_obo_namespace: chebi_ontology
has_related_synonym: Ameisensaeureamid
has_related_synonym: Formamid
has_related_synonym: Methanamid
has_related_synonym: Methanamide
has_related_synonym: carbamaldehyde
has_related_synonym: formimidic acid
id: CHEBI:16397
in_subset: 3 STAR

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
textual 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 Investigations

copper chelator
type: Class
subclass of: chelator
textual definition: A chelator that is any compound containing a ligand (typically organic) which is able to form a bond to a central copper atom at two or more points.
imported from: chebi.owl
database_cross_reference: PMID:24934357
database_cross_reference: PMID:29710396
has_exact_synonym: copper chelator
has_obo_namespace: chebi_ontology
has_related_synonym: copper chelate
has_related_synonym: copper chelating agent
has_related_synonym: copper chelating agents
has_related_synonym: copper chelators
id: CHEBI:166831
in_subset: 3 STAR

secondary fatty alcohol
type: Class
subclass of: fatty alcohol
textual definition: A fatty alcohol consisting of a chain of 3 to greater than 27 carbon atoms in which a hydroxy group is attached to a saturated carbon atom different from the terminal carbons. Secondary fatty alcohols may be saturated or unsaturated and may be branched or unbranched.
imported from: chebi.owl
charge: 0
formula: CH2OR2
mass: 30.026
monoisotopicmass: 30.01056
smiles: *C(O)*
has_obo_namespace: chebi_ontology
has_related_synonym: a secondary fatty alcohol
id: CHEBI:167095
in_subset: 2 STAR

benzene
type: Class
subclass of: volatile organic compound
subclass of: benzenes
subclass of: aromatic annulene
subclass of: Restriction
  on property: has role
  some values from: non-polar solvent
subclass of: Restriction
  on property: has role
  some values from: carcinogenic agent
subclass of: Restriction
  on property: has role
  some values from: environmental contaminant
textual definition: A six-carbon aromatic annulene in which each carbon atom donates one of its two 2p electrons into a delocalised pi system. A toxic, flammable liquid byproduct of coal distillation, it is used as an industrial solvent. Benzene is a carcinogen that also damages bone marrow and the central nervous system.
imported from: chebi.owl
charge: 0
formula: C6H6
inchi: InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
inchikey: UHOVQNZJYSORNB-UHFFFAOYSA-N
mass: 78.11184
monoisotopicmass: 78.04695
smiles: c1ccccc1
has_alternative_id: CHEBI:13876
has_alternative_id: CHEBI:22703
has_alternative_id: CHEBI:3025
has_alternative_id: CHEBI:41187
database_cross_reference: Beilstein:969212
database_cross_reference: CAS:71-43-2
database_cross_reference: Gmelin:1671
database_cross_reference: HMDB:HMDB0001505
database_cross_reference: KEGG:C01407
database_cross_reference: PDBeChem:BNZ
database_cross_reference: PMID:11684179
database_cross_reference: PMID:11993966
database_cross_reference: PMID:12857942
database_cross_reference: PMID:14677922
database_cross_reference: PMID:15468289
database_cross_reference: PMID:15935818
database_cross_reference: PMID:16161967
database_cross_reference: PMID:17373369
database_cross_reference: PMID:18072742
database_cross_reference: PMID:18407866
database_cross_reference: PMID:18409691
database_cross_reference: PMID:18836923
database_cross_reference: PMID:19228219
database_cross_reference: PMID:21325737
database_cross_reference: PMID:23088855
database_cross_reference: PMID:23222815
database_cross_reference: PMID:23534829
database_cross_reference: PMID:6353911
database_cross_reference: PMID:8124204
database_cross_reference: Reaxys:969212
database_cross_reference: UM-BBD_compID:c0142
database_cross_reference: Wikipedia:Benzene
has_exact_synonym: BENZENE
has_exact_synonym: Benzene
has_exact_synonym: benzene
has_obo_namespace: chebi_ontology
has_related_synonym: Benzen
has_related_synonym: Benzine
has_related_synonym: Benzol
has_related_synonym: Bicarburet of hydrogen
has_related_synonym: Coal naphtha
has_related_synonym: Mineral naphtha
has_related_synonym: Phene
has_related_synonym: Pyrobenzol
has_related_synonym: Pyrobenzole
has_related_synonym: [6]annulene
has_related_synonym: benzole
has_related_synonym: cyclohexatriene
has_related_synonym: phenyl hydride
id: CHEBI:16716
in_subset: 3 STAR

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: deoxyribonucleic acid
textual 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 Investigations

ketone
type: Class
subclass of: carbonyl compound
textual definition: A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
imported from: chebi.owl
charge: 0
formula: COR2
mass: 28.010
monoisotopicmass: 27.99491
smiles: [*]C([*])=O
has_alternative_id: CHEBI:13427
has_alternative_id: CHEBI:13646
has_alternative_id: CHEBI:24974
has_alternative_id: CHEBI:6127
has_alternative_id: CHEBI:8742
database_cross_reference: KEGG:C01450
database_cross_reference: Wikipedia:Ketone
has_exact_synonym: Ketone
has_exact_synonym: ketones
has_obo_namespace: chebi_ontology
has_related_synonym: Keton
has_related_synonym: R-CO-R'
has_related_synonym: a ketone
has_related_synonym: cetone
has_related_synonym: ketones
id: CHEBI:17087
in_subset: 3 STAR

hydrogen donor
type: Class
subclass of: electron donor
textual definition: A molecular entity that can undergo oxidation by the loss of hydrogen atom(s).
imported from: chebi.owl
charge: 0
formula: RH2
mass: 2.016
monoisotopicmass: 2.01565
smiles: *([H])[H]
has_alternative_id: CHEBI:13233
has_alternative_id: CHEBI:15018
has_alternative_id: CHEBI:8785
database_cross_reference: KEGG:C00030
has_obo_namespace: chebi_ontology
has_related_synonym: AH2
has_related_synonym: Donor
has_related_synonym: Hydrogen-donor
has_related_synonym: Reduced acceptor
id: CHEBI:17499
in_subset: 3 STAR

cyanide
type: Class
subclass of: pseudohalide anion
subclass of: Restriction
  on property: has role
  some values from: EC 1.9.3.1 (cytochrome c oxidase) inhibitor
subclass of: Restriction
  on property: is conjugate base of
  some values from: hydrogen cyanide
subclass of: Restriction
  on property: is conjugate base of
  some values from: hydrogen isocyanide
textual definition: A pseudohalide anion that is the conjugate base of hydrogen cyanide.
imported from: chebi.owl
charge: -1
formula: CN
inchi: InChI=1S/CN/c1-2/q-1
inchikey: XFXPMWWXUTWYJX-UHFFFAOYSA-N
mass: 26.01740
monoisotopicmass: 26.00362
smiles: [C-]#N
has_alternative_id: CHEBI:14038
has_alternative_id: CHEBI:3969
has_alternative_id: CHEBI:41780
database_cross_reference: Beilstein:1900509
database_cross_reference: CAS:57-12-5
database_cross_reference: Gmelin:89
database_cross_reference: HMDB:HMDB0002084
database_cross_reference: KEGG:C00177
database_cross_reference: MetaCyc:CPD-13584
database_cross_reference: PDBeChem:CYN
database_cross_reference: PMID:11386635
database_cross_reference: PMID:14871577
database_cross_reference: PMID:17554165
database_cross_reference: PMID:7839575
database_cross_reference: Reaxys:1900509
database_cross_reference: Wikipedia:Cyanide
has_exact_synonym: Cyanide
has_exact_synonym: cyanide
has_exact_synonym: nitridocarbonate(1-)
has_obo_namespace: chebi_ontology
has_related_synonym: CN(-)
has_related_synonym: CN-
has_related_synonym: CYANIDE ION
has_related_synonym: Prussiate
has_related_synonym: Zyanid
id: CHEBI:17514
in_subset: 3 STAR

toluene
type: Class
subclass of: volatile organic compound
subclass of: toluenes
subclass of: methylbenzene
textual definition: The simplest member of the class toluenes consisting of a benzene core which bears a single methyl substituent.
imported from: chebi.owl
charge: 0
formula: C7H8
inchi: InChI=1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3
inchikey: YXFVVABEGXRONW-UHFFFAOYSA-N
mass: 92.13842
monoisotopicmass: 92.06260
smiles: Cc1ccccc1
has_alternative_id: CHEBI:15248
has_alternative_id: CHEBI:27022
has_alternative_id: CHEBI:44023
has_alternative_id: CHEBI:9624
database_cross_reference: Beilstein:635760
database_cross_reference: CAS:108-88-3
database_cross_reference: DrugBank:DB01900
database_cross_reference: Gmelin:2456
database_cross_reference: KEGG:C01455
database_cross_reference: PDBeChem:MBN
database_cross_reference: PMID:11182169
database_cross_reference: PMID:11314682
database_cross_reference: PMID:11846266
database_cross_reference: PMID:11991009
database_cross_reference: PMID:12062755
database_cross_reference: PMID:12213539
database_cross_reference: PMID:12237258
database_cross_reference: PMID:12784113
database_cross_reference: PMID:12876426
database_cross_reference: PMID:14512097
database_cross_reference: PMID:14559343
database_cross_reference: PMID:14605898
database_cross_reference: PMID:15015825
database_cross_reference: PMID:15019953
database_cross_reference: PMID:15119846
database_cross_reference: PMID:15193425
database_cross_reference: PMID:15542760
database_cross_reference: PMID:15567510
database_cross_reference: PMID:15695158
database_cross_reference: PMID:15796064
database_cross_reference: PMID:16316648
database_cross_reference: PMID:16348226
database_cross_reference: PMID:16601996
database_cross_reference: PMID:17145141
database_cross_reference: PMID:17175136
database_cross_reference: PMID:17497535
database_cross_reference: PMID:17725881
database_cross_reference: PMID:18397809
database_cross_reference: PMID:18832024
database_cross_reference: PMID:19261054
database_cross_reference: PMID:19384711
database_cross_reference: PMID:19429395
database_cross_reference: PMID:19635754
database_cross_reference: PMID:19765629
database_cross_reference: PMID:19825861
database_cross_reference: PMID:19928203
database_cross_reference: PMID:19969016
database_cross_reference: PMID:20347282
database_cross_reference: PMID:20837561
database_cross_reference: PMID:21430649
database_cross_reference: PMID:21655021
database_cross_reference: PMID:21731073
database_cross_reference: PMID:21802510
database_cross_reference: PMID:21840036
database_cross_reference: Reaxys:635760
database_cross_reference: UM-BBD_compID:c0114
database_cross_reference: Wikipedia:Toluene
has_exact_synonym: TOLUENE
has_exact_synonym: Toluene
has_exact_synonym: toluene
has_obo_namespace: chebi_ontology
has_related_synonym: Toluen
has_related_synonym: Toluol
has_related_synonym: methylbenzene
has_related_synonym: phenylmethane
id: CHEBI:17578
in_subset: 3 STAR

electron acceptor
type: Class
subclass of: acceptor
textual definition: A substance to which an electron may be transferred.
imported from: chebi.owl
has_alternative_id: CHEBI:14207
has_alternative_id: CHEBI:14716
has_alternative_id: CHEBI:7835
database_cross_reference: KEGG:C02177
has_exact_synonym: electron acceptor
has_obo_namespace: chebi_ontology
has_related_synonym: Elektronenakzeptor
has_related_synonym: Oxidized donor
id: CHEBI:17654
in_subset: 3 STAR

N,N-dimethylformamide
type: Class
subclass of: volatile organic compound
subclass of: formamides
subclass of: Restriction
  on property: has role
  some values from: polar aprotic solvent
subclass of: Restriction
  on property: has role
  some values from: hepatotoxic agent
subclass of: Restriction
  on property: has functional parent
  some values from: formamide
textual definition: A member of the class of formamides that is formamide in which the amino hydrogens are replaced by methyl groups.
imported from: chebi.owl
charge: 0
formula: C3H7NO
inchi: InChI=1S/C3H7NO/c1-4(2)3-5/h3H,1-2H3
inchikey: ZMXDDKWLCZADIW-UHFFFAOYSA-N
mass: 73.09382
monoisotopicmass: 73.05276
smiles: [H]C(=O)N(C)C
has_alternative_id: CHEBI:12425
has_alternative_id: CHEBI:21454
has_alternative_id: CHEBI:42077
has_alternative_id: CHEBI:7076
database_cross_reference: CAS:68-12-2
database_cross_reference: DrugBank:DB01844
database_cross_reference: HMDB:HMDB0001888
database_cross_reference: KEGG:C03134
database_cross_reference: MetaCyc:CPD-581
database_cross_reference: PDBeChem:DMF
database_cross_reference: PMID:18666198
database_cross_reference: PMID:19608215
database_cross_reference: PMID:3824392
database_cross_reference: Reaxys:605365
database_cross_reference: Wikipedia:Dimethylformamide
has_exact_synonym: N,N-Dimethylformamide
has_exact_synonym: N,N-dimethylformamide
has_obo_namespace: chebi_ontology
has_related_synonym: DMF
has_related_synonym: Dimethylformamide
has_related_synonym: N,N-Dimethylmethanamide
has_related_synonym: N-Formyldimethylamine
id: CHEBI:17741
in_subset: 3 STAR

methanol
type: Class
subclass of: volatile organic compound
subclass of: primary alcohol
subclass of: alkyl alcohol
subclass of: one-carbon compound
subclass of: Restriction
  on property: has role
  some values from: Mycoplasma genitalium metabolite
subclass of: Restriction
  on property: has role
  some values from: fuel
subclass of: Restriction
  on property: has role
  some values from: amphiprotic solvent
subclass of: Restriction
  on property: has role
  some values from: mouse metabolite
subclass of: Restriction
  on property: has role
  some values from: Escherichia coli metabolite
subclass of: Restriction
  on property: has role
  some values from: human metabolite
subclass of: Restriction
  on property: is conjugate acid of
  some values from: methoxide
textual definition: The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
imported from: chebi.owl
charge: 0
formula: CH4O
inchi: InChI=1S/CH4O/c1-2/h2H,1H3
inchikey: OKKJLVBELUTLKV-UHFFFAOYSA-N
mass: 32.04186
monoisotopicmass: 32.02621
smiles: CO
has_alternative_id: CHEBI:14588
has_alternative_id: CHEBI:25227
has_alternative_id: CHEBI:44080
has_alternative_id: CHEBI:44553
has_alternative_id: CHEBI:6816
database_cross_reference: Beilstein:1098229
database_cross_reference: CAS:67-56-1
database_cross_reference: Gmelin:449
database_cross_reference: HMDB:HMDB0001875
database_cross_reference: KEGG:C00132
database_cross_reference: KEGG:D02309
database_cross_reference: MetaCyc:METOH
database_cross_reference: PDBeChem:MOH
database_cross_reference: PMID:11141607
database_cross_reference: PMID:11430978
database_cross_reference: PMID:11489599
database_cross_reference: PMID:11680737
database_cross_reference: PMID:11684179
database_cross_reference: PMID:14012711
database_cross_reference: PMID:14678513
database_cross_reference: PMID:14760634
database_cross_reference: PMID:15172721
database_cross_reference: PMID:15906011
database_cross_reference: PMID:16705261
database_cross_reference: PMID:17451998
database_cross_reference: PMID:17733096
database_cross_reference: PMID:19064074
database_cross_reference: PMID:19850112
database_cross_reference: PMID:20314698
database_cross_reference: Reaxys:1098229
database_cross_reference: UM-BBD_compID:c0132
database_cross_reference: Wikipedia:Methanol
has_exact_synonym: METHANOL
has_exact_synonym: Methanol
has_exact_synonym: methanol
has_obo_namespace: chebi_ontology
has_related_synonym: CH3OH
has_related_synonym: MeOH
has_related_synonym: Methyl alcohol
has_related_synonym: Methylalkohol
has_related_synonym: carbinol
has_related_synonym: spirit of wood
has_related_synonym: wood alcohol
has_related_synonym: wood naphtha
has_related_synonym: wood spirit
id: CHEBI:17790
in_subset: 3 STAR

propan-2-ol
type: Class
subclass of: secondary fatty alcohol
subclass of: secondary alcohol
subclass of: Restriction
  on property: has role
  some values from: protic solvent
textual definition: A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group.
imported from: chebi.owl
charge: 0
formula: C3H8O
inchi: InChI=1S/C3H8O/c1-3(2)4/h3-4H,1-2H3
inchikey: KFZMGEQAYNKOFK-UHFFFAOYSA-N
mass: 60.09502
monoisotopicmass: 60.05751
smiles: CC(C)O
has_alternative_id: CHEBI:14897
has_alternative_id: CHEBI:26280
has_alternative_id: CHEBI:43588
has_alternative_id: CHEBI:8467
database_cross_reference: Beilstein:635639
database_cross_reference: CAS:67-63-0
database_cross_reference: DrugBank:DB04402
database_cross_reference: Drug_Central:4215
database_cross_reference: Gmelin:1464
database_cross_reference: HMDB:HMDB0000863
database_cross_reference: KEGG:C01845
database_cross_reference: KEGG:D00137
database_cross_reference: KNApSAcK:C00048438
database_cross_reference: MetaCyc:ISO-PROPANOL
database_cross_reference: PDBeChem:IPA
database_cross_reference: PMID:24524727
database_cross_reference: PMID:24653974
database_cross_reference: Reaxys:635639
database_cross_reference: UM-BBD_compID:c0519
database_cross_reference: Wikipedia:Isopropyl_Alcohol
database_cross_reference: YMDB:YMDB01718
has_exact_synonym: Propan-2-ol
has_exact_synonym: propan-2-ol
has_obo_namespace: chebi_ontology
has_related_synonym: 1-methylethanol
has_related_synonym: 1-methylethyl alcohol
has_related_synonym: 2-Propanol
has_related_synonym: 2-hydroxypropane
has_related_synonym: IPA
has_related_synonym: ISOPROPYL ALCOHOL
has_related_synonym: Isopropanol
has_related_synonym: Isopropyl alcohol
has_related_synonym: Isopropylalkohol
has_related_synonym: i-Propylalkohol
has_related_synonym: i-propanol
has_related_synonym: isopropyl alcohol
has_related_synonym: sec-propanol
id: CHEBI:17824
in_subset: 3 STAR

donor
type: Class
subclass of: chemical role
textual definition: A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
imported from: chebi.owl
has_alternative_id: CHEBI:14202
has_alternative_id: CHEBI:4697
database_cross_reference: KEGG:C01351
has_exact_synonym: Donor
has_obo_namespace: chebi_ontology
has_related_synonym: Donator
has_related_synonym: donneur
id: CHEBI:17891
in_subset: 3 STAR

dialkyl ketone
type: Class
subclass of: ketone
imported from: chebi.owl
charge: 0
formula: COR2
mass: 28.01010
monoisotopicmass: 27.99491
smiles: [*]C([*])=O
has_alternative_id: CHEBI:14136
has_alternative_id: CHEBI:23663
has_alternative_id: CHEBI:4485
database_cross_reference: KEGG:C02146
has_exact_synonym: Dialkyl ketone
has_exact_synonym: dialkyl ketone
has_obo_namespace: chebi_ontology
has_related_synonym: dialkyl ketones
id: CHEBI:18044
in_subset: 3 STAR

lipid
type: Class
subclass of: organic molecular entity
textual 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

nitrile
type: Class
subclass of: cyanides
subclass of: Restriction
  on property: has part
  some values from: cyano group
textual definition: A compound having the structure RC#N; thus a C-substituted derivative of hydrocyanic acid, HC#N. In systematic nomenclature, the suffix nitrile denotes the triply bound #N atom, not the carbon atom attached to it.
imported from: chebi.owl
charge: 0
formula: CNR
mass: 26.01740
monoisotopicmass: 26.00307
smiles: [*]C#N
has_alternative_id: CHEBI:13212
has_alternative_id: CHEBI:13426
has_alternative_id: CHEBI:13660
has_alternative_id: CHEBI:25547
has_alternative_id: CHEBI:7584
database_cross_reference: KEGG:C00726
has_exact_synonym: Nitrile
has_exact_synonym: nitrile
has_exact_synonym: nitriles
has_obo_namespace: chebi_ontology
has_related_synonym: Nitril
has_related_synonym: R-CN
has_related_synonym: a nitrile
has_related_synonym: nitrilos
id: CHEBI:18379
in_subset: 3 STAR

hydrogen cyanide
type: Class
subclass of: hydracid
subclass of: one-carbon compound
subclass of: Restriction
  on property: has role
  some values from: poison
subclass of: Restriction
  on property: has role
  some values from: Escherichia coli metabolite
subclass of: Restriction
  on property: has role
  some values from: human metabolite
subclass of: Restriction
  on property: is conjugate acid of
  some values from: cyanide
subclass of: Restriction
  on property: is tautomer of
  some values from: hydrogen isocyanide
textual definition: A one-carbon compound consisting of a methine group triple bonded to a nitrogen atom
imported from: chebi.owl
charge: 0
formula: CHN
inchi: InChI=1S/CHN/c1-2/h1H
inchikey: LELOWRISYMNNSU-UHFFFAOYSA-N
mass: 27.02530
monoisotopicmass: 27.01090
smiles: C#N
has_alternative_id: CHEBI:13362
has_alternative_id: CHEBI:5786
database_cross_reference: CAS:74-90-8
database_cross_reference: HMDB:HMDB0060292
database_cross_reference: KEGG:C01326
database_cross_reference: KNApSAcK:C00007569
database_cross_reference: MetaCyc:HCN
database_cross_reference: PMID:19849830
database_cross_reference: PMID:26700190
database_cross_reference: PMID:26778429
database_cross_reference: PMID:26823582
database_cross_reference: PMID:26940198
database_cross_reference: PMID:27123778
database_cross_reference: Reaxys:1718793
database_cross_reference: Wikipedia:Hydrogen_cyanide
has_exact_synonym: Hydrogen cyanide
has_exact_synonym: hydridonitridocarbon
has_exact_synonym: hydrogen cyanide
has_exact_synonym: hydrogen(nitridocarbonate)
has_exact_synonym: methanenitrile
has_obo_namespace: chebi_ontology
has_related_synonym: Blausaeure
has_related_synonym: Cyanwasserstoff
has_related_synonym: HCN
has_related_synonym: [CHN]
has_related_synonym: formonitrile
has_related_synonym: hydrocyanic acid
id: CHEBI:18407
in_subset: 3 STAR

acyl group
type: Class
subclass of: organic group
textual definition: An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
imported from: chebi.owl
has_exact_synonym: acyl group
has_exact_synonym: alkanoyl
has_obo_namespace: chebi_ontology
has_related_synonym: acyl groups
has_related_synonym: alkanoyl group
has_related_synonym: groupe acyle
id: CHEBI:22221
in_subset: 3 STAR

alpha-1-microglobulin-Ig alpha complex chromophores
type: Class
subclass of: chromophore
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:22368
in_subset: 1 STAR

anion
type: Class
subclass of: ion
textual definition: A monoatomic or polyatomic species having one or more elementary charges of the electron.
imported from: chebi.owl
has_exact_synonym: Anion
has_exact_synonym: anion
has_obo_namespace: chebi_ontology
has_related_synonym: Anionen
has_related_synonym: aniones
has_related_synonym: anions
id: CHEBI:22563
in_subset: 3 STAR

antioxidant
type: Class
subclass of: chemical role
textual definition: A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: antioxidants
has_related_synonym: antioxydant
has_related_synonym: antoxidant
id: CHEBI:22586
in_subset: 3 STAR

base
type: Class
subclass of: chemical role
textual definition: A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
imported from: chebi.owl
database_cross_reference: KEGG:C00701
has_exact_synonym: Base
has_exact_synonym: base
has_obo_namespace: chebi_ontology
has_related_synonym: Base1
has_related_synonym: Base2
has_related_synonym: Basen
has_related_synonym: Nucleobase
has_related_synonym: bases
id: CHEBI:22695
in_subset: 3 STAR

benzenes
type: Class
subclass of: benzenoid aromatic compound
textual definition: Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:22712
in_subset: 3 STAR

butanone
type: Class
subclass of: ketone
textual definition: Any ketone that is butane substituted by an oxo group at unspecified position.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: butanones
id: CHEBI:22951
in_subset: 3 STAR

carbamoyl group
type: Class
subclass of: univalent carboacyl group
subclass of: Restriction
  on property: is substituent group from
  some values from: carbamic acid
textual definition: The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
imported from: chebi.owl
charge: 0
formula: CH2NO
mass: 44.03272
monoisotopicmass: 44.01364
smiles: *C(N)=O
database_cross_reference: PMID:24168430
has_exact_synonym: carbamoyl
has_obo_namespace: chebi_ontology
has_related_synonym: -C(O)NH2
has_related_synonym: -CONH2
has_related_synonym: aminocarbonyl
has_related_synonym: carbamyl
has_related_synonym: carbamyl group
has_related_synonym: carboxamide
id: CHEBI:23004
in_subset: 3 STAR

carbonyl group
type: Class
subclass of: organodiyl group
imported from: chebi.owl
charge: 0
formula: CO
mass: 28.01010
monoisotopicmass: 27.99491
smiles: O=C(*)*
has_exact_synonym: carbonyl
has_exact_synonym: carbonyl group
has_obo_namespace: chebi_ontology
has_related_synonym: >C=O
id: CHEBI:23019
in_subset: 3 STAR

chromophore
type: Class
subclass of: photochemical role
textual definition: The part (atom or group of atoms) of a molecular entity in which the electronic transition responsible for a given spectral band is approximately localized.
imported from: chebi.owl
database_cross_reference: Wikipedia:Chromophore
has_exact_synonym: chromophore
has_obo_namespace: chebi_ontology
has_related_synonym: chromophores
id: CHEBI:23240
in_subset: 3 STAR

cofactor
type: Class
subclass of: biochemical role
textual definition: An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
imported from: chebi.owl
database_cross_reference: Wikipedia:Cofactor_(biochemistry)
has_exact_synonym: cofactor
has_exact_synonym: cofactors
has_obo_namespace: chebi_ontology
id: CHEBI:23357
in_subset: 3 STAR

molecular entity
type: Class
subclass of: material entity
subclass of: chemical entity
editor preferred label: molecular entity
textual 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 Investigations
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

cyanides
type: Class
subclass of: organonitrogen compound
subclass of: Restriction
  on property: has parent hydride
  some values from: hydrogen cyanide
textual definition: Salts and C-organyl derivatives of hydrogen cyanide, HC#N.
imported from: chebi.owl
has_exact_synonym: cyanides
has_obo_namespace: chebi_ontology
id: CHEBI:23424
in_subset: 3 STAR

drug
type: Class
subclass of: pharmaceutical
textual definition: Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: drugs
has_related_synonym: medicine
id: CHEBI:23888
in_subset: 3 STAR

enzyme inhibitor
type: Class
subclass of: inhibitor
subclass of: biochemical role
textual definition: A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
imported from: chebi.owl
has_exact_synonym: enzyme inhibitor
has_obo_namespace: chebi_ontology
has_related_synonym: enzyme inhibitors
has_related_synonym: inhibidor enzimatico
has_related_synonym: inhibidores enzimaticos
has_related_synonym: inhibiteur enzymatique
has_related_synonym: inhibiteurs enzymatiques
id: CHEBI:23924
in_subset: 3 STAR

fatty alcohol
type: Class
subclass of: lipid
subclass of: alcohol
textual definition: An aliphatic alcohol consisting of a chain of 3 to greater than 27 carbon atoms. Fatty alcohols may be saturated or unsaturated and may be branched or unbranched.
imported from: chebi.owl
charge: 0
formula: HOR
mass: 17.007
monoisotopicmass: 17.00274
smiles: O[*]
database_cross_reference: LIPID_MAPS_class:LMFA05
database_cross_reference: MetaCyc:Fatty-Alcohols
database_cross_reference: Wikipedia:Fatty_alcohol
has_exact_synonym: fatty alcohol
has_obo_namespace: chebi_ontology
has_related_synonym: Fettalkohol
has_related_synonym: Fettalkohole
has_related_synonym: alcool gras
has_related_synonym: fatty alcohols
id: CHEBI:24026
in_subset: 3 STAR

iron(3+) chelator
type: Class
subclass of: iron chelator
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:24028
in_subset: 1 STAR

formamides
type: Class
subclass of: carboxamide
textual definition: Amides with the general formula R(1)R(2)NCHO (R(1) and R(2) can be H).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:24079
in_subset: 3 STAR

chemical entity
type: Class
subclass of: material entity
textual 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
textual 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

group
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: has part
  some values from: atom
textual definition: A defined linked collection of atoms or a single atom within a molecular entity.
imported from: chebi.owl
has_exact_synonym: group
has_obo_namespace: chebi_ontology
has_related_synonym: Gruppe
has_related_synonym: Rest
has_related_synonym: groupe
has_related_synonym: grupo
has_related_synonym: grupos
id: CHEBI:24433
in_subset: 3 STAR

organic heterocyclic compound
type: Class
subclass of: heteroorganic entity
subclass of: organic cyclic compound
subclass of: heterocyclic compound
textual definition: A cyclic compound having as ring members atoms of carbon and at least of one other element.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic heterocycle
has_related_synonym: organic heterocyclic compounds
id: CHEBI:24532
in_subset: 3 STAR

hydrocarbon
type: Class
subclass of: organic fundamental parent
textual definition: A compound consisting of carbon and hydrogen only.
imported from: chebi.owl
has_exact_synonym: hydrocarbon
has_exact_synonym: hydrocarbons
has_obo_namespace: chebi_ontology
has_related_synonym: Kohlenwasserstoff
has_related_synonym: Kohlenwasserstoffe
has_related_synonym: hidrocarburo
has_related_synonym: hidrocarburos
has_related_synonym: hydrocarbure
id: CHEBI:24632
in_subset: 3 STAR

hydroxides
type: Class
subclass of: oxygen molecular entity
subclass of: hydrogen molecular entity
subclass of: heteroatomic molecular entity
subclass of: Restriction
  on property: has part
  some values from: hydroxy group
textual definition: Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:24651
in_subset: 3 STAR

oxoacid
type: Class
subclass of: hydroxides
subclass of: Restriction
  on property: has role
  some values from: Bronsted acid
textual definition: A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
imported from: chebi.owl
has_exact_synonym: oxoacid
has_exact_synonym: oxoacids
has_obo_namespace: chebi_ontology
has_related_synonym: oxacids
has_related_synonym: oxiacids
has_related_synonym: oxo acid
has_related_synonym: oxy-acids
has_related_synonym: oxyacids
id: CHEBI:24833
in_subset: 3 STAR

inorganic anion
type: Class
subclass of: anion
subclass of: inorganic ion
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: inorganic anions
id: CHEBI:24834
in_subset: 3 STAR

inorganic molecular entity
type: Class
subclass of: molecular entity
textual definition: A molecular entity that contains no carbon.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: anorganische Verbindungen
has_related_synonym: inorganic compounds
has_related_synonym: inorganic entity
has_related_synonym: inorganic molecular entities
has_related_synonym: inorganics
id: CHEBI:24835
in_subset: 3 STAR

ionophore
type: Class
subclass of: membrane transport modulator
textual definition: A compound which can carry specific ions through membranes of cells or organelles.
imported from: chebi.owl
database_cross_reference: Wikipedia:Ionophore
has_exact_synonym: ionophore
has_obo_namespace: chebi_ontology
has_related_synonym: ionophores
id: CHEBI:24869
in_subset: 3 STAR

ion
type: Class
subclass of: molecular entity
textual definition: A molecular entity having a net electric charge.
imported from: chebi.owl
has_exact_synonym: Ion
has_exact_synonym: ion
has_obo_namespace: chebi_ontology
has_related_synonym: Ionen
has_related_synonym: iones
has_related_synonym: ions
id: CHEBI:24870
in_subset: 3 STAR

iron ionophore
type: Class
subclass of: ionophore
textual definition: Any ionophore capable of transportation of iron ions across membranes.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: iron ionophores
id: CHEBI:24874
in_subset: 3 STAR

luciferin
type: Class
subclass of: photobiochemical role
textual definition: A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:25078
in_subset: 3 STAR

metabolite
type: Class
subclass of: biochemical role
textual 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

mitochondrial respiratory-chain inhibitor
type: Class
subclass of: respiratory-chain inhibitor
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: mitochondrial electron transport chain inhibitors
has_related_synonym: mitochondrial electron-transport chain inhibitor
has_related_synonym: mitochondrial respiratory chain inhibitors
id: CHEBI:25355
in_subset: 3 STAR

molecule
type: Class
subclass of: polyatomic entity
textual definition: Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
imported from: chebi.owl
has_exact_synonym: molecule
has_obo_namespace: chebi_ontology
has_related_synonym: Molekuel
has_related_synonym: molecula
has_related_synonym: molecules
has_related_synonym: neutral molecular compounds
id: CHEBI:25367
in_subset: 3 STAR

monocarboxylic acid
type: Class
subclass of: carboxylic acid
subclass of: Restriction
  on property: is conjugate acid of
  some values from: monocarboxylic acid anion
textual definition: An oxoacid containing a single carboxy group.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: monocarboxylic acids
id: CHEBI:25384
in_subset: 3 STAR

nitrogen atom
type: Class
subclass of: nonmetal atom
subclass of: pnictogen
subclass of: Restriction
  on property: has role
  some values from: macronutrient
imported from: chebi.owl
charge: 0
formula: N
mass: 14.007
monoisotopicmass: 14.00307
database_cross_reference: WebElements:N
has_exact_synonym: nitrogen
has_obo_namespace: chebi_ontology
has_related_synonym: 7N
has_related_synonym: N
has_related_synonym: Stickstoff
has_related_synonym: azote
has_related_synonym: nitrogen
has_related_synonym: nitrogeno
id: CHEBI:25555
in_subset: 3 STAR

nonmetal atom
type: Class
subclass of: atom
imported from: chebi.owl
has_exact_synonym: nonmetal
has_obo_namespace: chebi_ontology
has_related_synonym: Nichtmetall
has_related_synonym: Nichtmetalle
has_related_synonym: no metal
has_related_synonym: no metales
has_related_synonym: non-metal
has_related_synonym: non-metaux
has_related_synonym: nonmetal
has_related_synonym: nonmetals
id: CHEBI:25585
in_subset: 3 STAR

organic heteromonocyclic compound
type: Class
subclass of: organic heterocyclic compound
subclass of: heteromonocyclic compound
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic heteromonocyclic compounds
id: CHEBI:25693
in_subset: 3 STAR

organic anion
type: Class
subclass of: anion
subclass of: organic ion
textual definition: Any organic ion with a net negative charge.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic anions
id: CHEBI:25696
in_subset: 3 STAR

ether
type: Class
subclass of: organooxygen compound
textual definition: An organooxygen compound with formula ROR, where R is not hydrogen.
imported from: chebi.owl
charge: 0
formula: OR2
mass: 15.99940
monoisotopicmass: 15.99491
smiles: [*]O[*]
has_exact_synonym: ether
has_exact_synonym: ethers
has_obo_namespace: chebi_ontology
has_related_synonym: ethers
id: CHEBI:25698
in_subset: 3 STAR

organic ion
type: Class
subclass of: ion
subclass of: organic molecular entity
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic ions
id: CHEBI:25699
in_subset: 3 STAR

aliphatic alcohol
type: Class
subclass of: alcohol
textual definition: An alcohol derived from an aliphatic compound.
imported from: chebi.owl
charge: 0
formula: HOR
mass: 17.007
monoisotopicmass: 17.00274
smiles: O*
database_cross_reference: KEGG:C02525
has_exact_synonym: Aliphatic alcohol
has_obo_namespace: chebi_ontology
has_related_synonym: aliphatic alcohols
has_related_synonym: an aliphatic alcohol
id: CHEBI:2571
in_subset: 3 STAR

oxide
type: Class
subclass of: oxygen molecular entity
subclass of: heteroatomic molecular entity
textual definition: An oxide is a chemical compound of oxygen with other chemical elements.
imported from: chebi.owl
has_exact_synonym: oxide
has_obo_namespace: chebi_ontology
has_related_synonym: oxides
id: CHEBI:25741
in_subset: 3 STAR

oxidized luciferins
type: Class
subclass of: luciferin
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:25747
in_subset: 1 STAR

oxygen atom
type: Class
subclass of: nonmetal atom
subclass of: chalcogen
subclass of: Restriction
  on property: has role
  some values from: macronutrient
imported from: chebi.owl
charge: 0
formula: O
inchi: InChI=1S/O
inchikey: QVGXLLKOCUKJST-UHFFFAOYSA-N
mass: 15.99940
monoisotopicmass: 15.99491
smiles: [O]
database_cross_reference: KEGG:C00007
database_cross_reference: WebElements:O
has_exact_synonym: oxygen
has_obo_namespace: chebi_ontology
has_related_synonym: 8O
has_related_synonym: O
has_related_synonym: Sauerstoff
has_related_synonym: oxigeno
has_related_synonym: oxygen
has_related_synonym: oxygene
id: CHEBI:25805
in_subset: 3 STAR

oxygen molecular entity
type: Class
subclass of: chalcogen molecular entity
subclass of: Restriction
  on property: has part
  some values from: oxygen atom
imported from: chebi.owl
has_exact_synonym: oxygen molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: oxygen molecular entities
id: CHEBI:25806
in_subset: 3 STAR

propanones
type: Class
subclass of: ketone
textual definition: A ketone that is propane carrying at least one oxo substituent.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:26292
in_subset: 3 STAR

sideramine
type: Class
subclass of: siderophore
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:26671
in_subset: 1 STAR

siderophore
type: Class
subclass of: cofactor
subclass of: iron(3+) chelator
subclass of: iron ionophore
textual definition: Any of low-molecular-mass iron(III)-chelating compounds produced by microorganisms for the purpose of the transport and sequestration of iron.
imported from: chebi.owl
has_exact_synonym: siderophore
has_obo_namespace: chebi_ontology
has_related_synonym: ferrioxamine
has_related_synonym: ferrioxamines
has_related_synonym: ironophore
has_related_synonym: siderochrome
has_related_synonym: siderochromes
has_related_synonym: siderophores
id: CHEBI:26672
in_subset: 3 STAR

oxolane
type: Class
subclass of: volatile organic compound
subclass of: oxolanes
subclass of: saturated organic heteromonocyclic parent
subclass of: cyclic ether
subclass of: Restriction
  on property: has role
  some values from: polar aprotic solvent
textual definition: A cyclic ether that is butane in which one hydrogen from each methyl group is substituted by an oxygen.
imported from: chebi.owl
charge: 0
formula: C4H8O
inchi: InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2
inchikey: WYURNTSHIVDZCO-UHFFFAOYSA-N
mass: 72.10570
monoisotopicmass: 72.05751
smiles: C1CCOC1
database_cross_reference: Beilstein:102391
database_cross_reference: CAS:109-99-9
database_cross_reference: Gmelin:1767
database_cross_reference: HMDB:HMDB0000246
database_cross_reference: PMID:12571688
database_cross_reference: PMID:1811956
database_cross_reference: PMID:1911404
database_cross_reference: PMID:19716170
database_cross_reference: PMID:21316415
database_cross_reference: PMID:21842397
database_cross_reference: PMID:2675957
database_cross_reference: Reaxys:102391
database_cross_reference: UM-BBD_compID:c0019
database_cross_reference: Wikipedia:THF
has_exact_synonym: oxolane
has_obo_namespace: chebi_ontology
has_related_synonym: 1,4-epoxybutane
has_related_synonym: THF
has_related_synonym: butane alpha,delta-oxide
has_related_synonym: butylene oxide
has_related_synonym: furanidine
has_related_synonym: tetrahydrofuran
has_related_synonym: tetramethylene oxide
id: CHEBI:26911
in_subset: 3 STAR

oxolanes
type: Class
subclass of: organic heteromonocyclic compound
subclass of: oxacycle
textual definition: Any oxacycle having an oxolane (tetrahydrofuran) skeleton.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:26912
in_subset: 3 STAR

toluenes
type: Class
subclass of: benzenes
textual definition: Any member of the class of benzenes that is a substituted benzene in which the substituents include one (and only one) methyl group.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:27024
in_subset: 3 STAR

univalent carboacyl group
type: Class
subclass of: carboacyl group
textual definition: A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: univalent acyl group
has_related_synonym: univalent carboacyl groups
has_related_synonym: univalent carboxylic acyl groups
id: CHEBI:27207
in_subset: 3 STAR

carbon atom
type: Class
subclass of: nonmetal atom
subclass of: carbon group element atom
subclass of: Restriction
  on property: has role
  some values from: macronutrient
imported from: chebi.owl
charge: 0
formula: C
inchi: InChI=1S/C
inchikey: OKTJSMMVPCPJKN-UHFFFAOYSA-N
mass: 12.01070
monoisotopicmass: 12.00000
smiles: [C]
has_alternative_id: CHEBI:23009
has_alternative_id: CHEBI:3399
database_cross_reference: CAS:7440-44-0
database_cross_reference: KEGG:C06265
database_cross_reference: WebElements:C
has_exact_synonym: carbon
has_obo_namespace: chebi_ontology
has_related_synonym: 6C
has_related_synonym: C
has_related_synonym: Carbon
has_related_synonym: Kohlenstoff
has_related_synonym: carbon
has_related_synonym: carbone
has_related_synonym: carbonium
has_related_synonym: carbono
id: CHEBI:27594
in_subset: 3 STAR

detergent
type: Class
subclass of: application
subclass of: surfactant
textual definition: A surfactant (or a mixture containing one or more surfactants) having cleaning properties in dilute solutions.
imported from: chebi.owl
has_alternative_id: CHEBI:23648
has_alternative_id: CHEBI:4456
database_cross_reference: KEGG:C01689
has_exact_synonym: detergent
has_obo_namespace: chebi_ontology
has_related_synonym: Detergents
id: CHEBI:27780
in_subset: 3 STAR

butan-2-one
type: Class
subclass of: volatile organic compound
subclass of: dialkyl ketone
subclass of: butanone
subclass of: methyl ketone
subclass of: Restriction
  on property: has role
  some values from: polar aprotic solvent
subclass of: Restriction
  on property: has role
  some values from: bacterial metabolite
textual definition: A dialkyl ketone that is a four-carbon ketone carrying a single keto- group at position C-2.
imported from: chebi.owl
charge: 0
formula: C4H8O
inchi: InChI=1S/C4H8O/c1-3-4(2)5/h3H2,1-2H3
inchikey: ZWEHNKRNPOVVGH-UHFFFAOYSA-N
mass: 72.10572
monoisotopicmass: 72.05751
smiles: CCC(C)=O
has_alternative_id: CHEBI:25249
has_alternative_id: CHEBI:6858
database_cross_reference: Beilstein:741880
database_cross_reference: CAS:78-93-3
database_cross_reference: Gmelin:25656
database_cross_reference: HMDB:HMDB0000474
database_cross_reference: KEGG:C02845
database_cross_reference: LIPID_MAPS_instance:LMFA12000043
database_cross_reference: MetaCyc:MEK
database_cross_reference: PMID:20403429
database_cross_reference: PMID:23050457
database_cross_reference: Reaxys:741880
database_cross_reference: UM-BBD_compID:c0020
database_cross_reference: Wikipedia:Butanone
has_exact_synonym: butan-2-one
has_obo_namespace: chebi_ontology
has_related_synonym: 2-Butanon
has_related_synonym: 2-Butanone
has_related_synonym: 3-butanone
has_related_synonym: Aethylmethylketon
has_related_synonym: C2H5COCH3
has_related_synonym: Ethyl methyl ketone
has_related_synonym: Ethylmethylketon
has_related_synonym: MEK
has_related_synonym: Methyl ethyl ketone
has_related_synonym: Methylethylketon
has_related_synonym: butanone
has_related_synonym: butanone 2
has_related_synonym: ethyl methyl cetone
has_related_synonym: ethyl(methyl) ketone
has_related_synonym: ethylmethyl ketone
has_related_synonym: meetco
has_related_synonym: methyl acetone
has_related_synonym: methyl ethyl cetone
has_related_synonym: methyl(ethyl) ketone
has_related_synonym: methylacetone
has_related_synonym: methylethyl ketone
has_related_synonym: oxobutane
id: CHEBI:28398
in_subset: 3 STAR

carbamic acid
type: Class
subclass of: organonitrogen compound
subclass of: carbon oxoacid
subclass of: one-carbon compound
subclass of: Restriction
  on property: has role
  some values from: Escherichia coli metabolite
subclass of: Restriction
  on property: is conjugate acid of
  some values from: carbamate
textual definition: A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
imported from: chebi.owl
charge: 0
formula: CH3NO2
inchi: InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)
inchikey: KXDHJXZQYSOELW-UHFFFAOYSA-N
mass: 61.04006
monoisotopicmass: 61.01638
smiles: NC(O)=O
has_alternative_id: CHEBI:22504
has_alternative_id: CHEBI:23002
has_alternative_id: CHEBI:3386
has_alternative_id: CHEBI:44573
database_cross_reference: Beilstein:1734754
database_cross_reference: CAS:463-77-4
database_cross_reference: DrugBank:DB04261
database_cross_reference: Gmelin:130345
database_cross_reference: KEGG:C01563
database_cross_reference: PDBeChem:OUT
database_cross_reference: Wikipedia:Carbamic_acid
has_exact_synonym: CARBAMIC ACID
has_exact_synonym: Carbamic acid
has_exact_synonym: carbamic acid
has_obo_namespace: chebi_ontology
has_related_synonym: Aminoameisensaeure
has_related_synonym: Aminoformic acid
has_related_synonym: Carbamate
has_related_synonym: Carbamidsaeure
id: CHEBI:28616
in_subset: 3 STAR

fatty acid anion
type: Class
subclass of: lipid
subclass of: monocarboxylic acid anion
subclass of: Restriction
  on property: is conjugate base of
  some values from: fatty acid
textual definition: The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid.
imported from: chebi.owl
charge: -1
formula: CO2R
mass: 44.00950
monoisotopicmass: 43.98983
smiles: [O-]C([*])=O
has_alternative_id: CHEBI:13634
has_alternative_id: CHEBI:24022
has_alternative_id: CHEBI:4985
database_cross_reference: KEGG:C02403
database_cross_reference: PMID:18628202
has_exact_synonym: Fatty acid anion
has_obo_namespace: chebi_ontology
has_related_synonym: Alkanate
has_related_synonym: Fettsaeureanion
has_related_synonym: Fettsaeureanionen
has_related_synonym: a fatty acid
has_related_synonym: acido graso anionico
has_related_synonym: acidos grasos anionicos
has_related_synonym: anion de l'acide gras
has_related_synonym: fatty acid anions
id: CHEBI:28868
in_subset: 3 STAR

ammonium
type: Class
subclass of: nitrogen hydride
subclass of: onium cation
subclass of: monovalent inorganic cation
subclass of: Restriction
  on property: has role
  some values from: cofactor
subclass of: Restriction
  on property: has role
  some values from: Saccharomyces cerevisiae metabolite
subclass of: Restriction
  on property: has role
  some values from: Escherichia coli metabolite
subclass of: Restriction
  on property: has role
  some values from: human metabolite
subclass of: Restriction
  on property: is conjugate acid of
  some values from: ammonia
textual definition: An onium cation obtained by protonation of ammonia.
imported from: chebi.owl
charge: +1
formula: H4N
inchi: InChI=1S/H3N/h1H3/p+1
inchikey: QGZKDVFQNNGYKY-UHFFFAOYSA-O
mass: 18.03850
monoisotopicmass: 18.03383
smiles: [H][N+]([H])([H])[H]
has_alternative_id: CHEBI:22534
has_alternative_id: CHEBI:49783
has_alternative_id: CHEBI:7435
database_cross_reference: CAS:14798-03-9
database_cross_reference: Gmelin:84
database_cross_reference: KEGG:C01342
database_cross_reference: MetaCyc:AMMONIUM
database_cross_reference: MolBase:929
database_cross_reference: PDBeChem:NH4
database_cross_reference: PMID:11319011
database_cross_reference: PMID:11341317
database_cross_reference: PMID:12096804
database_cross_reference: PMID:14512268
database_cross_reference: PMID:14879753
database_cross_reference: PMID:16345391
database_cross_reference: PMID:16903292
database_cross_reference: PMID:17392693
database_cross_reference: PMID:18515490
database_cross_reference: PMID:19199063
database_cross_reference: PMID:19596600
database_cross_reference: PMID:19682559
database_cross_reference: PMID:19716251
database_cross_reference: PMID:21993530
database_cross_reference: PMID:22265469
database_cross_reference: PMID:22524020
database_cross_reference: PMID:22562341
database_cross_reference: PMID:22631217
database_cross_reference: Reaxys:16093784
database_cross_reference: Wikipedia:Ammonium
has_exact_synonym: ammonium
has_exact_synonym: azanium
has_obo_namespace: chebi_ontology
has_related_synonym: Ammonium(1+)
has_related_synonym: NH4(+)
has_related_synonym: NH4+
has_related_synonym: [NH4](+)
has_related_synonym: ammonium cation
has_related_synonym: ammonium ion
id: CHEBI:28938
in_subset: 3 STAR

carboxylic acid anion
type: Class
subclass of: organic anion
subclass of: oxoanion
subclass of: Restriction
  on property: is conjugate base of
  some values from: carboxylic acid
textual definition: The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
imported from: chebi.owl
charge: -1
formula: CO2R
mass: 44.00950
monoisotopicmass: 43.98983
smiles: [O-]C([*])=O
has_alternative_id: CHEBI:13626
has_alternative_id: CHEBI:13945
has_alternative_id: CHEBI:23026
has_alternative_id: CHEBI:58657
has_obo_namespace: chebi_ontology
has_related_synonym: a carboxylate
has_related_synonym: carboxylic acid anions
has_related_synonym: carboxylic anions
id: CHEBI:29067
in_subset: 3 STAR

azanide
type: Class
subclass of: nitrogen hydride
subclass of: monovalent inorganic anion
subclass of: Restriction
  on property: is conjugate acid of
  some values from: hydridonitrate(2-)
subclass of: Restriction
  on property: is conjugate base of
  some values from: ammonia
imported from: chebi.owl
charge: -1
formula: H2N
inchi: InChI=1S/H2N/h1H2/q-1
inchikey: HYGWNUKOUCZBND-UHFFFAOYSA-N
mass: 16.02262
monoisotopicmass: 16.01927
smiles: [H][N-][H]
has_exact_synonym: amide
has_exact_synonym: azanide
has_exact_synonym: dihydridonitrate(1-)
has_obo_namespace: chebi_ontology
has_related_synonym: NH2(-)
id: CHEBI:29337
in_subset: 3 STAR

hydridonitrate(2-)
type: Class
subclass of: nitrogen hydride
subclass of: divalent inorganic anion
subclass of: Restriction
  on property: is conjugate base of
  some values from: azanide
textual definition: A divalent inorganic anion resulting from the removal of two protons from ammonia.
imported from: chebi.owl
charge: -2
formula: HN
inchi: InChI=1S/HN/h1H/q-2
inchikey: DZQYTNGKSBCIOE-UHFFFAOYSA-N
mass: 15.01468
monoisotopicmass: 15.01200
smiles: [N--][H]
has_exact_synonym: azanediide
has_exact_synonym: hydridonitrate(2-)
has_obo_namespace: chebi_ontology
has_related_synonym: NH(2-)
has_related_synonym: imide
id: CHEBI:29340
in_subset: 3 STAR

monocarboxylic acid amide
type: Class
subclass of: carboxamide
textual definition: A carboxamide derived from a monocarboxylic acid.
imported from: chebi.owl
charge: 0
formula: CNOR3
mass: 42.01680
monoisotopicmass: 41.99799
smiles: [*]N([*])C([*])=O
has_alternative_id: CHEBI:13211
has_alternative_id: CHEBI:22207
has_alternative_id: CHEBI:25383
has_alternative_id: CHEBI:6977
has_obo_namespace: chebi_ontology
has_related_synonym: monocarboxylic acid amides
id: CHEBI:29347
in_subset: 3 STAR

formic acid
type: Class
subclass of: monocarboxylic acid
subclass of: Restriction
  on property: has role
  some values from: metabolite
subclass of: Restriction
  on property: has role
  some values from: antibacterial agent
subclass of: Restriction
  on property: has role
  some values from: solvent
subclass of: Restriction
  on property: has role
  some values from: protic solvent
subclass of: Restriction
  on property: has role
  some values from: astringent
subclass of: Restriction
  on property: is conjugate acid of
  some values from: formate
textual definition: The simplest carboxylic acid, containing a single carbon. Occurs naturally in various sources including the venom of bee and ant stings, and is a useful organic synthetic reagent. Principally used as a preservative and antibacterial agent in livestock feed. Induces severe metabolic acidosis and ocular injury in human subjects.
imported from: chebi.owl
charge: 0
formula: CH2O2
inchi: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
inchikey: BDAGIHXWWSANSR-UHFFFAOYSA-N
mass: 46.02538
monoisotopicmass: 46.00548
smiles: [H]C(O)=O
has_alternative_id: CHEBI:24082
has_alternative_id: CHEBI:42460
has_alternative_id: CHEBI:5145
database_cross_reference: BPDB:1749
database_cross_reference: Beilstein:1209246
database_cross_reference: CAS:64-18-6
database_cross_reference: DrugBank:DB01942
database_cross_reference: Gmelin:1008
database_cross_reference: HMDB:HMDB0000142
database_cross_reference: KEGG:C00058
database_cross_reference: KNApSAcK:C00001182
database_cross_reference: LIPID_MAPS_instance:LMFA01010040
database_cross_reference: MetaCyc:FORMATE
database_cross_reference: PDBeChem:FMT
database_cross_reference: PMID:12591956
database_cross_reference: PMID:14637377
database_cross_reference: PMID:15811469
database_cross_reference: PMID:16120414
database_cross_reference: PMID:16185830
database_cross_reference: PMID:16222862
database_cross_reference: PMID:16230297
database_cross_reference: PMID:16445901
database_cross_reference: PMID:16465784
database_cross_reference: PMID:18034701
database_cross_reference: PMID:18397576
database_cross_reference: PMID:22080171
database_cross_reference: PMID:22280475
database_cross_reference: PMID:22304812
database_cross_reference: PMID:22385261
database_cross_reference: PMID:22447125
database_cross_reference: PMID:22483350
database_cross_reference: PMID:22499553
database_cross_reference: PMID:22540994
database_cross_reference: PMID:22606986
database_cross_reference: PMID:22622393
database_cross_reference: PMID:3946945
database_cross_reference: PMID:7361809
database_cross_reference: Patent:CN101481304
database_cross_reference: Reaxys:1209246
database_cross_reference: Wikipedia:Formic_acid
has_exact_synonym: FORMIC ACID
has_exact_synonym: Formic acid
has_exact_synonym: formic acid
has_obo_namespace: chebi_ontology
has_related_synonym: Acide formique
has_related_synonym: Ameisensaeure
has_related_synonym: H-COOH
has_related_synonym: HCO2H
has_related_synonym: HCOOH
has_related_synonym: Methanoic acid
has_related_synonym: aminic acid
has_related_synonym: bilorin
has_related_synonym: formylic acid
has_related_synonym: hydrogen carboxylic acid
has_related_synonym: methoic acid
id: CHEBI:30751
in_subset: 3 STAR

alcohol
type: Class
subclass of: organic hydroxy compound
textual definition: A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
imported from: chebi.owl
charge: 0
formula: HOR
mass: 17.007
monoisotopicmass: 17.00274
smiles: O[*]
has_alternative_id: CHEBI:13804
has_alternative_id: CHEBI:22288
has_alternative_id: CHEBI:2553
database_cross_reference: KEGG:C00069
has_exact_synonym: Alcohol
has_exact_synonym: alcohols
has_obo_namespace: chebi_ontology
has_related_synonym: an alcohol
id: CHEBI:30879
in_subset: 3 STAR

amide
type: Class
subclass of: nitrogen molecular entity
textual definition: An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
imported from: chebi.owl
has_alternative_id: CHEBI:22473
has_alternative_id: CHEBI:2633
database_cross_reference: KEGG:C00241
has_exact_synonym: Amide
has_exact_synonym: amides
has_obo_namespace: chebi_ontology
id: CHEBI:32988
in_subset: 3 STAR

application
type: Class
subclass of: role
textual definition: Intended use of the molecular entity or part thereof by humans.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:33232
in_subset: 3 STAR

fundamental particle
type: Class
subclass of: subatomic particle
textual definition: A particle not known to have substructure.
imported from: chebi.owl
has_exact_synonym: elementary particle
has_obo_namespace: chebi_ontology
has_related_synonym: elementary particles
id: CHEBI:33233
in_subset: 3 STAR

oxoacid derivative
type: Class
subclass of: heteroatomic molecular entity
subclass of: Restriction
  on property: has functional parent
  some values from: oxoacid
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: oxoacid derivatives
id: CHEBI:33241
in_subset: 3 STAR

inorganic hydride
type: Class
subclass of: inorganic molecular entity
subclass of: hydrides
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: inorganic hydrides
id: CHEBI:33242
in_subset: 3 STAR

organic fundamental parent
type: Class
subclass of: organic hydride
subclass of: organic molecular entity
textual definition: An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic fundamental parents
has_related_synonym: organic parent hydrides
id: CHEBI:33245
in_subset: 3 STAR

inorganic group
type: Class
subclass of: group
textual definition: Any substituent group which does not contain carbon.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: inorganic groups
id: CHEBI:33246
in_subset: 3 STAR

organic group
type: Class
subclass of: group
subclass of: Restriction
  on property: is substituent group from
  some values from: organic molecular entity
textual definition: Any substituent group or skeleton containing carbon.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic groups
id: CHEBI:33247
in_subset: 3 STAR

organyl group
type: Class
subclass of: organic univalent group
textual definition: Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
imported from: chebi.owl
has_exact_synonym: organyl group
has_exact_synonym: organyl groups
has_obo_namespace: chebi_ontology
has_related_synonym: groupe organyle
has_related_synonym: grupo organilo
has_related_synonym: grupos organilo
id: CHEBI:33249
in_subset: 3 STAR

atom
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: has part
  some values from: electron
subclass of: Restriction
  on property: has part
  some values from: atomic nucleus
textual definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
imported from: chebi.owl
has_alternative_id: CHEBI:22671
has_alternative_id: CHEBI:23907
has_exact_synonym: atom
has_obo_namespace: chebi_ontology
has_related_synonym: atome
has_related_synonym: atomo
has_related_synonym: atoms
has_related_synonym: atomus
has_related_synonym: element
has_related_synonym: elements
id: CHEBI:33250
in_subset: 3 STAR

atomic nucleus
type: Class
subclass of: nuclear particle
subclass of: Restriction
  on property: has part
  some values from: nucleon
textual definition: A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
imported from: chebi.owl
has_exact_synonym: nucleus
has_obo_namespace: chebi_ontology
has_related_synonym: Atomkern
has_related_synonym: Kern
has_related_synonym: noyau
has_related_synonym: noyau atomique
has_related_synonym: nuclei
has_related_synonym: nucleo
has_related_synonym: nucleo atomico
has_related_synonym: nucleus atomi
id: CHEBI:33252
in_subset: 3 STAR

nucleon
type: Class
subclass of: baryon
subclass of: nuclear particle
textual definition: Heavy nuclear particle: proton or neutron.
imported from: chebi.owl
has_exact_synonym: nucleon
has_obo_namespace: chebi_ontology
has_related_synonym: Nukleon
has_related_synonym: Nukleonen
has_related_synonym: nucleons
id: CHEBI:33253
in_subset: 3 STAR

primary amide
type: Class
subclass of: amide
textual definition: A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
imported from: chebi.owl
has_exact_synonym: primary amide
has_exact_synonym: primary amides
has_obo_namespace: chebi_ontology
id: CHEBI:33256
in_subset: 3 STAR

polyatomic anion
type: Class
subclass of: anion
subclass of: polyatomic ion
textual definition: An anion consisting of more than one atom.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: polyatomic anions
id: CHEBI:33273
in_subset: 3 STAR

antimicrobial agent
type: Class
subclass of: biological role
textual definition: A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
imported from: chebi.owl
has_alternative_id: CHEBI:22582
database_cross_reference: PMID:12964249
database_cross_reference: PMID:22117953
database_cross_reference: PMID:22439833
database_cross_reference: PMID:22849268
database_cross_reference: PMID:22849276
database_cross_reference: PMID:22958833
has_obo_namespace: chebi_ontology
has_related_synonym: Antibiotika
has_related_synonym: Antibiotikum
has_related_synonym: antibiotic
has_related_synonym: antibiotics
has_related_synonym: antibiotique
has_related_synonym: antimicrobial
has_related_synonym: antimicrobial agents
has_related_synonym: antimicrobials
has_related_synonym: microbicide
has_related_synonym: microbicides
id: CHEBI:33281
in_subset: 3 STAR

antibacterial agent
type: Class
subclass of: antimicrobial agent
textual definition: A substance (or active part thereof) that kills or slows the growth of bacteria.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: antibacterial agents
has_related_synonym: antibacterials
has_related_synonym: bactericide
has_related_synonym: bactericides
id: CHEBI:33282
in_subset: 3 STAR

nutrient
type: Class
subclass of: food component
textual definition: A nutrient is a food component that an organism uses to survive and grow.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: nutrients
id: CHEBI:33284
in_subset: 3 STAR

heteroorganic entity
type: Class
subclass of: organic molecular entity
textual definition: A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: heteroorganic entities
has_related_synonym: organoelement compounds
id: CHEBI:33285
in_subset: 3 STAR

fuel
type: Class
subclass of: application
textual definition: An energy-rich substance that can be transformed with release of usable energy.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:33292
in_subset: 3 STAR

pnictogen
type: Class
subclass of: p-block element atom
textual definition: Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
imported from: chebi.owl
has_exact_synonym: pnictogens
has_obo_namespace: chebi_ontology
has_related_synonym: group 15 elements
has_related_synonym: group V elements
has_related_synonym: nitrogenoideos
has_related_synonym: nitrogenoides
has_related_synonym: pnictogene
has_related_synonym: pnictogenes
id: CHEBI:33300
in_subset: 3 STAR

pnictogen molecular entity
type: Class
subclass of: p-block molecular entity
subclass of: Restriction
  on property: has part
  some values from: pnictogen
textual definition: A p-block molecular entity containing any pnictogen.
imported from: chebi.owl
has_exact_synonym: pnictogen molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: pnictogen molecular entities
id: CHEBI:33302
in_subset: 3 STAR

chalcogen
type: Class
subclass of: p-block element atom
textual definition: Any p-block element belonging to the group 16 family of the periodic table.
imported from: chebi.owl
database_cross_reference: PMID:17084588
has_exact_synonym: chalcogen
has_exact_synonym: chalcogens
has_obo_namespace: chebi_ontology
has_related_synonym: Chalkogen
has_related_synonym: Chalkogene
has_related_synonym: anfigeno
has_related_synonym: anfigenos
has_related_synonym: calcogeno
has_related_synonym: calcogenos
has_related_synonym: chalcogene
has_related_synonym: chalcogenes
has_related_synonym: group 16 elements
has_related_synonym: group VI elements
id: CHEBI:33303
in_subset: 3 STAR

chalcogen molecular entity
type: Class
subclass of: p-block molecular entity
subclass of: Restriction
  on property: has part
  some values from: chalcogen
textual definition: Any p-block molecular entity containing a chalcogen.
imported from: chebi.owl
has_exact_synonym: chalcogen molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: chalcogen compounds
has_related_synonym: chalcogen molecular entities
id: CHEBI:33304
in_subset: 3 STAR

carbon group element atom
type: Class
subclass of: p-block element atom
imported from: chebi.owl
has_exact_synonym: group 14 elements
has_obo_namespace: chebi_ontology
has_related_synonym: carbon group element
has_related_synonym: carbon group elements
has_related_synonym: carbonoides
has_related_synonym: cristallogene
has_related_synonym: cristallogenes
has_related_synonym: group IV elements
id: CHEBI:33306
in_subset: 3 STAR

main group element atom
type: Class
subclass of: atom
textual definition: An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
imported from: chebi.owl
has_exact_synonym: main group elements
has_obo_namespace: chebi_ontology
has_related_synonym: Hauptgruppenelement
has_related_synonym: Hauptgruppenelemente
has_related_synonym: main group element
id: CHEBI:33318
in_subset: 3 STAR

hydracid
type: Class
subclass of: hydrogen molecular entity
subclass of: Restriction
  on property: has role
  some values from: Bronsted acid
textual definition: A hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
imported from: chebi.owl
has_exact_synonym: hydracid
has_obo_namespace: chebi_ontology
has_related_synonym: hydracids
id: CHEBI:33405
in_subset: 3 STAR

s-block element atom
type: Class
subclass of: atom
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: s-block element
has_related_synonym: s-block elements
id: CHEBI:33559
in_subset: 3 STAR

p-block element atom
type: Class
subclass of: main group element atom
textual definition: Any main group element atom belonging to the p-block of the periodic table.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: p-block element
has_related_synonym: p-block elements
id: CHEBI:33560
in_subset: 3 STAR

carboxylic acid
type: Class
subclass of: carbon oxoacid
subclass of: carbonyl compound
subclass of: organic acid
subclass of: Restriction
  on property: has part
  some values from: carboxy group
subclass of: Restriction
  on property: is conjugate acid of
  some values from: carboxylic acid anion
textual definition: A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
imported from: chebi.owl
charge: 0
formula: CHO2R
mass: 45.01740
monoisotopicmass: 44.99765
smiles: OC([*])=O
has_alternative_id: CHEBI:13428
has_alternative_id: CHEBI:13627
has_alternative_id: CHEBI:23027
database_cross_reference: PMID:17147560
database_cross_reference: PMID:18433345
database_cross_reference: Wikipedia:Carboxylic_acid
has_exact_synonym: carboxylic acid
has_exact_synonym: carboxylic acids
has_obo_namespace: chebi_ontology
has_related_synonym: Carbonsaeure
has_related_synonym: Carbonsaeuren
has_related_synonym: Karbonsaeure
has_related_synonym: RC(=O)OH
has_related_synonym: acide carboxylique
has_related_synonym: acides carboxyliques
has_related_synonym: acido carboxilico
has_related_synonym: acidos carboxilicos
id: CHEBI:33575
in_subset: 3 STAR

main group molecular entity
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has part
  some values from: main group element atom
textual definition: A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: main group compounds
has_related_synonym: main group molecular entities
id: CHEBI:33579
in_subset: 3 STAR

carbon group molecular entity
type: Class
subclass of: p-block molecular entity
subclass of: Restriction
  on property: has part
  some values from: carbon group element atom
imported from: chebi.owl
has_exact_synonym: carbon group molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: carbon group molecular entities
id: CHEBI:33582
in_subset: 3 STAR

cyclic compound
type: Class
subclass of: molecule
textual definition: Any molecule that consists of a series of atoms joined together to form a ring.
imported from: chebi.owl
database_cross_reference: Wikipedia:Cyclic_compound
has_obo_namespace: chebi_ontology
has_related_synonym: cyclic compounds
id: CHEBI:33595
in_subset: 3 STAR

homocyclic compound
type: Class
subclass of: cyclic compound
textual definition: A cyclic compound having as ring members atoms of the same element only.
imported from: chebi.owl
has_exact_synonym: homocyclic compound
has_exact_synonym: homocyclic compounds
has_obo_namespace: chebi_ontology
has_related_synonym: isocyclic compounds
id: CHEBI:33597
in_subset: 3 STAR

carbocyclic compound
type: Class
subclass of: homocyclic compound
subclass of: organic cyclic compound
textual definition: A homocyclic compound in which all of the ring members are carbon atoms.
imported from: chebi.owl
has_exact_synonym: carbocyclic compound
has_exact_synonym: carbocyclic compounds
has_obo_namespace: chebi_ontology
has_related_synonym: carbocycle
id: CHEBI:33598
in_subset: 3 STAR

hydrogen molecular entity
type: Class
subclass of: s-block molecular entity
subclass of: Restriction
  on property: has part
  some values from: hydrogen atom
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: hydrogen compounds
has_related_synonym: hydrogen molecular entities
id: CHEBI:33608
in_subset: 3 STAR

aromatic compound
type: Class
subclass of: cyclic compound
textual definition: A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
imported from: chebi.owl
has_exact_synonym: aromatic compounds
has_exact_synonym: aromatic molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: aromatics
has_related_synonym: aromatische Verbindungen
id: CHEBI:33655
in_subset: 3 STAR

arene
type: Class
subclass of: organic aromatic compound
subclass of: cyclic hydrocarbon
textual definition: Any monocyclic or polycyclic aromatic hydrocarbon.
imported from: chebi.owl
has_exact_synonym: arene
has_exact_synonym: arenes
has_obo_namespace: chebi_ontology
has_related_synonym: aromatic hydrocarbons
id: CHEBI:33658
in_subset: 3 STAR

organic aromatic compound
type: Class
subclass of: aromatic compound
subclass of: organic cyclic compound
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic aromatic compounds
id: CHEBI:33659
in_subset: 3 STAR

monocyclic compound
type: Class
subclass of: cyclic compound
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: monocyclic compounds
id: CHEBI:33661
in_subset: 3 STAR

annulene
type: Class
subclass of: monocyclic hydrocarbon
textual definition: A mancude monocyclic hydrocarbon without side chains of the general formula CnHn (n is an even number) or CnHn+1 (n is an odd number). In systematic nomenclature an annulene with seven or more carbon atoms may be named [n]annulene, where n is the number of carbon atoms.
imported from: chebi.owl
has_exact_synonym: annulene
has_exact_synonym: annulenes
has_obo_namespace: chebi_ontology
id: CHEBI:33662
in_subset: 3 STAR

cyclic hydrocarbon
type: Class
subclass of: hydrocarbon
subclass of: carbocyclic compound
imported from: chebi.owl
has_exact_synonym: cyclic hydrocarbon
has_obo_namespace: chebi_ontology
has_related_synonym: cyclic hydrocarbons
id: CHEBI:33663
in_subset: 3 STAR

monocyclic hydrocarbon
type: Class
subclass of: cyclic hydrocarbon
imported from: chebi.owl
has_exact_synonym: monocyclic hydrocarbon
has_exact_synonym: monocyclic hydrocarbons
has_obo_namespace: chebi_ontology
has_related_synonym: monocyclic hydrocarbons
id: CHEBI:33664
in_subset: 3 STAR

heteromonocyclic compound
type: Class
subclass of: monocyclic compound
subclass of: heterocyclic compound
imported from: chebi.owl
has_exact_synonym: heteromonocyclic compound
has_exact_synonym: heteromonocyclic compounds
has_obo_namespace: chebi_ontology
id: CHEBI:33670
in_subset: 3 STAR

s-block molecular entity
type: Class
subclass of: main group molecular entity
subclass of: Restriction
  on property: has part
  some values from: s-block element atom
textual definition: An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
imported from: chebi.owl
has_exact_synonym: s-block molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: s-block compounds
has_related_synonym: s-block molecular entities
id: CHEBI:33674
in_subset: 3 STAR

p-block molecular entity
type: Class
subclass of: main group molecular entity
subclass of: Restriction
  on property: has part
  some values from: p-block element atom
textual definition: A main group molecular entity that contains one or more atoms of a p-block element.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: p-block compounds
has_related_synonym: p-block molecular entities
has_related_synonym: p-block molecular entitiy
id: CHEBI:33675
in_subset: 3 STAR

hydrides
type: Class
subclass of: hydrogen molecular entity
subclass of: heteroatomic molecular entity
textual definition: Hydrides are chemical compounds of hydrogen with other chemical elements.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:33692
in_subset: 3 STAR

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
textual 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 Investigations

ribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: ribonucleic acid
textual 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 Investigations

amino acid
type: Class
subclass of: carboxylic acid
subclass of: organic amino compound
subclass of: Restriction
  on property: is conjugate acid of
  some values from: amino-acid anion
textual definition: A carboxylic acid containing one or more amino groups.
imported from: chebi.owl
has_alternative_id: CHEBI:13815
has_alternative_id: CHEBI:22477
database_cross_reference: Wikipedia:Amino_acid
has_obo_namespace: chebi_ontology
has_related_synonym: Aminocarbonsaeure
has_related_synonym: Aminokarbonsaeure
has_related_synonym: Aminosaeure
has_related_synonym: amino acids
id: CHEBI:33709
in_subset: 3 STAR

organic hydroxy compound
type: Class
subclass of: hydroxides
subclass of: organic molecular entity
textual definition: An organic compound having at least one hydroxy group attached to a carbon atom.
imported from: chebi.owl
has_alternative_id: CHEBI:64710
has_exact_synonym: hydroxy compounds
has_obo_namespace: chebi_ontology
has_related_synonym: organic alcohol
has_related_synonym: organic hydroxy compounds
id: CHEBI:33822
in_subset: 3 STAR

organic cyclic compound
type: Class
subclass of: cyclic compound
subclass of: organic molecule
textual definition: Any organic molecule that consists of atoms connected in the form of a ring.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic cyclic compounds
id: CHEBI:33832
in_subset: 3 STAR

benzenoid aromatic compound
type: Class
subclass of: carbocyclic compound
subclass of: organic aromatic compound
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: benzenoid aromatic compounds
has_related_synonym: benzenoid compound
id: CHEBI:33836
in_subset: 3 STAR

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
textual 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 Investigations

aromatic annulene
type: Class
subclass of: annulene
subclass of: monocyclic arene
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: aromatic annulenes
id: CHEBI:33842
in_subset: 3 STAR

monocyclic arene
type: Class
subclass of: arene
textual definition: A monocyclic aromatic hydrocarbon.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: monocyclic arenes
id: CHEBI:33847
in_subset: 3 STAR

reagent
type: Class
subclass of: application
textual definition: A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
imported from: chebi.owl
has_exact_synonym: reagent
has_obo_namespace: chebi_ontology
has_related_synonym: reactif
has_related_synonym: reactivo
has_related_synonym: reagents
id: CHEBI:33893
in_subset: 3 STAR

macronutrient
type: Class
subclass of: nutrient
textual definition: Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: macronutrients
id: CHEBI:33937
in_subset: 3 STAR

nitrogen hydride
type: Class
subclass of: pnictogen hydride
subclass of: nitrogen molecular entity
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: nitrogen hydrides
id: CHEBI:35106
in_subset: 3 STAR

azane
type: Class
subclass of: nitrogen hydride
textual definition: Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: azanes
id: CHEBI:35107
in_subset: 3 STAR

surfactant
type: Class
subclass of: emulsifier
textual definition: A substance which lowers the surface tension of the medium in which it is dissolved, and/or the interfacial tension with other phases, and, accordingly, is positively adsorbed at the liquid/vapour and/or at other interfaces.
imported from: chebi.owl
has_exact_synonym: surfactant
has_obo_namespace: chebi_ontology
has_related_synonym: surface active agent
has_related_synonym: surfactants
id: CHEBI:35195
in_subset: 3 STAR

lumiphore
type: Class
subclass of: photochemical role
textual definition: A part of a molecular entity (atom or group of atoms) in which electronic excitation associated with a given emission band is approximately localized.
imported from: chebi.owl
has_exact_synonym: lumiphore
has_obo_namespace: chebi_ontology
has_related_synonym: luminophore
id: CHEBI:35197
in_subset: 3 STAR

inhibitor
type: Class
subclass of: biological role
textual definition: A substance that diminishes the rate of a chemical reaction.
imported from: chebi.owl
has_exact_synonym: inhibitor
has_obo_namespace: chebi_ontology
has_related_synonym: inhibidor
has_related_synonym: inhibiteur
has_related_synonym: inhibitors
id: CHEBI:35222
in_subset: 3 STAR

catalyst
type: Class
subclass of: chemical role
textual definition: A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction.
imported from: chebi.owl
has_exact_synonym: catalyst
has_obo_namespace: chebi_ontology
has_related_synonym: Katalysator
has_related_synonym: catalizador
has_related_synonym: catalyseur
id: CHEBI:35223
in_subset: 3 STAR

buffer
type: Class
subclass of: chemical role
textual definition: Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: buffer compound
has_related_synonym: buffer compounds
id: CHEBI:35225
in_subset: 3 STAR

organonitrogen compound
type: Class
subclass of: heteroorganic entity
subclass of: nitrogen molecular entity
textual definition: Any heteroorganic entity containing at least one carbon-nitrogen bond.
imported from: chebi.owl
has_exact_synonym: organonitrogen compounds
has_obo_namespace: chebi_ontology
has_related_synonym: organonitrogens
id: CHEBI:35352
in_subset: 3 STAR

fatty acid
type: Class
subclass of: lipid
subclass of: monocarboxylic acid
subclass of: Restriction
  on property: is conjugate acid of
  some values from: fatty acid anion
textual definition: Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax.
imported from: chebi.owl
charge: 0
formula: CHO2R
mass: 45.01740
monoisotopicmass: 44.99765
smiles: OC([*])=O
has_alternative_id: CHEBI:13633
has_alternative_id: CHEBI:24024
has_alternative_id: CHEBI:4984
database_cross_reference: KEGG:C00162
database_cross_reference: PMID:14287444
database_cross_reference: PMID:14300208
database_cross_reference: PMID:14328676
database_cross_reference: Wikipedia:Fatty_acid
has_exact_synonym: Fatty acid
has_exact_synonym: fatty acids
has_obo_namespace: chebi_ontology
has_related_synonym: Fettsaeure
has_related_synonym: Fettsaeuren
has_related_synonym: acide gras
has_related_synonym: acides gras
has_related_synonym: acido graso
has_related_synonym: acidos grasos
has_related_synonym: fatty acids
id: CHEBI:35366
in_subset: 3 STAR

oxoanion
type: Class
subclass of: oxide
subclass of: polyatomic anion
textual definition: An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
imported from: chebi.owl
has_alternative_id: CHEBI:33274
has_alternative_id: CHEBI:33436
has_exact_synonym: oxoanion
has_obo_namespace: chebi_ontology
has_related_synonym: oxoacid anions
has_related_synonym: oxoanions
id: CHEBI:35406
in_subset: 3 STAR

heterocyclic organic fundamental parent
type: Class
subclass of: organic fundamental parent
imported from: chebi.owl
has_exact_synonym: heterocyclic parent hydrides
has_obo_namespace: chebi_ontology
has_related_synonym: heterocyclic fundamental parent
has_related_synonym: heterocyclic organic fundamental parents
has_related_synonym: organic heterocyclic fundamental parents
id: CHEBI:35552
in_subset: 3 STAR

carbon oxoacid
type: Class
subclass of: oxoacid
subclass of: organooxygen compound
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: carbon oxoacids
has_related_synonym: oxoacids of carbon
id: CHEBI:35605
in_subset: 3 STAR

secondary alcohol
type: Class
subclass of: alcohol
textual definition: A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it.
imported from: chebi.owl
charge: 0
formula: CH2OR2
mass: 30.026
monoisotopicmass: 30.01056
smiles: *C(*)O
has_alternative_id: CHEBI:13425
has_alternative_id: CHEBI:13686
has_alternative_id: CHEBI:26617
has_alternative_id: CHEBI:58662
has_alternative_id: CHEBI:8741
has_alternative_id: CHEBI:9077
database_cross_reference: KEGG:C00432
database_cross_reference: KEGG:C01612
has_exact_synonym: Secondary alcohol
has_obo_namespace: chebi_ontology
has_related_synonym: R-CHOH-R'
has_related_synonym: a secondary alcohol
has_related_synonym: secondary alcohols
id: CHEBI:35681
in_subset: 3 STAR

monocarboxylic acid anion
type: Class
subclass of: carboxylic acid anion
subclass of: Restriction
  on property: is conjugate base of
  some values from: monocarboxylic acid
textual definition: A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
imported from: chebi.owl
charge: -1
formula: CO2R
mass: 44.01000
monoisotopicmass: 43.98983
smiles: [O-]C([*])=O
has_alternative_id: CHEBI:13657
has_alternative_id: CHEBI:25382
has_alternative_id: CHEBI:3407
database_cross_reference: KEGG:C00060
has_obo_namespace: chebi_ontology
has_related_synonym: Carboxylate
has_related_synonym: Monocarboxylate
has_related_synonym: a monocarboxylate
has_related_synonym: monocarboxylates
has_related_synonym: monocarboxylic acid anions
id: CHEBI:35757
in_subset: 3 STAR

pnictogen hydride
type: Class
subclass of: inorganic hydride
subclass of: pnictogen molecular entity
imported from: chebi.owl
has_exact_synonym: pnictogen hydride
has_obo_namespace: chebi_ontology
has_related_synonym: pnictogen hydrides
id: CHEBI:35881
in_subset: 3 STAR

neurotransmitter agent
type: Class
subclass of: drug
subclass of: pharmacological role
textual definition: A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: neurotransmitter agents
id: CHEBI:35942
in_subset: 3 STAR

lepton
type: Class
subclass of: fundamental particle
subclass of: fermion
textual definition: Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: leptons
id: CHEBI:36338
in_subset: 3 STAR

baryon
type: Class
subclass of: fermion
subclass of: hadron
textual definition: Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: baryons
id: CHEBI:36339
in_subset: 3 STAR

fermion
type: Class
subclass of: subatomic particle
textual definition: Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
imported from: chebi.owl
has_exact_synonym: fermion
has_obo_namespace: chebi_ontology
has_related_synonym: fermions
id: CHEBI:36340
in_subset: 3 STAR

subatomic particle
type: Class
subclass of: molecular entity
textual definition: A particle smaller than an atom.
imported from: chebi.owl
database_cross_reference: Wikipedia:Subatomic_particle
has_obo_namespace: chebi_ontology
has_related_synonym: subatomic particles
id: CHEBI:36342
in_subset: 3 STAR

composite particle
type: Class
subclass of: subatomic particle
textual definition: A subatomic particle known to have substructure (i.e. consisting of smaller particles).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: composite particles
id: CHEBI:36343
in_subset: 3 STAR

hadron
type: Class
subclass of: composite particle
textual definition: Hadron is a subatomic particle which experiences the strong force.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: hadrons
id: CHEBI:36344
in_subset: 3 STAR

nuclear particle
type: Class
subclass of: subatomic particle
textual definition: A nucleus or any of its constituents in any of their energy states.
imported from: chebi.owl
has_exact_synonym: nuclear particle
has_obo_namespace: chebi_ontology
id: CHEBI:36347
in_subset: 3 STAR

polyatomic entity
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has part
  some values from: group
textual definition: Any molecular entity consisting of more than one atom.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: polyatomic entities
id: CHEBI:36357
in_subset: 3 STAR

polyatomic ion
type: Class
subclass of: ion
subclass of: polyatomic entity
textual definition: An ion consisting of more than one atom.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: polyatomic ions
id: CHEBI:36358
in_subset: 3 STAR

saturated organic heterocyclic parent
type: Class
subclass of: heterocyclic organic fundamental parent
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: saturated heterocyclic parent hydride
has_related_synonym: saturated heterocyclic parent hydrides
has_related_synonym: saturated organic heterocyclic parents
id: CHEBI:36388
in_subset: 3 STAR

saturated organic heteromonocyclic parent
type: Class
subclass of: organic heteromonocyclic compound
subclass of: saturated organic heterocyclic parent
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: saturated heteromonocyclic parent hydride
has_related_synonym: saturated heteromonocyclic parent hydrides
has_related_synonym: saturated organic heteromonocyclic parents
id: CHEBI:36389
in_subset: 3 STAR

carbonyl compound
type: Class
subclass of: organic oxo compound
subclass of: organooxygen compound
subclass of: Restriction
  on property: has part
  some values from: carbonyl group
textual definition: Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
imported from: chebi.owl
has_exact_synonym: carbonyl compounds
has_obo_namespace: chebi_ontology
id: CHEBI:36586
in_subset: 3 STAR

organic oxo compound
type: Class
subclass of: organic molecule
subclass of: Restriction
  on property: has part
  some values from: oxo group
textual definition: Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
imported from: chebi.owl
has_exact_synonym: oxo compounds
has_obo_namespace: chebi_ontology
has_related_synonym: organic oxo compounds
id: CHEBI:36587
in_subset: 3 STAR

pseudohalo group
type: Class
subclass of: group
imported from: chebi.owl
has_exact_synonym: pseudohalide group
has_obo_namespace: chebi_ontology
has_related_synonym: halogenoid group
has_related_synonym: pseudohalido group
has_related_synonym: pseudohalo groups
has_related_synonym: pseudohalogen group
id: CHEBI:36823
in_subset: 3 STAR

pseudohalide anion
type: Class
subclass of: polyatomic monoanion
imported from: chebi.owl
has_exact_synonym: pseudohalide ions
has_obo_namespace: chebi_ontology
has_related_synonym: pseudohalide anions
has_related_synonym: pseudohalides
has_related_synonym: pseudohalogen anion
has_related_synonym: pseudohalogen ion
id: CHEBI:36828
in_subset: 3 STAR

polyatomic monoanion
type: Class
subclass of: polyatomic anion
subclass of: monoanion
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: polyatomic monoanions
id: CHEBI:36829
in_subset: 3 STAR

monoanion
type: Class
subclass of: anion
imported from: chebi.owl
charge: -1
has_obo_namespace: chebi_ontology
has_related_synonym: monoanions
id: CHEBI:36830
in_subset: 3 STAR

hydrogen isocyanide
type: Class
subclass of: hydracid
subclass of: Restriction
  on property: is conjugate acid of
  some values from: cyanide
subclass of: Restriction
  on property: is tautomer of
  some values from: hydrogen cyanide
imported from: chebi.owl
charge: 0
formula: CHN
inchi: InChI=1S/CHN/c1-2/h2H
inchikey: QIUBLANJVAOHHY-UHFFFAOYSA-N
mass: 27.02538
monoisotopicmass: 27.01090
smiles: [C-]#[NH+]
database_cross_reference: Beilstein:2069401
database_cross_reference: CAS:6914-07-4
database_cross_reference: Gmelin:113
has_exact_synonym: hydrogen isocyanide
has_exact_synonym: nitriliomethanide
has_obo_namespace: chebi_ontology
has_related_synonym: CNH
has_related_synonym: HN(+)#C(-)
has_related_synonym: HNC
has_related_synonym: hydroisocyanic acid
id: CHEBI:36856
in_subset: 3 STAR

inorganic ion
type: Class
subclass of: inorganic molecular entity
subclass of: ion
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: inorganic ions
id: CHEBI:36914
in_subset: 3 STAR

inorganic cation
type: Class
subclass of: inorganic ion
subclass of: cation
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: inorganic cations
id: CHEBI:36915
in_subset: 3 STAR

cation
type: Class
subclass of: ion
textual definition: A monoatomic or polyatomic species having one or more elementary charges of the proton.
imported from: chebi.owl
has_alternative_id: CHEBI:23058
has_alternative_id: CHEBI:3473
database_cross_reference: KEGG:C01373
has_exact_synonym: Cation
has_exact_synonym: cation
has_obo_namespace: chebi_ontology
has_related_synonym: Kation
has_related_synonym: Kationen
has_related_synonym: cationes
has_related_synonym: cations
id: CHEBI:36916
in_subset: 3 STAR

organochalcogen compound
type: Class
subclass of: heteroorganic entity
subclass of: chalcogen molecular entity
textual definition: An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
imported from: chebi.owl
has_exact_synonym: organochalcogen compound
has_obo_namespace: chebi_ontology
has_related_synonym: organochalcogen compounds
id: CHEBI:36962
in_subset: 3 STAR

organooxygen compound
type: Class
subclass of: oxygen molecular entity
subclass of: organochalcogen compound
textual definition: An organochalcogen compound containing at least one carbon-oxygen bond.
imported from: chebi.owl
database_cross_reference: PMID:17586126
has_exact_synonym: organooxygen compound
has_obo_namespace: chebi_ontology
has_related_synonym: organooxygen compounds
id: CHEBI:36963
in_subset: 3 STAR

amino-acid anion
type: Class
subclass of: carboxylic acid anion
subclass of: organonitrogen compound
subclass of: Restriction
  on property: is conjugate base of
  some values from: amino acid
imported from: chebi.owl
has_exact_synonym: amino-acid anion
has_obo_namespace: chebi_ontology
has_related_synonym: amino acid anions
has_related_synonym: amino-acid anions
id: CHEBI:37022
in_subset: 3 STAR

organic hydride
type: Class
subclass of: hydrides
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic hydrides
id: CHEBI:37175
in_subset: 3 STAR

mononuclear parent hydride
type: Class
subclass of: hydrides
imported from: chebi.owl
has_exact_synonym: mononuclear parent hydrides
has_obo_namespace: chebi_ontology
has_related_synonym: mononuclear hydride
has_related_synonym: mononuclear hydrides
id: CHEBI:37176
in_subset: 3 STAR

cyclic ether
type: Class
subclass of: ether
subclass of: oxacycle
textual definition: Any ether in which the oxygen atom forms part of a ring.
imported from: chebi.owl
has_alternative_id: CHEBI:37406
has_exact_synonym: cyclic ether
has_exact_synonym: cyclic ethers
has_exact_synonym: epoxy compounds
has_obo_namespace: chebi_ontology
has_related_synonym: cyclic ethers
has_related_synonym: epoxy compounds
id: CHEBI:37407
in_subset: 3 STAR

acid
type: Class
subclass of: chemical role
textual definition: An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
imported from: chebi.owl
has_alternative_id: CHEBI:13800
has_alternative_id: CHEBI:13801
has_alternative_id: CHEBI:22209
has_alternative_id: CHEBI:2426
database_cross_reference: KEGG:C00174
has_exact_synonym: Acid
has_exact_synonym: acid
has_obo_namespace: chebi_ontology
has_related_synonym: Saeure
has_related_synonym: Saeuren
has_related_synonym: acide
has_related_synonym: acido
has_related_synonym: acids
id: CHEBI:37527
in_subset: 3 STAR

heteroatomic molecular entity
type: Class
subclass of: polyatomic entity
textual definition: A molecular entity consisting of two or more chemical elements.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: chemical compound
has_related_synonym: heteroatomic molecular entities
id: CHEBI:37577
in_subset: 3 STAR

carboxamide
type: Class
subclass of: primary amide
subclass of: organonitrogen compound
subclass of: organooxygen compound
subclass of: Restriction
  on property: has part
  some values from: carbamoyl group
textual definition: An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
imported from: chebi.owl
charge: 0
formula: CNOR3
mass: 42.01680
monoisotopicmass: 41.99799
smiles: [*]C(=O)N([*])[*]
has_alternative_id: CHEBI:35354
has_alternative_id: CHEBI:35355
has_exact_synonym: carboxamides
has_obo_namespace: chebi_ontology
has_related_synonym: carboxamides
has_related_synonym: primary carboxamide
id: CHEBI:37622
in_subset: 3 STAR

carboacyl group
type: Class
subclass of: acyl group
subclass of: Restriction
  on property: is substituent group from
  some values from: carboxylic acid
textual definition: A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
imported from: chebi.owl
has_exact_synonym: carboacyl groups
has_exact_synonym: carboxylic acyl group
has_obo_namespace: chebi_ontology
has_related_synonym: carboxylic acyl groups
id: CHEBI:37838
in_subset: 3 STAR

oxacycle
type: Class
subclass of: organic heterocyclic compound
subclass of: organooxygen compound
textual definition: Any organic heterocyclic compound containing at least one ring oxygen atom.
imported from: chebi.owl
database_cross_reference: PMID:17134300
has_obo_namespace: chebi_ontology
has_related_synonym: heterocyclic organooxygen compounds
has_related_synonym: organooxygen heterocyclic compounds
has_related_synonym: oxacycles
id: CHEBI:38104
in_subset: 3 STAR

phytosiderophore
type: Class
subclass of: iron(3+) chelator
subclass of: iron ionophore
textual definition: Any of low-molecular-mass iron(III)-chelating compounds produced by plants for the purpose of the transport and sequestration of iron.
imported from: chebi.owl
has_alternative_id: CHEBI:26122
has_alternative_id: CHEBI:38117
has_obo_namespace: chebi_ontology
has_related_synonym: Phytosiderophor
has_related_synonym: phytosiderophores
id: CHEBI:38155
in_subset: 3 STAR

iron chelator
type: Class
subclass of: chelator
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: iron chelating agents
has_related_synonym: iron chelators
id: CHEBI:38157
in_subset: 3 STAR

chelator
type: Class
subclass of: ligand
textual definition: A ligand with two or more separate binding sites that can bind to a single metallic central atom, forming a chelate.
imported from: chebi.owl
has_alternative_id: CHEBI:23090
has_alternative_id: CHEBI:3585
has_alternative_id: CHEBI:6789
database_cross_reference: KEGG:C00917
database_cross_reference: KEGG:C02169
has_obo_namespace: chebi_ontology
has_related_synonym: Chelating agent
has_related_synonym: Metal chelator
has_related_synonym: chelating agents
has_related_synonym: chelators
has_related_synonym: complexon
id: CHEBI:38161
in_subset: 3 STAR

iron(2+) chelator
type: Class
subclass of: iron chelator
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:38162
in_subset: 1 STAR

cholinergic drug
type: Class
subclass of: neurotransmitter agent
textual definition: Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: cholinergic agent
has_related_synonym: cholinergic drugs
has_related_synonym: cholinomimetic
id: CHEBI:38323
in_subset: 3 STAR

acetonitrile
type: Class
subclass of: volatile organic compound
subclass of: aliphatic nitrile
subclass of: Restriction
  on property: has role
  some values from: polar aprotic solvent
subclass of: Restriction
  on property: has role
  some values from: EC 3.5.1.4 (amidase) inhibitor
textual 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: 41.02655
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: PPDB:1349
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

electron-transport chain inhibitor
type: Class
subclass of: pathway inhibitor
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:38496
in_subset: 1 STAR

respiratory-chain inhibitor
type: Class
subclass of: electron-transport chain inhibitor
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:38497
in_subset: 1 STAR

EC 1.9.3.1 (cytochrome c oxidase) inhibitor
type: Class
subclass of: mitochondrial respiratory-chain inhibitor
subclass of: EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor
textual definition: An EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor that interferes with the action of cytochrome c oxidase (EC 1.9.3.1).
imported from: chebi.owl
has_alternative_id: CHEBI:38501
has_alternative_id: CHEBI:62966
database_cross_reference: PMID:12969439
database_cross_reference: Wikipedia:Cytochrome_c_oxidase
has_obo_namespace: chebi_ontology
has_related_synonym: CcO inhibitor
has_related_synonym: EC 1.9.3.1 (cytochrome c oxidase) inhibitors
has_related_synonym: EC 1.9.3.1 inhibitor
has_related_synonym: EC 1.9.3.1 inhibitors
has_related_synonym: NADH cytochrome c oxidase inhibitor
has_related_synonym: NADH cytochrome c oxidase inhibitors
has_related_synonym: Warburg's respiratory enzyme inhibitor
has_related_synonym: Warburg's respiratory enzyme inhibitors
has_related_synonym: complex IV (mitochondrial electron transport) inhibitor
has_related_synonym: complex IV (mitochondrial electron transport) inhibitors
has_related_synonym: cytochrome a3 inhibitor
has_related_synonym: cytochrome a3 inhibitors
has_related_synonym: cytochrome aa3 inhibitor
has_related_synonym: cytochrome aa3 inhibitors
has_related_synonym: cytochrome c oxidase (EC 1.9.3.1) inhibitor
has_related_synonym: cytochrome c oxidase (EC 1.9.3.1) inhibitors
has_related_synonym: cytochrome c oxidase inhibitor
has_related_synonym: cytochrome c oxidase inhibitors
has_related_synonym: cytochrome oxidase inhibitor
has_related_synonym: cytochrome oxidase inhibitors
has_related_synonym: cytochrome-c oxidase inhibitor
has_related_synonym: cytochrome-c oxidase inhibitors
has_related_synonym: ferrocytochrome c oxidase inhibitor
has_related_synonym: ferrocytochrome c oxidase inhibitors
has_related_synonym: ferrocytochrome-c:oxygen oxidoreductase inhibitor
has_related_synonym: ferrocytochrome-c:oxygen oxidoreductase inhibitors
has_related_synonym: indophenol oxidase inhibitor
has_related_synonym: indophenol oxidase inhibitors
has_related_synonym: indophenolase inhibitor
has_related_synonym: indophenolase inhibitors
has_related_synonym: mitochondrial complex IV inhibitor
has_related_synonym: mitochondrial complex IV inhibitors
has_related_synonym: mitochondrial cytochrome-c oxidase inhibitors
id: CHEBI:38500
in_subset: 3 STAR

membrane transport modulator
type: Class
subclass of: biophysical role
textual definition: Any agent that affects the transport of molecular entities across a biological membrane.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: membrane transport modulators
id: CHEBI:38632
in_subset: 3 STAR

nonionic surfactant
type: Class
subclass of: surfactant
textual definition: A surfactant with an uncharged hydrophilic headgroup.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: non-ionic surfactant
has_related_synonym: nonionic surfactants
id: CHEBI:38828
in_subset: 3 STAR

methylbenzene
type: Class
subclass of: alkylbenzene
textual definition: Any alkylbenzene that is benzene substituted with one or more methyl groups.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: methylbenzenes
id: CHEBI:38975
in_subset: 3 STAR

alkylbenzene
type: Class
subclass of: benzenes
subclass of: monocyclic arene
subclass of: Restriction
  on property: has parent hydride
  some values from: benzene
textual definition: A monocyclic arene that is benzene substituted with one or more alkyl groups.
imported from: chebi.owl
has_exact_synonym: alkylbenzene
has_obo_namespace: chebi_ontology
has_related_synonym: Alkylbenzol
has_related_synonym: alkylbenzenes
id: CHEBI:38976
in_subset: 3 STAR

Good's buffer substance
type: Class
subclass of: buffer
textual definition: Any member of a collection of zwitterionic buffer substances selected or devised for suitability in experimental biological systems according to a number of predetermined criteria. Named after Dr. Norman Good.
imported from: chebi.owl
database_cross_reference: Wikipedia:Good's_buffers
has_obo_namespace: chebi_ontology
has_related_synonym: Good buffer substance
has_related_synonym: Good's buffer
has_related_synonym: Good's buffers
id: CHEBI:39011
in_subset: 3 STAR

Bronsted acid
type: Class
subclass of: donor
subclass of: acid
textual definition: A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
imported from: chebi.owl
has_exact_synonym: Bronsted acid
has_obo_namespace: chebi_ontology
has_related_synonym: Bronsted-Saeure
has_related_synonym: acide de Bronsted
has_related_synonym: donneur d'hydron
has_related_synonym: hydron donor
id: CHEBI:39141
in_subset: 3 STAR

Bronsted base
type: Class
subclass of: acceptor
subclass of: base
textual definition: A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
imported from: chebi.owl
has_exact_synonym: Bronsted base
has_obo_namespace: chebi_ontology
has_related_synonym: Bronsted-Base
has_related_synonym: accepteur d'hydron
has_related_synonym: base de Bronsted
has_related_synonym: hydron acceptor
id: CHEBI:39142
in_subset: 3 STAR

Lewis acid
type: Class
subclass of: acceptor
subclass of: acid
textual definition: A molecular entity that is an electron-pair acceptor and therefore able to form a covalent bond with an electron-pair donor (Lewis base), thereby producing a Lewis adduct.
imported from: chebi.owl
has_exact_synonym: Lewis acid
has_obo_namespace: chebi_ontology
has_related_synonym: Lewis-Saeure
has_related_synonym: accepteur d'une paire d'electrons
has_related_synonym: acide de Lewis
has_related_synonym: electron acceptor
has_related_synonym: electron-pair acceptor
id: CHEBI:39143
in_subset: 3 STAR

Lewis base
type: Class
subclass of: donor
subclass of: base
textual definition: A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.
imported from: chebi.owl
has_exact_synonym: Lewis base
has_obo_namespace: chebi_ontology
has_related_synonym: Lewis-Base
has_related_synonym: base de Lewis
has_related_synonym: donneur d'une paire d'electrons
has_related_synonym: electron donor
id: CHEBI:39144
in_subset: 3 STAR

hydroxy group
type: Class
subclass of: inorganic group
imported from: chebi.owl
charge: 0
formula: HO
mass: 17.00734
monoisotopicmass: 17.00274
smiles: *O[H]
has_alternative_id: CHEBI:24706
has_alternative_id: CHEBI:43171
database_cross_reference: PDBeChem:OH
has_exact_synonym: HYDROXY GROUP
has_exact_synonym: hydroxy
has_exact_synonym: hydroxy group
has_obo_namespace: chebi_ontology
has_related_synonym: -OH
has_related_synonym: hydroxyl
has_related_synonym: hydroxyl group
id: CHEBI:43176
in_subset: 3 STAR

oxo group
type: Class
subclass of: inorganic group
imported from: chebi.owl
charge: 0
formula: O
mass: 15.99940
monoisotopicmass: 15.99491
smiles: O=*
has_alternative_id: CHEBI:29353
has_alternative_id: CHEBI:44607
database_cross_reference: PDBeChem:O
has_exact_synonym: OXO GROUP
has_exact_synonym: oxo
has_obo_namespace: chebi_ontology
has_related_synonym: =O
id: CHEBI:46629
in_subset: 3 STAR

solvent
type: Class
subclass of: application
subclass of: chemical role
textual definition: A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
imported from: chebi.owl
database_cross_reference: Wikipedia:Solvent
has_obo_namespace: chebi_ontology
has_related_synonym: Loesungsmittel
has_related_synonym: solvant
has_related_synonym: solvents
id: CHEBI:46787
in_subset: 3 STAR

carboxy group
type: Class
subclass of: organyl group
imported from: chebi.owl
charge: 0
formula: CHO2
mass: 45.01744
monoisotopicmass: 44.99765
smiles: *C(=O)O
has_alternative_id: CHEBI:23025
has_alternative_id: CHEBI:41420
database_cross_reference: PDBeChem:FMT
has_exact_synonym: CARBOXY GROUP
has_exact_synonym: carboxy
has_obo_namespace: chebi_ontology
has_related_synonym: -C(O)OH
has_related_synonym: -CO2H
has_related_synonym: -COOH
has_related_synonym: carboxyl group
id: CHEBI:46883
in_subset: 3 STAR

dioxane
type: Class
subclass of: saturated organic heteromonocyclic parent
subclass of: dioxanes
textual definition: Any member of the class of dioxanes that is a cyclohexane in which two carbon atoms are replaced by oxygen atoms.
imported from: chebi.owl
charge: 0
formula: C4H8O2
mass: 88.105
monoisotopicmass: 88.05243
has_exact_synonym: dioxane
has_obo_namespace: chebi_ontology
id: CHEBI:46923
in_subset: 3 STAR

dioxanes
type: Class
subclass of: organic heteromonocyclic compound
subclass of: oxacycle
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:46926
in_subset: 3 STAR

1,4-dioxane
type: Class
subclass of: volatile organic compound
subclass of: dioxane
subclass of: Restriction
  on property: has role
  some values from: metabolite
subclass of: Restriction
  on property: has role
  some values from: non-polar solvent
subclass of: Restriction
  on property: has role
  some values from: carcinogenic agent
textual 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: 88.05243
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: PPDB:1638
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
editor preferred label: double-stranded DNA
imported from: chebi.owl
imported from: Ontology for Biomedical Investigations

polar solvent
type: Class
subclass of: solvent
textual definition: A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
imported from: chebi.owl
has_exact_synonym: polar solvent
has_obo_namespace: chebi_ontology
has_related_synonym: polar solvents
id: CHEBI:48354
in_subset: 3 STAR

non-polar solvent
type: Class
subclass of: solvent
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:48355
in_subset: 1 STAR

protic solvent
type: Class
subclass of: Bronsted acid
subclass of: polar solvent
textual definition: A polar solvent that is capable of acting as a hydron (proton) donor.
imported from: chebi.owl
has_exact_synonym: protogenic solvent
has_obo_namespace: chebi_ontology
id: CHEBI:48356
in_subset: 3 STAR

aprotic solvent
type: Class
subclass of: solvent
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:48357
in_subset: 1 STAR

polar aprotic solvent
type: Class
subclass of: polar solvent
subclass of: aprotic solvent
textual definition: A solvent with a comparatively high relative permittivity (or dielectric constant), greater than ca. 15, and a sizable permanent dipole moment, that cannot donate suitably labile hydrogen atoms to form strong hydrogen bonds.
imported from: chebi.owl
has_exact_synonym: dipolar aprotic solvent
has_obo_namespace: chebi_ontology
id: CHEBI:48358
in_subset: 3 STAR

protophilic solvent
type: Class
subclass of: Bronsted base
subclass of: polar solvent
textual definition: Solvent that is capable of acting as a hydron (proton) acceptor.
imported from: chebi.owl
has_exact_synonym: protophilic solvent
has_obo_namespace: chebi_ontology
has_related_synonym: HBA solvent
has_related_synonym: hydrogen bond acceptor solvent
id: CHEBI:48359
in_subset: 3 STAR

amphiprotic solvent
type: Class
subclass of: protic solvent
subclass of: protophilic solvent
textual definition: Self-ionizing solvent possessing both characteristics of Bronsted acids and bases.
imported from: chebi.owl
has_exact_synonym: amphiprotic solvent
has_obo_namespace: chebi_ontology
id: CHEBI:48360
in_subset: 3 STAR

imidic acid
type: Class
subclass of: oxoacid derivative
subclass of: nitrogen molecular entity
textual definition: Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing =O by =NR; thus tautomers of amides. In organic chemistry an unspecified imidic acid is generally a carboximidic acid, RC(=NR)(OH).
imported from: chebi.owl
has_exact_synonym: imidic acid
has_exact_synonym: imidic acids
has_obo_namespace: chebi_ontology
has_related_synonym: imidic acids
has_related_synonym: imino acids
id: CHEBI:48377
in_subset: 3 STAR

carboximidic acid
type: Class
subclass of: organonitrogen compound
subclass of: imidic acid
imported from: chebi.owl
has_exact_synonym: carboximidic acid
has_exact_synonym: carboximidic acids
has_obo_namespace: chebi_ontology
has_related_synonym: carboximidic acids
id: CHEBI:48378
in_subset: 3 STAR

formimidic acid
type: Class
subclass of: carboximidic acid
subclass of: one-carbon compound
subclass of: Restriction
  on property: has functional parent
  some values from: formic acid
subclass of: Restriction
  on property: is tautomer of
  some values from: formamide
textual definition: A carboximidic acid that is formic acid in which the carbonyl oxygen is replaced by an imino group.
imported from: chebi.owl
charge: 0
formula: CH3NO
inchi: InChI=1S/CH3NO/c2-1-3/h1H,(H2,2,3)
inchikey: ZHNUHDYFZUAESO-UHFFFAOYSA-N
mass: 45.04066
monoisotopicmass: 45.02146
smiles: [H]C(O)=N
database_cross_reference: Beilstein:1918433
database_cross_reference: PMID:16331898
database_cross_reference: Reaxys:1918433
has_exact_synonym: imidoformic acid
has_obo_namespace: chebi_ontology
id: CHEBI:48431
in_subset: 3 STAR

radical scavenger
type: Class
subclass of: antioxidant
textual definition: A role played by a substance that can react readily with, and thereby eliminate, radicals.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: free radical scavengers
has_related_synonym: free-radical scavenger
id: CHEBI:48578
in_subset: 3 STAR

cyano group
type: Class
subclass of: pseudohalo group
subclass of: Restriction
  on property: is substituent group from
  some values from: hydrogen cyanide
imported from: chebi.owl
charge: 0
formula: CN
mass: 26.017
monoisotopicmass: 26.00307
smiles: C(#N)*
has_alternative_id: CHEBI:36824
has_alternative_id: CHEBI:48818
database_cross_reference: PDBeChem:CYN
has_exact_synonym: cyanido
has_exact_synonym: cyano
has_obo_namespace: chebi_ontology
has_related_synonym: -C#N
has_related_synonym: -CN
has_related_synonym: CYANIDE GROUP
has_related_synonym: NC-
has_related_synonym: carbonitrile group
id: CHEBI:48819
in_subset: 3 STAR

cholinergic antagonist
type: Class
subclass of: cholinergic drug
textual definition: Any drug that binds to but does not activate cholinergic receptors, thereby blocking the actions of acetylcholine or cholinergic agonists.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: Anticholinergika
has_related_synonym: Anticholinergikum
has_related_synonym: acetylcholine antagonists
has_related_synonym: acetylcholine receptor antagonist
has_related_synonym: agent anticholinergique
has_related_synonym: agente anticolinergico
has_related_synonym: agentes anticolinergicos
has_related_synonym: anticholinergic agents
has_related_synonym: anticholinergics
has_related_synonym: anticholinergiques
has_related_synonym: anticolinergicos
has_related_synonym: cholinergic-blocking agents
id: CHEBI:48873
in_subset: 3 STAR

hydrogen atom
type: Class
subclass of: inorganic molecular entity
subclass of: nonmetal atom
subclass of: s-block element atom
subclass of: Restriction
  on property: has role
  some values from: macronutrient
imported from: chebi.owl
charge: 0
formula: H
inchi: InChI=1S/H
inchikey: YZCKVEUIGOORGS-UHFFFAOYSA-N
mass: 1.00794
monoisotopicmass: 1.00783
smiles: [H]
has_alternative_id: CHEBI:24634
has_alternative_id: CHEBI:49636
database_cross_reference: WebElements:H
has_exact_synonym: hydrogen
has_obo_namespace: chebi_ontology
has_related_synonym: 1H
has_related_synonym: H
has_related_synonym: Wasserstoff
has_related_synonym: hidrogeno
has_related_synonym: hydrogen
has_related_synonym: hydrogene
id: CHEBI:49637
in_subset: 3 STAR

organic amino compound
type: Class
subclass of: organonitrogen compound
subclass of: organic molecular entity
subclass of: Restriction
  on property: has role
  some values from: Bronsted base
subclass of: Restriction
  on property: has parent hydride
  some values from: ammonia
textual definition: A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic amino compounds
id: CHEBI:50047
in_subset: 3 STAR

protective agent
type: Class
subclass of: drug
textual definition: Synthetic or natural substance which is given to prevent a disease or disorder or are used in the process of treating a disease or injury due to a poisonous agent.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: chemoprotectant
has_related_synonym: chemoprotectants
has_related_synonym: chemoprotective agent
has_related_synonym: chemoprotective agents
has_related_synonym: protective agents
id: CHEBI:50267
in_subset: 3 STAR

onium compound
type: Class
subclass of: heteroatomic molecular entity
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:50312
in_subset: 1 STAR

onium cation
type: Class
subclass of: onium compound
textual definition: Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
imported from: chebi.owl
has_exact_synonym: onium cations
has_obo_namespace: chebi_ontology
has_related_synonym: onium cations
has_related_synonym: onium ion
has_related_synonym: onium ions
id: CHEBI:50313
in_subset: 3 STAR

nitric oxide donor
type: Class
subclass of: donor
textual definition: An agent, with unique chemical structure and biochemical requirements, which generates nitric oxide.
imported from: chebi.owl
has_alternative_id: CHEBI:77704
has_obo_namespace: chebi_ontology
has_related_synonym: NO donor
has_related_synonym: NO donors
has_related_synonym: NO generator
has_related_synonym: NO generators
has_related_synonym: NO releasing agent
has_related_synonym: NO releasing agents
has_related_synonym: nitric oxide donors
has_related_synonym: nitric oxide generators
has_related_synonym: nitric oxide releasing agent
has_related_synonym: nitric oxide releasing agents
id: CHEBI:50566
in_subset: 3 STAR

alkyl alcohol
type: Class
subclass of: aliphatic alcohol
textual definition: An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position.
imported from: chebi.owl
has_alternative_id: CHEBI:22937
has_alternative_id: CHEBI:50581
has_obo_namespace: chebi_ontology
has_related_synonym: alkyl alcohols
has_related_synonym: hydroxyalkane
has_related_synonym: hydroxyalkanes
id: CHEBI:50584
in_subset: 3 STAR

organic molecular entity
type: Class
subclass of: carbon group molecular entity
subclass of: Restriction
  on property: has part
  some values from: carbon atom
textual definition: Any molecular entity that contains carbon.
imported from: chebi.owl
has_alternative_id: CHEBI:25700
has_alternative_id: CHEBI:33244
has_obo_namespace: chebi_ontology
has_related_synonym: organic compounds
has_related_synonym: organic entity
has_related_synonym: organic molecular entities
id: CHEBI:50860
in_subset: 3 STAR

carcinogenic agent
type: Class
subclass of: aetiopathogenetic role
textual definition: A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: agente carcinogeno
has_related_synonym: cancerigene
has_related_synonym: cancerogene
has_related_synonym: carcinogen
has_related_synonym: carcinogene
has_related_synonym: carcinogenic agents
has_related_synonym: carcinogeno
has_related_synonym: carcinogens
id: CHEBI:50903
in_subset: 3 STAR

deaminating agent
type: Class
subclass of: chemical role
textual definition: A deaminating agent is a role played by a chemical agent which exhibits the capability of causing the loss of an amine functional group on another molecular entity (e.g. DNA or protein).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:50907
in_subset: 3 STAR

hepatotoxic agent
type: Class
subclass of: aetiopathogenetic role
textual definition: A role played by a chemical compound exihibiting itself through the ability to induce damage to the liver in animals.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: agente hepatotoxico
has_related_synonym: hepatotoxic agents
has_related_synonym: hepatotoxicant
has_related_synonym: hepatotoxicants
has_related_synonym: hepatotoxin
has_related_synonym: hepatotoxins
has_related_synonym: hepatoxic agent
has_related_synonym: hepatoxicant
id: CHEBI:50908
in_subset: 3 STAR

neurotoxin
type: Class
subclass of: aetiopathogenetic role
subclass of: poison
textual definition: A poison that interferes with the functions of the nervous system.
imported from: chebi.owl
has_alternative_id: CHEBI:50911
database_cross_reference: Wikipedia:Neurotoxin
has_obo_namespace: chebi_ontology
has_related_synonym: agente neurotoxico
has_related_synonym: nerve poison
has_related_synonym: nerve poisons
has_related_synonym: neurotoxic agent
has_related_synonym: neurotoxic agents
has_related_synonym: neurotoxicant
has_related_synonym: neurotoxins
id: CHEBI:50910
in_subset: 3 STAR

chemical role
type: Class
subclass of: role
textual definition: A role played by the molecular entity or part thereof within a chemical context.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:51086
in_subset: 3 STAR

nitrogen molecular entity
type: Class
subclass of: pnictogen molecular entity
subclass of: Restriction
  on property: has part
  some values from: nitrogen atom
imported from: chebi.owl
has_alternative_id: CHEBI:25556
has_alternative_id: CHEBI:7594
database_cross_reference: KEGG:C06061
has_obo_namespace: chebi_ontology
has_related_synonym: Nitrogenous compounds
has_related_synonym: nitrogen compounds
has_related_synonym: nitrogen molecular entities
id: CHEBI:51143
in_subset: 3 STAR

drying control chemical additive
type: Class
subclass of: solvent
textual definition: A role played by a compound that facilitates the rapid drying of gels without their cracking.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:51268
in_subset: 3 STAR

organodiyl group
type: Class
subclass of: organic divalent group
textual definition: Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organodiyl groups
id: CHEBI:51422
in_subset: 3 STAR

organic divalent group
type: Class
subclass of: organic group
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:51446
in_subset: 1 STAR

organic univalent group
type: Class
subclass of: organic group
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:51447
in_subset: 1 STAR

methyl ketone
type: Class
subclass of: ketone
textual definition: A ketone of formula RC(=O)CH3 (R =/= H).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: methyl ketones
id: CHEBI:51867
in_subset: 3 STAR

methoxide
type: Class
subclass of: organic anion
subclass of: Restriction
  on property: has role
  some values from: human metabolite
subclass of: Restriction
  on property: is conjugate base of
  some values from: methanol
textual definition: An organic anion that is the conjugate base of methanol.
imported from: chebi.owl
charge: -1
formula: CH3O
inchi: InChI=1S/CH3O/c1-2/h1H3/q-1
inchikey: NBTOZLQBSIZIKS-UHFFFAOYSA-N
mass: 31.03390
monoisotopicmass: 31.01894
smiles: C[O-]
database_cross_reference: Reaxys:1839368
has_obo_namespace: chebi_ontology
has_related_synonym: methoxide ion
id: CHEBI:52090
in_subset: 3 STAR

biochemical role
type: Class
subclass of: biological role
textual 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

biophysical role
type: Class
subclass of: biological role
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:52208
in_subset: 1 STAR

aetiopathogenetic role
type: Class
subclass of: biological role
textual definition: A role played by the molecular entity or part thereof which causes the development of a pathological process.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: etiopathogenetic agent
has_related_synonym: etiopathogenetic role
id: CHEBI:52209
in_subset: 3 STAR

pharmacological role
type: Class
subclass of: biological role
textual definition: A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:52210
in_subset: 3 STAR

physiological role
type: Class
subclass of: biological role
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:52211
in_subset: 1 STAR

ligand
type: Class
subclass of: chemical role
textual definition: Any molecule or ion capable of binding to a central metal atom to form coordination complexes.
imported from: chebi.owl
database_cross_reference: Wikipedia:Ligand
has_obo_namespace: chebi_ontology
has_related_synonym: ligands
id: CHEBI:52214
in_subset: 3 STAR

photochemical role
type: Class
subclass of: chemical role
textual definition: A chemical role played by the molecular entity or part thereof in a photochemical process.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: photochemical roles
id: CHEBI:52215
in_subset: 3 STAR

photobiochemical role
type: Class
subclass of: biochemical role
subclass of: photochemical role
textual definition: A role played by a molecular entity or part thereof in a photobiochemical process.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
id: CHEBI:52216
in_subset: 3 STAR

pharmaceutical
type: Class
subclass of: application
textual definition: Any substance introduced into a living organism with therapeutic or diagnostic purpose.
imported from: chebi.owl
has_alternative_id: CHEBI:33293
has_alternative_id: CHEBI:33294
has_obo_namespace: chebi_ontology
has_related_synonym: farmaco
has_related_synonym: medicament
has_related_synonym: pharmaceuticals
id: CHEBI:52217
in_subset: 3 STAR

chain carrier
type: Class
subclass of: chemical role
textual definition: The role played by a molecular entity, such as an atom or free radical, which is involved in chain-propagating reactions.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: chain carriers
id: CHEBI:53431
in_subset: 3 STAR

heterocyclic compound
type: Class
subclass of: cyclic compound
textual definition: A cyclic compound having as ring members atoms of at least two different elements.
imported from: chebi.owl
has_exact_synonym: Heterocyclic compound
has_obo_namespace: chebi_ontology
has_related_synonym: compuesto heterociclico
has_related_synonym: compuestos heterociclicos
has_related_synonym: heterocycle
has_related_synonym: heterocyclic compounds
id: CHEBI:5686
in_subset: 3 STAR

electrophilic reagent
type: Class
subclass of: reagent
subclass of: Lewis acid
textual definition: A reagent that forms a bond to its reaction partner (the nucleophile) by accepting both bonding electrons from that reaction partner.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: electrophile
has_related_synonym: electrophiles
has_related_synonym: electrophilic reagents
id: CHEBI:59739
in_subset: 3 STAR

nucleophilic reagent
type: Class
subclass of: reagent
subclass of: Lewis base
textual definition: A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: nucleophile
has_related_synonym: nucleophiles
has_related_synonym: nucleophilic reagents
id: CHEBI:59740
in_subset: 3 STAR

bolaamphiphile
type: Class
subclass of: surfactant
textual definition: A surfactant molecule with hydrophilic groups at both ends of a hydrophobic hydrocarbon chain
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: alpha-omega-type surfactant
has_related_synonym: bolaamphiphiles
has_related_synonym: bolaform surfactant
has_related_synonym: bolaphile
id: CHEBI:59752
in_subset: 3 STAR

amphiphile
type: Class
subclass of: surfactant
textual definition: A surfactant molecule possessing both hydrophilic and lipophilic properties.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: amphiphiles
id: CHEBI:59941
in_subset: 3 STAR

monovalent inorganic cation
type: Class
subclass of: inorganic cation
textual definition: An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: a monovalent cation
id: CHEBI:60242
in_subset: 3 STAR

fatty acid derivative
type: Class
subclass of: organic molecular entity
subclass of: Restriction
  on property: has functional parent
  some values from: fatty acid
textual definition: Any organic molecular entity derived from a fatty acid.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: FA derivative
has_related_synonym: FA derivatives
has_related_synonym: fatty acid derivatives
id: CHEBI:61697
in_subset: 3 STAR

acyl donor
type: Class
subclass of: donor
textual definition: Any donor that can transfer acyl groups between molecular entities.
imported from: chebi.owl
database_cross_reference: PMID:16100120
database_cross_reference: PMID:19052863
has_obo_namespace: chebi_ontology
id: CHEBI:62049
in_subset: 3 STAR

fuel additive
type: Class
subclass of: chemical role
textual definition: Any additive that enhances the efficiency of fuel.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: fuel additives
has_related_synonym: fuel enhancer
id: CHEBI:62803
in_subset: 3 STAR

emulsifier
type: Class
subclass of: chemical role
textual definition: The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: emulgent
has_related_synonym: emulgents
has_related_synonym: emulsifiers
id: CHEBI:63046
in_subset: 3 STAR

food emulsifier
type: Class
subclass of: emulsifier
subclass of: food additive
textual definition: A food additive used to form or maintain a uniform emulsion of two (or more) phases in a food.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: food emulsifiers
id: CHEBI:63047
in_subset: 3 STAR

phase-transfer catalyst
type: Class
subclass of: catalyst
textual definition: A catalyst that facilitates the migration of a reactant from one phase into another phase where reaction occurs.
imported from: chebi.owl
database_cross_reference: Wikipedia:Phase_transfer_catalyst
has_obo_namespace: chebi_ontology
has_related_synonym: PTC
has_related_synonym: phase transfer catalyst
has_related_synonym: phase transfer catalysts
has_related_synonym: phase-transfer catalysts
id: CHEBI:63060
in_subset: 3 STAR

crystallisation adjutant
type: Class
subclass of: chemical role
textual definition: Chemical role played by a material when used to promote crystallisation.
imported from: chebi.owl
database_cross_reference: Wikipedia:Crystallization_adjutant
has_obo_namespace: chebi_ontology
has_related_synonym: crystallisation adjutants
has_related_synonym: crystallization adjutant
has_related_synonym: crystallization adjutants
id: CHEBI:63064
in_subset: 3 STAR

reducing agent
type: Class
subclass of: chemical role
textual definition: The element or compound in a reduction-oxidation (redox) reaction that donates an electron to another species.
imported from: chebi.owl
database_cross_reference: Wikipedia:Reducing_agent
has_obo_namespace: chebi_ontology
has_related_synonym: reducer
has_related_synonym: reducers
has_related_synonym: reducing agents
has_related_synonym: reductant
has_related_synonym: reductants
id: CHEBI:63247
in_subset: 3 STAR

oxidising agent
type: Class
subclass of: chemical role
textual definition: A substance that removes electrons from another reactant in a redox reaction.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: oxidant
has_related_synonym: oxidants
has_related_synonym: oxidiser
has_related_synonym: oxidisers
has_related_synonym: oxidising agents
has_related_synonym: oxidizer
has_related_synonym: oxidizers
has_related_synonym: oxidizing agent
has_related_synonym: oxidizing agents
id: CHEBI:63248
in_subset: 3 STAR

explosive
type: Class
subclass of: chemical role
textual definition: A substance capable of undergoing rapid and highly exothermic decomposition.
imported from: chebi.owl
database_cross_reference: Wikipedia:Explosive_material
has_obo_namespace: chebi_ontology
has_related_synonym: explosive compound
has_related_synonym: explosive compounds
has_related_synonym: explosive material
has_related_synonym: explosives
has_related_synonym: explosives chemical
has_related_synonym: explosives chemicals
id: CHEBI:63490
in_subset: 3 STAR

neuroprotective agent
type: Class
subclass of: protective agent
textual definition: Any compound that can be used for the treatment of neurodegenerative disorders.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: neuroprotectant
has_related_synonym: neuroprotectants
has_related_synonym: neuroprotective agents
id: CHEBI:63726
in_subset: 3 STAR

film-forming compound
type: Class
subclass of: chemical role
textual definition: Any compound that leaves a pliable, cohesive, and continuous covering over a surface when applied to it.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: film-forming agent
has_related_synonym: film-forming agents
has_related_synonym: film-forming compounds
id: CHEBI:63908
in_subset: 3 STAR

food additive
type: Class
subclass of: application
subclass of: food component
textual definition: Any substance which is added to food to preserve or enhance its flavour and/or appearance.
imported from: chebi.owl
database_cross_reference: Wikipedia:Food_additive
has_obo_namespace: chebi_ontology
has_related_synonym: food additives
id: CHEBI:64047
in_subset: 3 STAR

reaction intermediate
type: Class
subclass of: chemical role
textual definition: Any chemical substance produced during the conversion of a reactant to a product.
imported from: chebi.owl
database_cross_reference: Wikipedia:Reaction_intermediate
has_obo_namespace: chebi_ontology
has_related_synonym: chemical intermediate
id: CHEBI:64297
in_subset: 3 STAR

one-carbon compound
type: Class
subclass of: organic molecular entity
textual definition: An organic molecular entity containing a single carbon atom (C1).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: one-carbon compounds
id: CHEBI:64708
in_subset: 3 STAR

organic acid
type: Class
subclass of: organic molecular entity
textual definition: Any organic molecular entity that is acidic and contains carbon in covalent linkage.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic acids
id: CHEBI:64709
in_subset: 3 STAR

poison
type: Class
subclass of: biological role
textual definition: Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.
imported from: chebi.owl
database_cross_reference: Wikipedia:Poison
has_obo_namespace: chebi_ontology
has_related_synonym: poisonous agent
has_related_synonym: poisonous agents
has_related_synonym: poisonous substance
has_related_synonym: poisonous substances
has_related_synonym: poisons
has_related_synonym: toxic agent
has_related_synonym: toxic agents
has_related_synonym: toxic substance
has_related_synonym: toxic substances
id: CHEBI:64909
in_subset: 3 STAR

food preservative
type: Class
subclass of: food additive
textual definition: Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: food preservatives
id: CHEBI:65255
in_subset: 3 STAR

reactive oxygen species generator
type: Class
subclass of: chemical role
textual definition: Any entity used to generate reactive oxygen species.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: ROS generator
has_related_synonym: ROS generators
has_related_synonym: reactive oxygen species generators
id: CHEBI:70982
in_subset: 3 STAR

organic molecule
type: Class
subclass of: molecule
subclass of: organic molecular entity
textual definition: Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: organic compound
has_related_synonym: organic compounds
has_related_synonym: organic molecules
id: CHEBI:72695
in_subset: 3 STAR

ultraviolet filter
type: Class
subclass of: photochemical role
textual definition: A photochemical role realized in the absorption of ultraviolet light, for example to protect skin cells from damage.
imported from: chebi.owl
database_cross_reference: Wikipedia:UV_filter
has_obo_namespace: chebi_ontology
has_related_synonym: UV filter
has_related_synonym: UV filters
has_related_synonym: ultraviolet filters
id: CHEBI:73335
in_subset: 3 STAR

ketone body
type: Class
subclass of: carbonyl compound
subclass of: fatty acid derivative
subclass of: Restriction
  on property: has role
  some values from: metabolite
subclass of: Restriction
  on property: has role
  some values from: neuroprotective agent
textual definition: A carbonyl compound produced as a water-soluble byproduct when fatty acids are broken down for energy in the liver. There are three endogenous ketone bodies: acetone, acetoacetic acid, and (R)-3-hydroxybutyric acid; others may be produced as a result of the metabolism of synthetic triglycerides.
imported from: chebi.owl
database_cross_reference: PMID:10634967
database_cross_reference: PMID:19159745
database_cross_reference: PMID:22259088
database_cross_reference: PMID:22268909
database_cross_reference: PMID:22524563
database_cross_reference: PMID:22879057
database_cross_reference: PMID:23082721
database_cross_reference: PMID:23148246
database_cross_reference: PMID:23396451
database_cross_reference: PMID:23466063
database_cross_reference: PMID:23557707
database_cross_reference: Wikipedia:Ketone_body
has_obo_namespace: chebi_ontology
has_related_synonym: ketone bodies
id: CHEBI:73693
in_subset: 3 STAR

polymerisation monomer
type: Class
subclass of: chemical role
textual definition: Any compound used as a monomer for a polymerisation process. The term is generally used in relation to industrial polymerisation processes.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: polymerization monomer
id: CHEBI:74236
in_subset: 3 STAR

astringent
type: Class
subclass of: drug
textual definition: A compound that causes the contraction of body tissues, typically used to reduce bleeding from minor abrasions.
imported from: chebi.owl
database_cross_reference: Wikipedia:Astringent
has_obo_namespace: chebi_ontology
has_related_synonym: adstringent
has_related_synonym: adstringents
has_related_synonym: astringents
id: CHEBI:74783
in_subset: 3 STAR

eukaryotic metabolite
type: Class
subclass of: metabolite
textual definition: Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: eukaryotic metabolites
id: CHEBI:75763
in_subset: 3 STAR

animal metabolite
type: Class
subclass of: eukaryotic metabolite
textual definition: Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
imported from: chebi.owl
has_alternative_id: CHEBI:77721
has_alternative_id: CHEBI:77743
has_obo_namespace: chebi_ontology
has_related_synonym: animal metabolites
id: CHEBI:75767
in_subset: 3 STAR

mammalian metabolite
type: Class
subclass of: animal metabolite
textual definition: Any animal metabolite produced during a metabolic reaction in mammals.
imported from: chebi.owl
has_alternative_id: CHEBI:77464
has_alternative_id: CHEBI:77744
has_obo_namespace: chebi_ontology
has_related_synonym: mammalian metabolites
id: CHEBI:75768
in_subset: 3 STAR

mouse metabolite
type: Class
subclass of: mammalian metabolite
textual definition: Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: Mus musculus metabolite
has_related_synonym: Mus musculus metabolites
has_related_synonym: mouse metabolites
id: CHEBI:75771
in_subset: 3 STAR

Saccharomyces cerevisiae metabolite
type: Class
subclass of: fungal metabolite
textual definition: Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
imported from: chebi.owl
has_alternative_id: CHEBI:76949
has_alternative_id: CHEBI:76951
has_obo_namespace: chebi_ontology
has_related_synonym: S. cerevisiae metabolite
has_related_synonym: S. cerevisiae metabolites
has_related_synonym: S. cerevisiae secondary metabolite
has_related_synonym: S. cerevisiae secondary metabolites
has_related_synonym: Saccharomyces cerevisiae metabolites
has_related_synonym: Saccharomyces cerevisiae secondary metabolites
has_related_synonym: baker's yeast metabolite
has_related_synonym: baker's yeast metabolites
has_related_synonym: baker's yeast secondary metabolite
has_related_synonym: baker's yeast secondary metabolites
id: CHEBI:75772
in_subset: 3 STAR

prokaryotic metabolite
type: Class
subclass of: metabolite
textual definition: Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: prokaryotic metabolites
id: CHEBI:75787
in_subset: 3 STAR

greenhouse gas
type: Class
subclass of: chemical role
textual definition: A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.
imported from: chebi.owl
database_cross_reference: Wikipedia:Greenhouse_gas
has_obo_namespace: chebi_ontology
has_related_synonym: greenhouse gases
id: CHEBI:76413
in_subset: 3 STAR

fluorescence quencher
type: Class
subclass of: chemical role
textual definition: A compound used to return an excited fluorophore to the ground state by transfer of energy from fluorophore to quencher without the emission of light, with the quencher being promoted to its own excited state.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: fluorescence quenchers
id: CHEBI:76648
in_subset: 3 STAR

EC 1.* (oxidoreductase) inhibitor
type: Class
subclass of: enzyme inhibitor
textual definition: An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*).
imported from: chebi.owl
database_cross_reference: Wikipedia:Oxidoreductase
has_obo_namespace: chebi_ontology
has_related_synonym: EC 1.* (oxidoreductase) inhibitors
has_related_synonym: EC 1.* inhibitor
has_related_synonym: EC 1.* inhibitors
has_related_synonym: oxidoreductase (EC 1.*) inhibitor
has_related_synonym: oxidoreductase (EC 1.*) inhibitors
has_related_synonym: oxidoreductase inhibitor
has_related_synonym: oxidoreductase inhibitors
id: CHEBI:76725
in_subset: 3 STAR

EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor
type: Class
subclass of: EC 1.* (oxidoreductase) inhibitor
textual definition: An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on a heme group of donors (EC 1.9.*.*).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitor
has_related_synonym: EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitors
has_related_synonym: EC 1.9.* (oxidoreductase acting on donor heme group) inhibitors
has_related_synonym: EC 1.9.* inhibitor
has_related_synonym: EC 1.9.* inhibitors
has_related_synonym: oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitor
has_related_synonym: oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitors
id: CHEBI:76736
in_subset: 3 STAR

EC 3.* (hydrolase) inhibitor
type: Class
subclass of: enzyme inhibitor
textual definition: Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
imported from: chebi.owl
database_cross_reference: Wikipedia:Hydrolase
has_obo_namespace: chebi_ontology
has_related_synonym: EC 3.* (hydrolase) inhibitors
has_related_synonym: EC 3.* inhibitor
has_related_synonym: EC 3.* inhibitors
has_related_synonym: EC 3.*.*.* inhibitor
has_related_synonym: EC 3.*.*.* inhibitors
has_related_synonym: hydrolase (EC 3.*) inhibitor
has_related_synonym: hydrolase (EC 3.*) inhibitors
has_related_synonym: hydrolase inhibitor
has_related_synonym: hydrolase inhibitors
id: CHEBI:76759
in_subset: 3 STAR

EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
type: Class
subclass of: EC 3.* (hydrolase) inhibitor
textual definition: Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor
has_related_synonym: EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors
has_related_synonym: EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor
has_related_synonym: EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors
has_related_synonym: EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors
has_related_synonym: EC 3.5.* inhibitor
has_related_synonym: EC 3.5.* inhibitors
id: CHEBI:76764
in_subset: 3 STAR

EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
type: Class
subclass of: EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
textual definition: An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors
has_related_synonym: EC 3.5.1.* inhibitor
has_related_synonym: EC 3.5.1.* inhibitors
has_related_synonym: non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor
has_related_synonym: non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors
id: CHEBI:76807
in_subset: 3 STAR

EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor
type: Class
subclass of: EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor
textual definition: An EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.9.3.*).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitors
has_related_synonym: EC 1.9.3.* inhibitor
has_related_synonym: EC 1.9.3.* inhibitors
has_related_synonym: oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitor
has_related_synonym: oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitors
id: CHEBI:76870
in_subset: 3 STAR

pathway inhibitor
type: Class
subclass of: enzyme inhibitor
textual definition: An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: metabolic pathway inhibitor
has_related_synonym: metabolic pathway inhibitors
has_related_synonym: pathway inhibitors
id: CHEBI:76932
in_subset: 3 STAR

fungal metabolite
type: Class
subclass of: eukaryotic metabolite
textual definition: Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
imported from: chebi.owl
has_alternative_id: CHEBI:75765
has_alternative_id: CHEBI:76947
has_obo_namespace: chebi_ontology
has_related_synonym: fungal metabolites
id: CHEBI:76946
in_subset: 3 STAR

bacterial metabolite
type: Class
subclass of: prokaryotic metabolite
textual definition: Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
imported from: chebi.owl
has_alternative_id: CHEBI:75760
has_alternative_id: CHEBI:76970
has_obo_namespace: chebi_ontology
id: CHEBI:76969
in_subset: 3 STAR

Escherichia coli metabolite
type: Class
subclass of: bacterial metabolite
textual definition: Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: E.coli metabolite
has_related_synonym: E.coli metabolites
has_related_synonym: Escherichia coli metabolites
id: CHEBI:76971
in_subset: 3 STAR

thermal degradation product
type: Class
subclass of: chemical role
textual definition: Any product obtained as a result of thermally induced non-enzymatic degradation.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: thermal artefact
has_related_synonym: thermal artefacts
has_related_synonym: thermal degradation products
id: CHEBI:77521
in_subset: 3 STAR

Maillard reaction product
type: Class
subclass of: thermal degradation product
textual definition: Any thermal degradation product obtained as a result of a chemical reaction between an amino acid and a reducing sugar (Maillard reaction, a non-enzymatic browning procedure that usually imparts flavour to starch-based food products).
imported from: chebi.owl
database_cross_reference: PMID:23588491
database_cross_reference: PMID:23612540
database_cross_reference: PMID:24246231
database_cross_reference: Wikipedia:Maillard_reaction
has_obo_namespace: chebi_ontology
has_related_synonym: Maillard product
has_related_synonym: Maillard products
has_related_synonym: maillard reaction products
id: CHEBI:77523
in_subset: 3 STAR

human metabolite
type: Class
subclass of: mammalian metabolite
textual definition: Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
imported from: chebi.owl
has_alternative_id: CHEBI:75770
has_alternative_id: CHEBI:77123
has_obo_namespace: chebi_ontology
has_related_synonym: H. sapiens metabolite
has_related_synonym: H. sapiens metabolites
has_related_synonym: Homo sapiens metabolite
has_related_synonym: Homo sapiens metabolites
id: CHEBI:77746
in_subset: 3 STAR

persistent organic pollutant
type: Class
subclass of: environmental contaminant
textual definition: Any environmental contaminant that is resistant to environmental degradation through photolytic, biological or chemical processes. Such substances can have significant impact on health and the environment, as they persist in the environment, bioaccumulate in animal tissue and so biomagnify in food chains.
imported from: chebi.owl
database_cross_reference: Wikipedia:Persistant_organic_pollutant
has_obo_namespace: chebi_ontology
has_related_synonym: POP
has_related_synonym: POPs
has_related_synonym: persistent organic pollutants
id: CHEBI:77853
in_subset: 3 STAR

EC 3.5.1.4 (amidase) inhibitor
type: Class
subclass of: EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
textual definition: An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).
imported from: chebi.owl
database_cross_reference: Wikipedia:Amidase
has_obo_namespace: chebi_ontology
has_related_synonym: EC 3.5.1.4 (amidase) inhibitors
has_related_synonym: EC 3.5.1.4 inhibitor
has_related_synonym: EC 3.5.1.4 inhibitors
has_related_synonym: N-acetylaminohydrolase inhibitor
has_related_synonym: N-acetylaminohydrolase inhibitors
has_related_synonym: acylamidase inhibitor
has_related_synonym: acylamidase inhibitors
has_related_synonym: acylamide amidohydrolase inhibitor
has_related_synonym: acylamide amidohydrolase inhibitors
has_related_synonym: amidase (EC 3.5.1.4) inhibitor
has_related_synonym: amidase (EC 3.5.1.4) inhibitors
has_related_synonym: amidase inhibitor
has_related_synonym: amidase inhibitors
has_related_synonym: amidohydrolase inhibitor
has_related_synonym: amidohydrolase inhibitors
has_related_synonym: deaminase inhibitor
has_related_synonym: deaminase inhibitors
has_related_synonym: fatty acylamidase inhibitor
has_related_synonym: fatty acylamidase inhibitors
id: CHEBI:77941
in_subset: 3 STAR

food antioxidant
type: Class
subclass of: antioxidant
subclass of: food preservative
textual definition: An antioxidant that used as a food additives to help guard against food deterioration.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: food antioxidants
id: CHEBI:77962
in_subset: 3 STAR

sequestrant
type: Class
subclass of: chelator
subclass of: food preservative
textual definition: A food preservative that acts by chelating with metal cations (particularly those of copper, iron and nickel) that catalyse the oxidation of fats in food.
imported from: chebi.owl
database_cross_reference: Wikipedia:Sequestrant
has_obo_namespace: chebi_ontology
has_related_synonym: sequestrants
id: CHEBI:77963
in_subset: 3 STAR

food component
type: Class
subclass of: physiological role
textual definition: A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: dietary component
has_related_synonym: dietary components
has_related_synonym: food components
id: CHEBI:78295
in_subset: 3 STAR

environmental contaminant
type: Class
subclass of: chemical role
textual definition: Any minor or unwanted substance introduced into the environment that can have undesired effects.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: environmental contaminants
id: CHEBI:78298
in_subset: 3 STAR

environmental food contaminant
type: Class
subclass of: food component
subclass of: environmental contaminant
textual definition: Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: environmental food contaminants
id: CHEBI:78299
in_subset: 3 STAR

refrigerant
type: Class
subclass of: application
textual definition: A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.
imported from: chebi.owl
database_cross_reference: Wikipedia:Refrigerant
has_obo_namespace: chebi_ontology
has_related_synonym: refrigerants
id: CHEBI:78433
in_subset: 3 STAR

divalent inorganic anion
type: Class
subclass of: inorganic anion
textual definition: Any inorganic anion with a valency of two.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: divalent inorganic anions
id: CHEBI:79388
in_subset: 3 STAR

monovalent inorganic anion
type: Class
subclass of: inorganic anion
textual definition: Any inorganic anion with a valency of one.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: monovalent inorganic anions
id: CHEBI:79389
in_subset: 3 STAR

aliphatic nitrile
type: Class
subclass of: nitrile
textual definition: Any nitrile derived from an aliphatic compound.
imported from: chebi.owl
charge: 0
formula: CNR
mass: 26.017
monoisotopicmass: 26.00307
smiles: [*]C#N
database_cross_reference: KEGG:C16072
has_obo_namespace: chebi_ontology
has_related_synonym: an aliphatic nitrile
id: CHEBI:80291
in_subset: 3 STAR

phytochrome chromophore
type: Class
subclass of: chromophore
textual definition: A chromophore that is a linear tetrapyrrolic prosthetic group covalently attached to a large soluble protein phytochrome. Light absorption by the phytochrome chromophore triggers photoconversion between two spectrally distinct forms of the photoreceptor: Pr, the red light absorbing form, and Pfr, the far-red light absorbing form.
imported from: chebi.owl
database_cross_reference: PMID:2909515
has_obo_namespace: chebi_ontology
has_related_synonym: phytochrome chromophores
id: CHEBI:82632
in_subset: 3 STAR

corrosion inhibitor
type: Class
subclass of: chemical role
textual definition: A chemical compound that, when added to a liquid or gas, decreases the corrosion rate of a material, typically a metal or an alloy.
imported from: chebi.owl
database_cross_reference: PMID:23636692
database_cross_reference: PMID:25594340
database_cross_reference: PMID:25839822
database_cross_reference: PMID:25912625
database_cross_reference: PMID:25955130
database_cross_reference: PMID:26160863
database_cross_reference: PMID:26343626
database_cross_reference: PMID:26347374
database_cross_reference: PMID:26364631
database_cross_reference: PMID:26727190
database_cross_reference: Wikipedia:Corrosion_inhibitor
has_obo_namespace: chebi_ontology
has_related_synonym: corrosion inhibitors
id: CHEBI:91015
in_subset: 3 STAR

portion of material
type: Class
subclass of: material entity
textual definition: An independent material continuant that is self-connected and retains its identity over time.
imported from: chmo.owl
id: CHMO:0000993

chromatography column
type: Class
subclass of: device
textual definition: A piece of apparatus that has the form of a tube with a diameter between 5 to 50 mm and hosts the stationary bed in chromatography.
imported from: chmo.owl
id: CHMO:0000997

separation method
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: A method that results in the separation of two or more components according to some property.
imported from: chmo.owl
has_alternative_id: FIX:0000002
has_exact_synonym: partition
id: CHMO:0000999

chromatography
type: Class
subclass of: separation method
textual definition: A separation method where the components are distributed between two phases, one of which is stationary, while the other moves in a definite direction.
imported from: chmo.owl
has_alternative_id: FIX:0000053
has_exact_synonym: analytical chromatography
has_exact_synonym: chromatographic analysis
has_exact_synonym: preparative chromatography
id: CHMO:0001000

column chromatography
type: Class
equivalent class: Class
  intersection of: chromatography
  intersection of: Restriction
    on property: has participant
    some values from: chromatography column
subclass of: chromatography
subclass of: Restriction
  on property: has participant
  some values from: chromatography column
textual definition: A chromatography method where the stationary bed is within a tube (of standard length 25 cm). The particles of the solid stationary phase or support coated with a liquid stationary phase may fill the whole inside volume of the tube (packed column) or be concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube (open-tubular column).
imported from: chmo.owl
has_alternative_id: CHMO:0002118
has_narrow_synonym: preparative column chromatography
id: CHMO:0001001

affinity chromatography
type: Class
subclass of: column chromatography
textual definition: Chromatography where the separation is caused by differing biological specificity of the analyte-ligand interactions.
imported from: chmo.owl
has_exact_synonym: bioaffinity chromatography
id: CHMO:0001006

adsorption chromatography
type: Class
subclass of: chromatography
textual definition: Chromatography in which separation is based mainly on differences between the adsorption affinities of the sample components for the surface of an active solid.
imported from: chmo.owl
created by: batchelorc
creation date: 2009-03-06T04:48:25Z
id: CHMO:0001128

displacement chromatography
type: Class
subclass of: chromatography
textual definition: Chromatography where the mobile phase contains a compound (the displacer) more strongly retained than the components of the sample under examination. The sample is fed into the system as a finite slug.
imported from: chmo.owl
created by: batchelorc
creation date: 2009-03-06T04:48:37Z
has_alternative_id: FIX:0000618
id: CHMO:0001129

synthesis method
type: Class
subclass of: material processing
textual definition: A method used to synthesise a sample.
imported from: chmo.owl
id: CHMO:0001301

sample deposition
type: Class
subclass of: synthesis method
textual definition: The process of the settling of particles (atoms or molecules) from a solution, suspension or vapour onto a pre-existing surface, resulting in the growth of a new phase.
imported from: chmo.owl
has_related_synonym: deposition
id: CHMO:0001310

ionothermal synthesis
type: Class
subclass of: synthesis method
textual definition: A synthesis method for growing single crystals from an ionic liquid in an autoclave (a thick-walled steel vessel) at high temperature (400 °C) and pressure.
imported from: chmo.owl
id: CHMO:0001387

solvothermal synthesis
type: Class
subclass of: synthesis method
textual definition: A synthesis method for growing single crystals from a non-aqueous solution in an autoclave (a thick-walled steel vessel) at high temperature (400 °C) and pressure.
imported from: chmo.owl
has_exact_synonym: solvothermal method
has_exact_synonym: solvothermal process
has_exact_synonym: solvothermal reaction
has_exact_synonym: solvothermal treatment
id: CHMO:0001458

ageing
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: Any time-dependent change of the properties of a precipitate e.g. loss of water or growth of crystals as a result of prolonged heat treatment.
imported from: chmo.owl
has_exact_synonym: age hardening
has_exact_synonym: aging
has_exact_synonym: dispersion hardening
has_exact_synonym: precipitate ageing
has_exact_synonym: precipitation hardening
id: CHMO:0001464

annealing
type: Class
subclass of: sample heating
textual definition: A heat treatment that alters the microstructure of a material causing changes in its properties such as strength and hardness
imported from: chmo.owl
id: CHMO:0001465

crystallisation
type: Class
subclass of: sample solidification
textual definition: The formation of a crystalline solid from a solution, melt vapour, or a different solid phase, generally by lowering the temperature or by evaporation of a solvent.
imported from: chmo.owl
has_exact_synonym: crystallization
id: CHMO:0001477

cocrystallisation
type: Class
subclass of: crystallisation
textual definition: The simultaneous crystallisation of two different substances or two different structural elements of the same substance.
imported from: chmo.owl
has_exact_synonym: co crystallisation
has_exact_synonym: co crystallization
has_exact_synonym: co-crystallisation
has_exact_synonym: co-crystallization
has_exact_synonym: cocrystallization
id: CHMO:0001478

fractional crystallisation
type: Class
subclass of: crystallisation
textual definition: The stepwise crystallisation of two or more different substances induced by changes in concentration or temperature. The sample is mixed with a solvent, heated, and then gradually cooled so that, as each of its constituent components crystallises, it can be removed in its pure form from the solution.
imported from: chmo.owl
has_exact_synonym: fractional crystallization
id: CHMO:0001479

distillation
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a sample mixture are vaporised by the application of heat and then cooled by the action of cold water in a condenser.
imported from: chmo.owl
id: CHMO:0001532

batch distillation
type: Class
subclass of: distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a sample mixture are vaporised by the application of heat and then cooled by the action of cold water in a condenser. Distillation is completed before more sample mixture is added.
imported from: chmo.owl
id: CHMO:0001533

continuous distillation
type: Class
subclass of: distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a sample mixture are vaporised by the application of heat and then cooled by the action of cold water in a condenser. The distillation is ongoing with sample mixture being continuously added.
imported from: chmo.owl
id: CHMO:0001534

extractive distillation
type: Class
subclass of: distillation
textual definition: A method of separating two components of very similar boiling point from a mixture. A third, miscible and high-boiling-point solvent is added to the mixture which causes a change in the volatilities of the components. These components are then vaporised by the application of heat and cooled by the action of cold water in a condenser.
imported from: chmo.owl
id: CHMO:0001535

fractional distillation
type: Class
subclass of: distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. As the sample mixture to be purified is heated, its vapours rise into a condenser where they are cooled by water. The vapours stick to the inside surface of the condenser where they continue to be heated until they vaporise again.
imported from: chmo.owl
id: CHMO:0001536

reactive distillation
type: Class
subclass of: distillation
textual definition: A method of separating a lower-boiling-point product from its reactants in a reaction mixture. The product is vaporised by the application of heat and then cooled by the action of cold water in a condenser.
imported from: chmo.owl
id: CHMO:0001537

simple distillation
type: Class
subclass of: distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a sample mixture are vaporised by the application of heat and then immediately cooled by the action of cold water in a condenser. This method can only be used to separate mixtures where the components differ widely in boiling point (by approx. 25°).
imported from: chmo.owl
id: CHMO:0001538

steam distillation
type: Class
subclass of: distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a sample mixture are vaporised by bubbling steam through it and then cooled by the action of cold water in a condenser.
imported from: chmo.owl
id: CHMO:0001539

vacuum distillation
type: Class
subclass of: distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a high-boiling-point sample mixture are vaporised by the application of heat at low pressure and then cooled by the action of cold water in a condenser.
imported from: chmo.owl
has_exact_synonym: low temperature distillation
has_exact_synonym: low-temperature distillation
id: CHMO:0001540

air-sensitive vacuum distillation
type: Class
subclass of: vacuum distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a high-boiling-point sample mixture are vaporised by the application of heat at low pressure and then cooled by the action of cold water in a condenser. The vacuum is replaced by an inert gas once the distillation is complete.
imported from: chmo.owl
id: CHMO:0001541

molecular distillation
type: Class
subclass of: vacuum distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. The components in a high-boiling-point sample mixture are vaporised by the application of heat at low pressure (< 0.01 Torr) and then cooled by the action of cold water in a condenser.
imported from: chmo.owl
id: CHMO:0001542

sample drying
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The process of removing a solvent from a substance.
imported from: chmo.owl
has_related_synonym: drying
id: CHMO:0001549

dielectric drying
type: Class
subclass of: sample drying
textual definition: The removal of solvent from a sample by the application of radio frequency (3 Hz to 300 GHz) or microwave (1–1000 mm) radiation.
imported from: chmo.owl
id: CHMO:0001550

direct drying
type: Class
subclass of: blow drying
textual definition: The removal of solvent from a sample by the application of heated air.
imported from: chmo.owl
id: CHMO:0001551

drum drying
type: Class
subclass of: sample drying
textual definition: The removal of solvent from a sample by applying it as a thin layer to the surface of a heated drum.
imported from: chmo.owl
id: CHMO:0001552

freeze drying
type: Class
subclass of: sample drying
textual definition: The removal of solvent from a sample without passing through the liquid–gas boundary. The sample is frozen at liquid nitrogen temperature (-80 °C) then the surrounding pressure is reduced to allow the water in the sample to sublime.
imported from: chmo.owl
has_exact_synonym: cryodesiccation
has_exact_synonym: freeze-drying
has_exact_synonym: lyophilization
id: CHMO:0001553

oven drying
type: Class
subclass of: sample drying
textual definition: The removal of solvent from a sample by heating in an oven.
imported from: chmo.owl
id: CHMO:0001554

spray drying
type: Class
subclass of: sample drying
textual definition: The removal of water from a liquid sample by pumping it through an atomiser (to produce a spray of fine droplets) then passing a hot gas (e.g. air or N2) through it.
imported from: chmo.owl
has_exact_synonym: spray-drying
id: CHMO:0001555

supercritical drying
type: Class
subclass of: sample drying
textual definition: The removal of solvent from a sample without passing through the liquid–gas boundary, by immersion in a supercritical fluid and de-pressurisation.
imported from: chmo.owl
has_exact_synonym: critical point drying
has_exact_synonym: critical-point drying
has_exact_synonym: super-critical point drying
id: CHMO:0001556

vacuum drying
type: Class
subclass of: sample drying
textual definition: The removal of water from a sample by placing it under reduced pressure. This allows water to evaporate from (heat-sensitive) samples at a lower temperature.
imported from: chmo.owl
id: CHMO:0001557

evaporation
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The physical process by which a liquid substance is converted to a gas or vapour. This may occur at or below the normal boiling point of the liquid (the temperature at which a liquid boils at 1 atmosphere pressure) and the process is endothermic.
imported from: chmo.owl
id: CHMO:0001574

centrifugal evaporation
type: Class
subclass of: solvent evaporation
textual definition: The evaporation of solvent from a sample by placing it a centrifuge and spinning it rapidly.
imported from: chmo.owl
id: CHMO:0001575

rotary evaporation
type: Class
subclass of: solvent evaporation
textual definition: The removal of solvent from a sample by applying heat and lowering the pressure above the sample whilst rotating it at 10–300 rpm.
imported from: chmo.owl
id: CHMO:0001576

extraction
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it.
imported from: chmo.owl
id: CHMO:0001577

coextraction
type: Class
subclass of: extraction
textual definition: The transfer of two solutes from a liquid phase to a (low-polarity) organic liquid phase in contact with it. The solutes form mixed-species aggregates in the organic phase.
imported from: chmo.owl
has_exact_synonym: co-extraction
id: CHMO:0001578

liquid-solid extraction
type: Class
subclass of: extraction
textual definition: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (e.g. silica particles).
imported from: chmo.owl
has_exact_synonym: liquid-solid extraction
has_exact_synonym: solid phase extraction
has_exact_synonym: solid-phase extraction
has_exact_synonym: sorbent extraction
has_exact_synonym: sorptive extraction
has_related_synonym: LSE
has_related_synonym: SPE
id: CHMO:0001583

membrane extraction
type: Class
subclass of: extraction
textual definition: The transfer of a solute from one phase (the 'donor' or 'feed' phase) to another (the 'acceptor' or 'strip' phase) across a nonporous membrane.
imported from: chmo.owl
id: CHMO:0001593

membrane extraction with a sorbent interface
type: Class
subclass of: membrane extraction
textual definition: The transfer of a solute from one phase (the 'donor' or 'feed' phase) to another (the 'acceptor' or 'strip' phase) across a non-porous non-polar polymer membrane. The membrane first extracts the analytes from their matrix, and these are subsequently trapped on a polymeric trap with a porous sorbent using a carrier gas stream.
imported from: chmo.owl
has_exact_synonym: MESI
has_exact_synonym: membrane extraction sorbent interface
has_exact_synonym: membrane extraction with sorbent interface
has_exact_synonym: membrane extraction with trapping on a sorbent interface
id: CHMO:0001594

polymeric membrane extraction
type: Class
subclass of: membrane extraction
textual definition: The transfer of a solute from one phase (the 'donor' or 'feed' phase) to another (the 'acceptor' or 'strip' phase) across a nonporous sillicon rubber membrane.
imported from: chmo.owl
has_exact_synonym: PME
id: CHMO:0001595

supported liquid membrane extraction
type: Class
subclass of: membrane extraction
textual definition: The transfer of a solute from one phase (the 'donor' or 'feed' phase) to another (the 'acceptor' or 'strip' phase) across a non-porous liquid membrane.
imported from: chmo.owl
has_exact_synonym: SLM extraction
has_exact_synonym: SLME
has_exact_synonym: supported liquid membrane (SLM) extraction
id: CHMO:0001596

sequentional extraction
type: Class
subclass of: extraction
textual definition: An analytical process that sequentially chemically leaches metals from soils, sludges or sediments.
imported from: chmo.owl
has_exact_synonym: sequential chemical extraction
id: CHMO:0001597

solvent extraction
type: Class
subclass of: extraction
textual definition: The process of transferring a substance from any matrix to an appropriate liquid phase.
imported from: chmo.owl
id: CHMO:0001598

gas–liquid extraction
type: Class
subclass of: solvent extraction
textual definition: A flotation process in which the material of interest, adsorbed on the surface of gas bubbles in a liquid, is collected on an upper layer of immiscible liquid.
imported from: chmo.owl
has_exact_synonym: gas-liquid extraction
has_exact_synonym: sublation
id: CHMO:0001599

liquid–liquid extraction
type: Class
subclass of: solvent extraction
textual definition: The process of transferring a dissolved substance from one liquid phase to another (immiscible or partially miscible) liquid phase in contact with it.
imported from: chmo.owl
has_exact_synonym: LLE
has_exact_synonym: liquid phase extraction
has_exact_synonym: liquid-liquid distribution
has_exact_synonym: liquid-liquid extraction
has_exact_synonym: liquid-liquid partition
has_exact_synonym: liquid-phase extraction
id: CHMO:0001600

cloud-point extraction
type: Class
subclass of: liquid–liquid extraction
textual definition: The process of transferring a non-ionic surfactant from one liquid phase to another by heating. As the temperature of the solution rises, the surfactant molecules form micelles, if the temperature increases above the cloud point (CPT) the micelles become dehydrated and aggregate. This leads to macroscopic phase separation of the solution into a surfactant-rich phase and a solvent phase.
imported from: chmo.owl
has_exact_synonym: CPE
has_exact_synonym: cloud point extraction
id: CHMO:0001601

pressurised-fluid extraction
type: Class
subclass of: liquid–liquid extraction
textual definition: The process of transferring a dissolved substance from one liquid phase to another (immiscible or partially miscible) liquid phase in contact with it using solvents at elevated temperature (50–200 °C) and pressure (7–20 MPa).
imported from: chmo.owl
has_exact_synonym: PFE
has_exact_synonym: PLE
has_exact_synonym: PSE
has_exact_synonym: accelerated solvent extraction
has_exact_synonym: accelerated-solvent extraction
has_exact_synonym: pressurised fluid extraction
has_exact_synonym: pressurised liquid extraction
has_exact_synonym: pressurised solvent extraction
has_exact_synonym: pressurised-liquid extraction
has_exact_synonym: pressurised-solvent extraction
has_exact_synonym: pressurized fluid extraction
has_exact_synonym: pressurized liquid extraction
has_exact_synonym: pressurized solvent extraction
has_exact_synonym: pressurized-fluid extraction
has_exact_synonym: pressurized-liquid extraction
has_exact_synonym: pressurized-solvent extraction
id: CHMO:0001604

shake-flask extraction
type: Class
subclass of: solvent extraction
textual definition: The process of transferring a substance from any matrix to an appropriate liquid phase, during which the sample and solvent are kept in contact in a mechanical shaker.
imported from: chmo.owl
has_exact_synonym: shake flask extraction
id: CHMO:0001606

solid–liquid extraction
type: Class
subclass of: solvent extraction
textual definition: The process of transferring the soluble components of a solid to the liquid phase using a solvent.
imported from: chmo.owl
has_exact_synonym: solid-liquid extraction dry extraction
id: CHMO:0001607

supercritical fluid extraction
type: Class
subclass of: solvent extraction
textual definition: The process of transferring a substance from any matrix to a liquid phase using a supercritical fluid.
imported from: chmo.owl
has_exact_synonym: SCFE
has_exact_synonym: SFE
has_exact_synonym: supercritical extraction
has_exact_synonym: supercritical fluid extraction
id: CHMO:0001610

substoichiometric extraction
type: Class
subclass of: extraction
textual definition: The process of transferring a substance from any matrix to another where the amount of reagent used is lower than that dictated by stoichiometry.
imported from: chmo.owl
id: CHMO:0001612

fermentation
type: Class
subclass of: planned process
subclass of: material processing
textual definition: The process in which cells (microorganisms, plant or animal cells) are cultured in a bioreactor in a liquid or solid medium to convert organic substances into biomass (growth) or into products.
imported from: chmo.owl
id: CHMO:0001624

fractionation
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The process of dividing up a sample mixture into smaller quantities according to their physical (e.g. size, solubility) or chemical (e.g. bonding, reactivity) properties.
imported from: chmo.owl
id: CHMO:0001625

foam fractionation
type: Class
subclass of: fractionation
textual definition: A method of separation in which a component of the bulk liquid is preferentially adsorbed at the liquid–vapour interface and is removed by foaming.
imported from: chmo.owl
id: CHMO:0001636

freeze distillation
type: Class
subclass of: fractionation
textual definition: The process of enriching a solution by partially freezing it and removing frozen material that contains less of the dissolved material than the remaining solution.
imported from: chmo.owl
has_exact_synonym: normal freezing
has_exact_synonym: progressive freezing
id: CHMO:0001637

filtration
type: Class
subclass of: purification
textual definition: The process of segregation of phases; the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.
imported from: chmo.owl
id: CHMO:0001640

micro-filtration
type: Class
subclass of: filtration
textual definition: A pressure-driven membrane-based separation process in which particles and dissolved macromolecules larger than 0.1 micrometre are rejected.
imported from: chmo.owl
has_exact_synonym: microfiltration
id: CHMO:0001641

nano-filtration
type: Class
subclass of: filtration
textual definition: A pressure-driven membrane-based separation process in which particles and dissolved macromolecules larger 200 Da are rejected.
imported from: chmo.owl
has_exact_synonym: NF
has_exact_synonym: nanofiltration
id: CHMO:0001642

reverse osmosis
type: Class
subclass of: filtration
textual definition: A separation process which involves using pressure to force a solution through a membrane, retaining the solute on one side and allowing the pure solvent to pass to the other side. (This is the reverse of the normal osmosis process, which is the natural movement of solvent from an area of low solute concentration, through a membrane, to an area of high solute concentration.)
imported from: chmo.owl
has_exact_synonym: RO
id: CHMO:0001643

suction filtration
type: Class
subclass of: filtration
textual definition: The separation of a solid phase from a liquid phase by passing the sample through a porous medium under pressure.
imported from: chmo.owl
has_exact_synonym: vacuum filtration
id: CHMO:0001644

ultra-filtration
type: Class
subclass of: filtration
textual definition: A separation process whereby a solution containing a solute of molecular size significantly greater than that of the solvent molecule is removed from the solvent by the application of hydraulic pressure which forces only the solvent to flow through a suitable membrane, usually having a pore size in the range 0.001–0.1 \μm.
imported from: chmo.owl
has_exact_synonym: UF
has_exact_synonym: ultrafiltration
id: CHMO:0001645

grinding
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting.
imported from: chmo.owl
has_exact_synonym: dry grinding
has_exact_synonym: milling
has_exact_synonym: solid-state grinding
has_exact_synonym: solvent-free grinding
id: CHMO:0001652

liquid-assisted grinding
type: Class
subclass of: grinding
textual definition: The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting in the presence of a small amount of solvent.
imported from: chmo.owl
has_exact_synonym: LAG
has_exact_synonym: solvent-drop grinding
id: CHMO:0001653

ball milling
type: Class
subclass of: grinding
textual definition: The mechanical reduction of the particle size of a solid sample by grinding with one or more inert balls (ceramic, flint, or stainless steel, 2–8 mm diameter) rotating around a horizontal axis.
imported from: chmo.owl
id: CHMO:0001654

high-speed ball milling
type: Class
subclass of: ball milling
textual definition: The mechanical reduction of the particle size of a solid sample by grinding with one or more inert balls (ceramic, flint or stainless steel, 2–8 mm diameter) rotating at high speed around a horizontal axis. A high-speed agitator is used to increase the speed of the balls.
imported from: chmo.owl
has_exact_synonym: HSBM
has_exact_synonym: high speed ball milling
id: CHMO:0001655

high-energy ball milling
type: Class
subclass of: ball milling
textual definition: The mechanical reduction of the particle size of a solid sample by grinding with one or more inert balls (ceramic, flint or stainless steel, 2–8 mm diameter) rotating at high speed (up to 650 rpm) around a horizontal axis. A high-speed agitator is used to increase the speed of the balls which are held in vacuum or in an inert gas (e.g. Ar).
imported from: chmo.owl
has_exact_synonym: HEBM
has_exact_synonym: high energy ball milling
id: CHMO:0001656

wet grinding
type: Class
subclass of: grinding
textual definition: The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting in the presence of a small amount of liquid (which is not a solvent for the solid).
imported from: chmo.owl
id: CHMO:0001657

mixing
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process μst not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system.
imported from: chmo.owl
id: CHMO:0001685

Ostwald ripening
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The growth of larger crystals from those of smaller size, which have a higher solubility than the larger ones.
imported from: chmo.owl
has_exact_synonym: Ostwald-ripening
id: CHMO:0001686

precipitation
type: Class
subclass of: sample solidification
textual definition: The sedimentation of a solid material (a 'precipitate') from a liquid solution in which the material is present in amounts greater than its solubility in the liquid.
imported from: chmo.owl
id: CHMO:0001688

affinity precipitation
type: Class
subclass of: precipitation
textual definition: The selective sedimentation of a solid material (a 'precipitate') from a liquid sample containing a ligand and a target protein. The precipitate evolves after the application of a suitable stimulus (e.g. Ca2+ or Ba2+).
imported from: chmo.owl
id: CHMO:0001689

co-precipitation
type: Class
subclass of: precipitation
textual definition: The simultaneous precipitation of a normally soluble component with a macro-component from the same solution by the formation of mixed crystals, by adsorption, occlusion or mechanical entrapment.
imported from: chmo.owl
has_exact_synonym: coprecipitation
id: CHMO:0001690

postprecipitation
type: Class
subclass of: precipitation
textual definition: The subsequent precipitation of a chemically different species upon the surface of an initial precipitate usually, but not necessarily, including a common ion.
imported from: chmo.owl
id: CHMO:0001696

reprecipitation
type: Class
subclass of: precipitation
textual definition: The planned repetition of a precipitation to remove impurities from a precipitate or improve its stoichiometry.
imported from: chmo.owl
id: CHMO:0001697

supercritical fluid method
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: Any material processing method that uses a supercritical fluid.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-03T09:36:47Z
id: CHMO:0001904

supercritical antisolvent technique
type: Class
subclass of: supercritical fluid method
textual definition: A solid sample is dissolved in a common (organic or inorganic) solvent then injected into a supercritical fluid (held under pressure) resulting in a large decrease in solution density. This effect leads to the reduction in solubility of the solid and precipitation.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-03T09:44:30Z
has_exact_synonym: SAS
has_exact_synonym: SF antisolvent process
has_exact_synonym: supercritical anti-solvent fractionation
has_exact_synonym: supercritical anti-solvent precipitation
has_exact_synonym: supercritical anti-solvent process
has_exact_synonym: supercritical antisolvent fractionation
has_exact_synonym: supercritical antisolvent precipitation
has_exact_synonym: supercritical fluid antisolvent process
id: CHMO:0001905

gas antisolvent technique
type: Class
subclass of: supercritical fluid method
textual definition: A technique where a solid sample is first partially dissolved in a organic solvent in a vessel. The solution is then pressurised with a dense gas or supercritical fluid resulting in precipitation of the solid as a fine powder.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-10T10:59:22Z
has_exact_synonym: GAS
has_exact_synonym: GAS recrystallisation
has_exact_synonym: GAS recrystallization
has_exact_synonym: GASP
has_exact_synonym: GASR
has_exact_synonym: gas anti-solvent precipitation
has_exact_synonym: gas anti-solvent reaction
has_exact_synonym: gas anti-solvent recrystallisation
has_exact_synonym: gas anti-solvent recrystallization
has_exact_synonym: gas antisolvent precipitation
has_exact_synonym: gas antisolvent reaction
has_exact_synonym: gas antisolvent recrystallisation
has_exact_synonym: gas antisolvent recrystallization
id: CHMO:0001945

precipitation with compressed antisolvent
type: Class
subclass of: supercritical antisolvent technique
textual definition: A technique where a solid sample is dissolved in a common (organic or inorganic) solvent then sprayed into a vessel pressurised with a dense gas (e.g. supercritical CO2) This results in a large decrease in solution density and precipitation.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-10T11:02:33Z
has_exact_synonym: precipitation using compressed anti-solvent
has_exact_synonym: precipitation using compressed antisolvent
has_exact_synonym: precipitation with compressed anti-solvent
has_related_synonym: PCA
id: CHMO:0001947

supercritical carbon dioxide drying
type: Class
subclass of: supercritical drying
textual definition: The removal of solvent from a sample without passing through the liquid–gas boundary, by immersion in supercritical CO2 and de-pressurisation.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-18T10:00:03Z
has_exact_synonym: CO2 critical point drying
has_exact_synonym: CO2 critical-point drying
has_exact_synonym: CO2 super-critical point drying
has_exact_synonym: supercritical CO2 drying
id: CHMO:0001987

ethanol extraction
type: Class
subclass of: solvent extraction
textual definition: The process of transferring a substance from any matrix into ethanol.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-18T10:18:25Z
has_exact_synonym: EtOH extraction
id: CHMO:0001989

sequential centrifugation
type: Class
subclass of: centrifugation
textual definition: A separation method where the components of a sample are separated on the basis of their density in a centrifuge according to the centrifugal force they experience. The sample is centrifuged in a number of separate, sequential steps.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-19T01:59:21Z
id: CHMO:0002011

low-speed centrifugation
type: Class
subclass of: centrifugation
textual definition: A separation method where the components of a sample are separated on the basis of their density in a centrifuge according to the centrifugal force they experience. Samples are spun at <5000 rpm.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-19T02:00:33Z
has_exact_synonym: low speed centrifugation
id: CHMO:0002012

preparative centrifugation
type: Class
subclass of: centrifugation
textual definition: A method where a sample is purified by removing impurities on the basis of their density in a centrifuge.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-19T02:05:24Z
id: CHMO:0002014

differential centrifugation
type: Class
subclass of: sequential centrifugation
textual definition: A separation method where the components of a cell are separated on the basis of their density in a centrifuge according to the centrifugal force they experience. The sample is centrifuged in a number of separate, sequential steps; each time the pellet is removed and the speed increased.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-19T02:10:04Z
id: CHMO:0002015

homogenisation
type: Class
subclass of: mixing
textual definition: The intensive mixing of μtually insoluble phases (sometimes with addition of surfactants) to obtain a soluble suspension or emulsion.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-06-19T02:29:46Z
has_exact_synonym: homogenation
has_exact_synonym: homogenization
id: CHMO:0002020

trituration
type: Class
subclass of: purification
textual definition: Purification of crude chemical compounds containing solid impurities where a solvent is chosen in which the desired product is insoluble and the undesired by-products are very soluble (or vice versa). The crude material is washed with the solvent and filtered away, leaving the purified product in solid form and any impurities in solution.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-01T02:42:13Z
id: CHMO:0002066

physical blending
type: Class
subclass of: mixing
textual definition: The process of making a polymer blend by mechanically mixing different polymers together in the melt.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-06T11:06:28Z
has_exact_synonym: mechanical mixing
id: CHMO:0002106

blow drying
type: Class
subclass of: sample drying
textual definition: The removal of solvent from a sample by the application of an inert gas or air.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-08T04:06:02Z
id: CHMO:0002124

deionisation method
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: The removal of ions from a solution using an ion-exchange method.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-13T01:17:32Z
has_exact_synonym: deionization
id: CHMO:0002157

Czochralski process
type: Class
subclass of: crystal growth method
textual definition: A method of producing large single crystals (of semiconductors or metals) by inserting a small seed crystal into a crucible filled with similar molten material, then slowly pulling the seed up from the melt while rotating it.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-13T01:35:58Z
id: CHMO:0002158

Verneuil process
type: Class
subclass of: crystal growth method
textual definition: A method for preparing synthetic gemstones. A finely powdered sample is melted in an hydrogen-oxygen flame (2000 °C) and crystallising the melted droplets on a boule (a single crystal).
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-13T01:37:26Z
has_exact_synonym: flame fusion
id: CHMO:0002159

Bridgeman technique
type: Class
subclass of: crystal growth method
textual definition: A method of growing a single crystal 'ingot' or 'boule'. The polycrystalline sample is heated in a container above its melting point and slowly cooled from one end where a seed crystal is located. Single crystal material is then progressively formed along the length of the container.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-13T01:43:03Z
has_exact_synonym: Bridgman technique
has_exact_synonym: Bridgman-Stockbarger technique
id: CHMO:0002160

recrystallisation
type: Class
subclass of: crystallisation
textual definition: A technique for purifying a crystalline sample where the impure sample is dissolved in a small volume of solvent, forming a supersaturated solution. As the temperature of the solution drops, pure crystals form, the impurities remaining dissolved in the solvent.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-22T09:23:11Z
has_exact_synonym: re-crystallisation
has_exact_synonym: re-crystallization
has_exact_synonym: recrystallization
id: CHMO:0002198

solvent evaporation
type: Class
subclass of: evaporation
textual definition: The removal of solvent from a sample, usually by the application of heat.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-24T02:31:03Z
has_exact_synonym: drying
id: CHMO:0002208

sample sublimation
type: Class
subclass of: purification
textual definition: Any technique used to purify a sample by forcing it to pass from the solid to gas phase without passing through an intermediate liquid phase.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T03:22:04Z
id: CHMO:0002217

fractional sublimation
type: Class
subclass of: sample sublimation
textual definition: A method for purifying samples by heating the sample under reduced pressure and allowing the fractions to sublime order of increasing sublimation temperature (a function of vapor pressure).
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T03:22:24Z
id: CHMO:0002218

vacuum sublimation
type: Class
subclass of: sample sublimation
textual definition: A technique for purifying solid samples by heating the sample under vacuum. The sample sublimes and the vapours condense as a purified compound on a cooled surface, leaving the non-volatile residue impurities behind.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T03:23:24Z
has_exact_synonym: vacuum-sublimation method
id: CHMO:0002219

high-vacuum sublimation
type: Class
subclass of: vacuum sublimation
textual definition: A technique for purifying solid samples by heating the sample under high vacuum (<0.1 Pa). The sample sublimes and the vapours condense as a purified compound on a cooled surface, leaving the non-volatile residue impurities behind.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T03:23:35Z
has_exact_synonym: high vacuum sublimation
id: CHMO:0002220

Lely method
type: Class
subclass of: crystal growth method
textual definition: A method for crystal growth where polycrystalline SiC lumps are carefully packed between two concentric graphite tubes. The inner tube is then withdrawn leaving a porous SiC layer inside the outer tube. The outer tube is then heated (~2500 °C) in Ar, causing the SiC powder to sublime and nucleate on a cooler surface.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T04:03:12Z
has_exact_synonym: Lely technique
id: CHMO:0002221

seeded sublimation
type: Class
subclass of: crystal growth method
textual definition: A technique for growing crystals of SiC by heating a source (polycrystalline SiC or powder) at high temperature (1800-2600 °C) and low pressure in an Ar atmosphere causing it to sublime. The vapours then condense on a single crystal of SiC (the 'seed').
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T03:25:09Z
has_exact_synonym: modified Lely method
has_exact_synonym: seed sublimation
has_exact_synonym: seeded sublimation method
has_exact_synonym: seeded sublimation technique
has_exact_synonym: seeded-sublimation growth technique
has_exact_synonym: seeded-sublimation method
has_exact_synonym: seeded-sublimation technique
id: CHMO:0002222

sandwich sublimation
type: Class
subclass of: seeded sublimation
textual definition: A technique for growing thick (micrometre) epitaxial layers of SiC by heating a source (polycrystalline SiC or powder) at high temperature (1800-2600 °C) and low pressure in an Ar atmosphere causing it to sublime. The vapours then condense on a single crystal of SiC (the 'seed') placed a few mm away.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T03:26:30Z
has_exact_synonym: SSM
has_exact_synonym: close space sublimation
has_exact_synonym: close-space sublimation
has_exact_synonym: sandwich sublimation method
has_exact_synonym: sandwich sublimation technique
has_exact_synonym: sandwich-sublimation method
has_exact_synonym: sublimation sandwich method
has_exact_synonym: sublimation-sandwich method
id: CHMO:0002223

crystal growth method
type: Class
subclass of: sample deposition
textual definition: Any synthesis method used to grow crystals.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T04:05:29Z
id: CHMO:0002224

Acheson method
type: Class
subclass of: crystal growth method
textual definition: A method for growing low-purity polycrystalline SiC. A mixture of silica, carbon, sawdust and NaCl is heated to 2700 °C in a furnace, and the temperature gradually decreased.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-28T04:20:26Z
has_exact_synonym: Acheson technique
id: CHMO:0002225

purification
type: Class
subclass of: separation method
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: purification objective
textual definition: Any technique used to physically separate an analyte from byproducts, reagents or contaminating substances.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-07-29T03:59:53Z
id: CHMO:0002231

solvent precipitation
type: Class
subclass of: precipitation
textual definition: The sedimentation of a solid material (a 'precipitate') from a liquid solution caused by the addition of an additional different solvent.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-09-28T11:52:22Z
id: CHMO:0002465

protein precipitation
type: Class
subclass of: precipitation
textual definition: The sedimentation of a solid protein (a 'precipitate') from an aqueous solution caused by the addition of an organic solvent (e.g. methanol), a polyelectrolyte (e.g. alginate) or a salt (e.g. ammonium sulfate) in a process known as 'salting out'.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-09-28T11:55:08Z
id: CHMO:0002466

vapour-phase extraction
type: Class
subclass of: extraction
textual definition: The process of transferring a substance from a vapour to a solid phase by passing the vapour sample through a stationary phase (e.g. silica particles) and then desorbing it using a desorbent or carrier gas.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-10-13T11:06:56Z
has_exact_synonym: vapor phase extraction
has_exact_synonym: vapor-phase extraction
has_exact_synonym: vapour phase extraction
id: CHMO:0002523

dual-phase extraction
type: Class
subclass of: extraction
textual definition: An extraction method for soil samples that uses a high-vacuum system to remove liquid and gas from low-permeability or heterogeneous soil. By removing water from the sample (liquid-phase extraction) the water table is lowered exposing the solid sample to vapor-phase extraction.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-10-13T11:10:28Z
has_exact_synonym: DPE
has_exact_synonym: bioslurping
has_exact_synonym: dual phase extraction
has_exact_synonym: multi-phase extraction
has_exact_synonym: multiphase extraction
has_exact_synonym: vacuum-enhanced extraction
id: CHMO:0002524

azeotropic distillation
type: Class
subclass of: distillation
textual definition: A method of separating mixtures based on differences in their volatilities in a boiling liquid mixture. An azeotrope (a mixture of two or more liquids which produces vapor with the same ratio of constituents as the original mixture) cannot be separated by normal distillation, therefore an additional third component (known as an 'entrainer') is added to the mixture. This has the effect of changing the volatility of one of liquids in the azeotrope to a greater extent than the other, allowing separation to occur.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2009-12-07T05:40:30Z
id: CHMO:0002634

chemical vapour transport
type: Class
subclass of: crystal growth method
textual definition: A crystal growth method for metal dichalcogenides in which the starting materials (high purity metal and chalcogen) are placed in a quartz ampoule together with a transport agent (e.g. iodine) and heated in a furnace under a temperature gradient.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2010-01-05T11:46:52Z
has_exact_synonym: CVT
has_exact_synonym: chemical vapor transport
id: CHMO:0002652

surface-assisted chemical vapour transport
type: Class
subclass of: chemical vapour transport
textual definition: A crystal growth method for metal dichalcogenides in which the starting materials (high-purity metal and chalcogen powders) are placed in one half of a quartz ampoule together with a transport agent (e.g. iodine) and heated in a furnace under a temperature gradient. The product crystals are grown on the surface of a sheet of high-purity metal in the other half of the ampoule.
imported from: chmo.owl
created by: https://orcid.org/0000-0001-5985-7429
creation date: 2010-01-05T11:50:07Z
has_exact_synonym: SA-CVT
has_exact_synonym: SACVT
has_exact_synonym: surface assisted CVT
has_exact_synonym: surface assisted chemical vapor transport
has_exact_synonym: surface assisted chemical vapour transport
has_exact_synonym: surface-assisted CVT
has_exact_synonym: surface-assisted chemical vapor transport
has_exact_synonym: surface-assisted chemical-vapor-transport
has_exact_synonym: surface-assisted chemical-vapour-transport
id: CHMO:0002653

elution
type: Class
subclass of: extraction
textual definition: A process wherein one material is extracted from another by interaction with a solvent.
imported from: chmo.owl
id: CHMO:0002742

sample heating
type: Class
subclass of: material processing
textual definition: A sample preparation step involving the increase in temperature of a sample.
imported from: chmo.owl
id: CHMO:0002770
comment: ought to be in OBI. Will put here pro tem.

concentrating
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: A preparative step where the concentration of one component is increased.
imported from: chmo.owl
id: CHMO:0002771

degassing
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: A preparative step involving the removal of dissolved gases from a sample.
imported from: chmo.owl
database_cross_reference: http://en.wikipedia.org/wiki/Degasification
has_exact_synonym: degasification
id: CHMO:0002772

dissolving
type: Class
subclass of: mixing
textual definition: A mixing step where a soluble component is mixed with a liquid component.
imported from: chmo.owl
id: CHMO:0002773

stirring
type: Class
subclass of: mixing
textual definition: Mixing involving the agitation of a solution through circular motion.
imported from: chmo.owl
id: CHMO:0002774

magnetic stirring
type: Class
subclass of: stirring
textual definition: Stirring achieved by rotating a magnetic stir bar in a solution.
imported from: chmo.owl
id: CHMO:0002775

spiking
type: Class
subclass of: material processing
textual definition: A material processing step that involves taking a test material with an adequately low background level of the intended analyte and mixing it with a known amount of analyte.
imported from: chmo.owl
id: CHMO:0002852

dispersive solid phase extraction
type: Class
subclass of: liquid-solid extraction
imported from: chmo.owl
has_exact_synonym: dispersive solid-phase extraction
id: CHMO:0002863

sample solidification
type: Class
subclass of: material processing
subclass of: unit operation in chemical processing
textual definition: Material processing in which a liquid or gas transitions into a solid.
imported from: chmo.owl
id: CHMO:0002916

sample quenching
type: Class
subclass of: material processing
textual definition: Material processing in which a sample is cooled by immersion in a fluid.
imported from: chmo.owl
id: CHMO:0002917

reaction property
type: Class
subclass of: process profile
imported from: fix.owl
has_obo_namespace: fix.ontology
id: FIX:0000277

Gibbs free energy change
type: Class
subclass of: thermodynamic reaction property
imported from: fix.owl
has_obo_namespace: fix.ontology
has_related_synonym: Gibbs energy change
id: FIX:0000279

Gibbs free energy of activation
type: Class
subclass of: thermodynamic reaction property
textual definition: The activation energy (Ea) of a reaction is the magnitude of the potential barrier (sometimes called the energy barrier) separating minima of the potential energy surface pertaining to the initial and final thermodynamic state. For a chemical reaction to proceed at a reasonable rate, the temperature of the system should be high enough such that there exists an appreciable number of molecules with translational energy equal to or greater than the activation energy.
definition source: [Wikipedia]
imported from: fix.owl
has_obo_namespace: fix.ontology
has_related_synonym: Gibbs energy of activation
id: FIX:0000280

redox reaction property
type: Class
subclass of: reaction property
imported from: fix.owl
has_obo_namespace: fix.ontology
has_related_synonym: oxidation-reduction reaction property
id: FIX:0000281

redox potential change
type: Class
subclass of: redox reaction property
subclass of: thermodynamic reaction property
imported from: fix.owl
has_obo_namespace: fix.ontology
has_related_synonym: oxidation-reduction potential change
id: FIX:0000285

kinetic reaction property
type: Class
subclass of: reaction property
imported from: fix.owl
has_obo_namespace: fix.ontology
id: FIX:0000368

thermodynamic reaction property
type: Class
subclass of: reaction property
imported from: fix.owl
has_obo_namespace: fix.ontology
id: FIX:0000369

molecular_function
type: Class
subclass of: process
editor preferred label: molecular_function
textual definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
imported from: go.owl
imported from: Ontology for Biomedical Investigations

catalytic activity
type: Class
subclass of: molecular_function
editor preferred label: catalytic activity
textual 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 Investigations

protein-containing complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: protein
editor preferred label: protein-containing complex
example of usage: A ribosome is a protein complex.
textual definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
alternative term: protein complex
imported from: go.owl
imported from: Ontology for Biomedical Investigations

DNA polymerase activity
type: Class
subclass of: catalytic activity
editor preferred label: DNA polymerase activity
textual definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
imported from: go.owl
imported from: Ontology for Biomedical Investigations

DNA polymerase complex
type: Class
subclass of: protein-containing complex
subclass of: enzyme
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: DNA polymerase activity
editor preferred label: DNA polymerase complex
textual definition: A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
imported from: go.owl
imported from: Ontology for Biomedical Investigations

measurement unit label
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
textual definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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: chmo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
id: IAO:0000005

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
has curation status: metadata incomplete
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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: chmo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
id: IAO:0000030

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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: chmo.owl
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
id: IAO:0000033

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
textual 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 Investigations

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

data about an ontology part
type: Class
subclass of: data item
editor preferred label: data about an ontology part
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations
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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: document
editor preferred label: document part
example of usage: An abstract, introduction, method or results section.
has curation status: metadata complete
textual definition: An information content entity that is part of a document.
term editor: PERSON: Lawrence Hunter
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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 Investigations

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

centrally registered identifier
type: Class
subclass of: information content entity
subclass of: identifier
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has curation status: metadata complete
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

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
textual 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: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

written name
type: Class
subclass of: textual entity
editor preferred label: written name
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
has curation status: pending final vetting
textual definition: A textual entity that denotes a particular in reality.
term editor: PERSON: Bill Hogan
definition source: https://github.com/information-artifact-ontology/IAO/issues/114
curator note: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
imported from: Information Artifact Ontology (IAO)
imported from: Ontology for Biomedical Investigations

identifier
type: Class
subclass of: information content entity
editor preferred label: identifier
textual definition: An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
imported from: Information Artifact Ontology (IAO)
imported from: pno.owl

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
textual definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: chmo.owl
imported from: Ontology for Biomedical Investigations
has_alternative_id: CHMO:0001840
id: OBI:0000011

reference substance role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
editor preferred label: reference substance role
example of usage: Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
has curation status: metadata complete
textual definition: a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
term editor: Person:Jennifer Fostel
alternative term: reference substance
definition source: OBI
imported from: Ontology for Biomedical Investigations

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
textual definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
imported from: Ontology for Biomedical Investigations

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
textual 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 Investigations
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
textual 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 Investigations

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
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
textual 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: Ontology for Biomedical Investigations
ISA alternative term: study assay
IEDB alternative term: any method

reagent role
type: Class
subclass of: ingredient role
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
textual 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 Investigations
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…
alternative label: reagent
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. [OBI]

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  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
textual definition: A planned process which results in physical changes in a specified input material
textual 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: chmo.owl
imported from: Ontology for Biomedical Investigations
has_alternative_id: CHMO:0001131
has_alternative_id: CHMO:0001267
has_alternative_id: CHMO:0001461
has_alternative_id: FIX:0000258
has_exact_synonym: material transformations
has_exact_synonym: preparative method
has_exact_synonym: sample preparation
has_exact_synonym: sample preparation step
has_exact_synonym: sample preparative method
id: OBI:0000094

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
textual 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 Investigations
ISA alternative term: study protocol

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
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
textual 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 Investigations

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
textual 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 Investigations

synthesizing function
type: Class
subclass of: function
editor preferred label: synthesizing function
has curation status: ready for release
textual definition: A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: Ontology for Biomedical Investigations

PCR product
type: Class
equivalent class: Class
  intersection of: double-stranded DNA
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: polymerase chain reaction
subclass of: double-stranded DNA
subclass of: amplified DNA
editor preferred label: PCR product
example of usage: PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
has curation status: ready for release
textual definition: is double stranded DNA that is the specified output of a polymerase chain reaction
editor note: We are using PCR and not the written out words, as this is the most common used.
term editor: GROUP: OBI BIomaterial Branch
definition source: GROUP: OBI BIomaterial Branch
imported from: Ontology for Biomedical Investigations

nucleic acid template role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: inheres in
  some values from: nucleic acid
subclass of: Restriction
  on property: realized in
  all values from: polymerase chain reaction
editor preferred label: nucleic acid template role
example of usage: a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
has curation status: metadata incomplete
textual definition: a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
imported from: Ontology for Biomedical Investigations

polymerase chain reaction
type: Class
subclass of: enzymatic amplification
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: synthesizing function
    intersection of: Restriction
      on property: inheres in
      some values from: DNA polymerase complex
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: PCR product
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: polymerase chain reaction
example of usage: Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
has curation status: metadata incomplete
textual definition: PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
term editor: OBI Plan
alternative term: PCR
definition source: adapted from wikipedai
imported from: Ontology for Biomedical Investigations

enzyme
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Class
    union of: ribonucleic acid
    union of: protein-containing 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-containing complex
    union of: Restriction
      on property: has part
      some values from: protein
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: realized in
      all values from: catalytic activity
subclass of: material entity
editor preferred label: enzyme
has curation status: pending final vetting
textual 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 Investigations

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
textual 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 Investigations

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
textual 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 Investigations

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
textual 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 Investigations

manufacturer role
type: Class
subclass of: role
alternative label: manufacturer
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. [OBI]
example: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. [OBI]
example: With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. [OBI]
example: With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. [OBI]

data set of predicted values according to fitted curve
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: curve fitting data transformation
subclass of: data set
editor preferred label: data set of predicted values according to fitted curve
has curation status: pending final vetting
textual definition: A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
imported from: Ontology for Biomedical Investigations

purification objective
type: Class
subclass of: objective specification
textual definition: The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest.
imported from: chmo.owl
id: OBI:0000796

amplified DNA
type: Class
equivalent class: Class
  intersection of: deoxyribonucleic acid
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: enzymatic amplification
subclass of: deoxyribonucleic acid
subclass of: processed material
editor preferred label: amplified DNA
example of usage: Amplied DNA created by PCR
has curation status: ready for release
textual definition: DNA that has been produced in an enzymatic amplification process
term editor: PERSON: Alan Ruttenberg
definition source: Alan Ruttenberg
imported from: Ontology for Biomedical Investigations

device
type: Class
subclass of: portion of material
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
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
textual 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: chmo.owl
imported from: Ontology for Biomedical Investigations
has_alternative_id: CHMO:0000998
id: OBI:0000968

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
textual 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 Investigations

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
textual 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 Investigations

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
textual 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 Investigations

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
textual 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 Investigations

pipette
type: Class
subclass of: device
editor preferred label: pipette
has curation status: metadata complete
textual definition: A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser.
term editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://en.wikipedia.org/wiki/Pipette
imported from: Ontology for Biomedical Investigations

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
  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
textual 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 Investigations

curve fitting data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: data set of predicted values according to fitted curve
  union of: Restriction
    on property: achieves_planned_objective
    some values from: curve fitting objective
subclass of: data transformation
editor preferred label: curve fitting data transformation
has curation status: ready for release
textual definition: A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Curve_fitting
imported from: Ontology for Biomedical Investigations

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
textual 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 Investigations

curve fitting objective
type: Class
subclass of: data transformation objective
editor preferred label: curve fitting objective
has curation status: pending final vetting
textual definition: A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
imported from: Ontology for Biomedical Investigations

centrifugation
type: Class
subclass of: material component separation
textual definition: A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation.
imported from: chmo.owl
has_alternative_id: CHMO:0001047
has_alternative_id: FIX:0000259
has_alternative_id: FIX:0000260
id: OBI:0302886

washing
type: Class
subclass of: elution
textual definition: Washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
imported from: chmo.owl
has_exact_synonym: rinsing
id: OBI:0302888

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
textual 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 Investigations

material component separation
type: Class
subclass of: material processing
textual definition: A material processing in which components of an input material become segregated in space.
imported from: chmo.owl
id: OBI:0600014

enzymatic amplification
type: Class
subclass of: material processing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: inheres in
      some values from: enzyme
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: nucleic acid template role
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: enzymatic amplification
example of usage: the use of a polymerase chain reaction to amplify a fragment of DNA
has curation status: pending final vetting
textual definition: the use of enzymes to increase the number of molecules of a biomaterial
term editor: PERSON:Kevin Clancy
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigations

quality
type: Class
subclass of: quality
textual definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
imported from: pato.owl
OBO foundry unique label: quality (PATO)
has_alternative_id: PATO:0000072
has_obo_namespace: quality
id: PATO:0000001

concentration of
type: Class
subclass of: molecular quality
textual definition: A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
imported from: pato.owl
has_exact_synonym: concentration
has_obo_namespace: quality
id: PATO:0000033
in_subset: attribute slim
in_subset: relational slim
in_subset: scalar slim

morphology
type: Class
subclass of: quality
textual definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000051
in_subset: attribute slim

length
type: Class
subclass of: morphology
textual definition: A 1-D extent quality which is equal to the distance between two points.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000122
in_subset: attribute slim
in_subset: mpath slim
in_subset: scalar slim

mass
type: Class
subclass of: quality
textual definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000125
in_subset: attribute slim
in_subset: relational slim
in_subset: scalar slim

symmetry
type: Class
subclass of: morphology
textual definition: A pattern quality of inhering in a bearer by virtue of the correspondence in size, shape, and relative position of the bearer's parts on opposite sides of a dividing line or median plane or about a center or axis.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000965
in_subset: attribute slim

solubility
type: Class
subclass of: molecular quality
textual definition: A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001536
in_subset: attribute slim
in_subset: disposition slim
in_subset: relational slim
in_subset: scalar slim

flow rate
type: Class
subclass of: quality
textual definition: A physical quality inhering in a bearer by virtue of the bearer's motion characteristic.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001574
in_subset: attribute slim
in_subset: scalar slim

molecular quality
type: Class
subclass of: quality
textual definition: A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
imported from: pato.owl
created by: George Gkoutos
creation date: 2010-03-10T03:18:15Z
has_alternative_id: PATO:0002061
has_exact_synonym: relational molecular quality
has_obo_namespace: quality
id: PATO:0002182

synthetic chemical process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: synthesizing function
subclass of: Restriction
  on property: has_specified_input
  some values from: starting material for synthesis
subclass of: Restriction
  on property: has_specified_output
  some values from: chemical product
textual definition: Synthesis is a planned material process that combines, changes or converts material to produce a new material. [Allotrope]
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

Plackett–Burman design
type: Class
subclass of: experimental design
textual definition: An experimental design to limit the number of experiments covering the space by assuming the Interactions between the factors are negligible
definition source: [PROCO]

prior art
type: Class
subclass of: information content entity
textual definition: All information that has been made available to the public in any form before a given date that might be relevant to a patent's claims of originality.
definition source: [wikipedia]

design space
type: Class
subclass of: directive information entity
textual definition: A direct information entity that describes the multidimensional combination and interaction of input variables (e.g., material attributes) and process parameters that have been demonstrated to provide assurance of quality. Working within the design space is not considered as a change. Movement out of the design space is considered to be a change and would normally initiate a regulatory post-approval change process. Design space is proposed by the applicant and is subject to regulatory assessment and approval.
definition source: [ICH Q8(R2)]

factor
type: Class
subclass of: data item
textual definition: A data item that is a member of a minimal set of independent variables that can be used to model the dependent reponses in a set of related experiments.
term editor: W Schafer
definition source: [wikipedia]

equation
type: Class
subclass of: information content entity
textual definition: An information content entity that asserts the equality of two expressions.
definition source: [Wikipedia]

factorial design
type: Class
subclass of: experimental design
textual definition: An experimental design consisting of two or more factors, each with discrete possible values or "levels", and whose experimental units take on all or a subset of the possible combinations of these levels across all such factors.
definition source: [wikipedia]

route scouting
type: Class
subclass of: route related process
subclass of: Restriction
  on property: part of
  some values from: chemical process development
textual definition: A process of systematically selecting possible synthetic routes to make a particular product or intermediate.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

route selection milestone
type: Class
subclass of: process boundary
textual definition: A process boundary that represents a milestone decision on route selection.
term editor: Wes, Oliver
definition source: [PROCO]

reaction process profile
type: Class
subclass of: process profile
subclass of: Restriction
  on property: is about
  some values from: synthetic chemical process
textual definition: A process profile that tracks some aspect of a reaction.
definition source: [PROCO]

synthesis reaction time
type: Class
subclass of: temporal region
textual definition: A temporal region that describes the length of time that a synthesis occurs.
term editor: W Schafer
definition source: [PROCO]

critical quality attribute
type: Class
subclass of: quality
textual definition: A physical, chemical, biological, or microbiological property or characteristic that should be within an appropriate limit, range, or distribution to ensure the desired product quality.
alternative term: CQA
definition source: [ICH Q8(R2)]

experiment
type: Class
subclass of: investigation
textual definition: An investigation carried out to support or refute a hypothesis. Experiments provide insight into cause-and-effect by demonstrating what outcome occurs when a particular factor is manipulated.
definition source: [Wikipedia]

process profile specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: SIO_000338
  some values from: process profile
textual definition: A directive information entity that specifies allowed ranges recorded for a process profile.
definition source: [PROCO]

critical process parameter specification
type: Class
subclass of: process profile specification
subclass of: Restriction
  on property: SIO_000338
  some values from: Class
    intersection of: critical process parameter
    intersection of: Restriction
      on property: profile of
      some values from: quality
textual definition: A process profile specification that is associated with a critical process parameter (CPP). Critical process parameters (CPPs) in pharmaceutical manufacturing are key variables affecting the production process.
term editor: Wes, Oliver
alternative term: CPP specification
definition source: https://en.wikipedia.org/wiki/Critical_process_parameters
comment: CPP 'has facet' some specification (note: like has part, but it is for info).

quality specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: SIO_000338
  some values from: Class
    intersection of: quality
    intersection of: Restriction
      on property: bearer of
      some values from: material entity
textual definition: A directive information entity that species the acceptable range of values associated with a material quality
term editor: W Schafer
definition source: [PROCO]

CQA specification
type: Class
subclass of: quality specification
subclass of: Restriction
  on property: SIO_000338
  some values from: critical quality attribute
textual definition: A quality specification set against a critical quality attribute of a material
definition source: [PROCO]

chemical product
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: synthetic chemical process
    intersection of: Restriction
      on property: has role
      some values from: product role
textual definition: A chemical entity that is the end point product generated from a synthetic chemical process.
term editor: Oliver He, Wes Schafer
definition source: https://en.wikipedia.org/wiki/Product_(chemistry)

commercial chemical product
type: Class
subclass of: chemical product
textual definition: A chemical product that is used for commercial purpose.
term editor: Oliver, Wes
definition source: [PROCO]

temperature profile in synthesis process
type: Class
subclass of: quality process profile
textual definition: A process profile that is about temperature.
term editor: Oliver, Wes
definition source: [PROCO]

starting material for synthesis
type: Class
equivalent class: Restriction
  on property: has role
  some values from: starting material role
subclass of: chemical entity
textual definition: A chemcial entity with the role starting material in a synthesis.
definition source: [PROCO]

intermediate material for synthesis
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: RO_0002353
  some values from: synthetic chemical process
textual definition: A chemical entity that is the product of a chemical reaction but not the last step in a synthesis.
definition source: [PROCO]

chemical impurity
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: RO_0002353
  some values from: synthetic chemical process
textual definition: Chemical substance that is inside a confined amount of liquid, gas, or solid, and differs from the chemical composition of the material or compound. Impurities are either naturally occurring or added during synthesis of a chemical or commercial product. During production, impurities may be purposely, accidentally, inevitably, or incidentally added into the substance.
term editor: Oliver He, Wes Schafer
definition source: [Wikipedia]
definition source: https://en.wikipedia.org/wiki/Impurity

GMP starting material
type: Class
subclass of: starting material for synthesis
textual definition: A raw material, intermediate, or an AP chemical entity that is used in the production of an API and that is incorporated as a significant structural fragment into the structure of the API.
definition source: [ICH Q7]

GMP synthetic process
type: Class
subclass of: synthetic chemical process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: GMP specification of synthetic process
subclass of: Restriction
  on property: has_specified_output
  some values from: chemical product
textual definition: A synthetic process governed by the cGMP regulations.
term editor: Wes Schafer, Oliver He
alternative term: commercial synthetic process
definition source: [PROCO]

temperature measurement
type: Class
subclass of: process monitoring
textual definition: A process measurement of the temperature in a process
term editor: Wes, Oliver
definition source: [PROCO]

charging material
type: Class
subclass of: unit operation in chemical processing
textual definition: A unit operation of adding a reagent or starting material to a chemical reaction
term editor: Wes, Oliver
alternative term: inserting material
definition source: [PROCO]

GLP synthetic process
type: Class
subclass of: synthetic chemical process
textual definition: A synthetic process governed by the GLP regulations.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

GMP specification of synthetic process
type: Class
subclass of: route specification
textual definition: A plan specification that specifies the action and objective of a synthetic process, as defined in CFR - Code of Federal Regulations Title 21.
term editor: Wes, Oliver
definition source: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm

stir rate profile
type: Class
subclass of: quality process profile
subclass of: Restriction
  on property: profile of
  some values from: stirring
textual definition: A process profile that represents the number of revolution of stirs given a specific time period
term editor: Wes, Oliver
alternative term: stirring profile in synthesis process
definition source: [PROCO]

material flow profile in synthesis process
type: Class
subclass of: quality process profile
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: flow rate
    intersection of: Restriction
      on property: inheres in
      some values from: portion of material
textual definition: A process profile in synthesis process that is about material flow
term editor: Oliver, Wes
definition source: [PROCO]

process chemistry filing
type: Class
subclass of: planned process
subclass of: Restriction
  on property: RO_0002180
  some values from: critical process parameter specification
textual definition: A planned process.
term editor: Wes, Oliver
definition source: [PROCO]

quality process profile
type: Class
subclass of: process profile
textual definition: A process profile that tracks the quality of some process participant.
definition source: [PROCO]

reaction rate profile
type: Class
subclass of: reaction process profile
textual definition: Reaction rate is the rate of the changing concentration of a product during a reaction process.
term editor: Wes, Oliver
definition source: https://en.wikipedia.org/wiki/Reaction_rate

filtering
type: Class
subclass of: unit operation in chemical processing
textual definition: A unit operation to remove portions of material from a synthesis stream by trapping it on a filter.
term editor: Wes, Oliver
definition source: [PROCO]

unit operation in chemical processing
type: Class
subclass of: planned process
textual definition: A basic and unit step in a process
alternative term: unit operation
definition source: https://en.wikipedia.org/wiki/Unit_operation
comment: Unit operations involve a physical change or chemical transformation such as separation, crystallization, evaporation, filtration, polymerization, isomerization, and other reactions. For example, in milk processing, homogenization, pasteurization, and packaging are each unit operations which are connected to create the overall process. A process may require many unit operations to obtain the desired product from the starting materials, or feedstocks.

crystallization
type: Class
subclass of: unit operation in chemical processing
subclass of: Restriction
  on property: RO_0002234
  some values from: crystalline solid
textual definition: A process that has as a material output a crystalline solid or a mixture that has as an ingredient a crystalline solid.
term editor: Wes Schafer, Oliver He
alternative term: crystallization
definition source: https://en.wikipedia.org/wiki/Crystallization
comment: The formation of a crystalline solid from a solution, melt vapour, or a different solid phase, generally by lowering the temperature or by evaporation of a solvent. [CHMO]
comment: Wes and Oliver: This term is currently defined as a planned process term although crystallization may occur in nature. Here we use to term to represent those synthetic chemical process processes that are man made and planned.

process mass intensity
type: Class
subclass of: process chemistry datum
textual definition: The process mass intensity (PMI) calculates the ratio of the total mass of materials to the mass of the isolated product
alternative term: PMI
definition source: [wikipedia]
definition source: https://en.wikipedia.org/wiki/Process_chemistry

polymer
type: Class
subclass of: chemical entity
textual definition: A substance or material consisting of very large molecules, or macromolecules, composed of many repeating subunits.
definition source: https://en.wikipedia.org/wiki/Polymer

impurity fate and purge determination
type: Class
subclass of: process validation
textual definition: A process that determines the fate of impurities (organic, inorganic, elemental, or residual solvents) of pharmaceutical substances produced by chemical syntheses to ensure the desired product quality, and the ability of the synthetic route to purge them.
term editor: Wes, Oliver
alternative term: fate and purge
alternative term: fate and purge of impurity
definition source: [PROCO]

route specification
type: Class
subclass of: plan specification
textual definition: A sequenced plan of synthetic steps and defined intermediates to make a specific product from commercially available starting materials
term editor: Wes, Oliver
definition source: [PROCO]

synthetic step specification
type: Class
subclass of: action specification
textual definition: A sequenced set of unit operations for a single synthetic reaction or simultaneous reactions that are executed in a single equipment train.
term editor: Wes, Oliver
definition source: [PROCO]
comment: https://www.chemistryworld.com/opinion/what-counts-as-a-step-during-chemical-synthesis/2500261.article#/

product filing milestone
type: Class
subclass of: process boundary
textual definition: A process boundary that represents a milestone of filing the documentation required to obtain regulatory approval to sell a new product.
term editor: Wes, Oliver
definition source: [PROCO]

fate of impurity
type: Class
subclass of: disposition
subclass of: process chemistry datum
textual definition: A process chemistry datum describing the ultimate final state and location of an impurity in a synthetic process.
definition source: [PROCO]

rate constant
type: Class
subclass of: kinetic constant
textual definition: Numerical parameter that quantifies the velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants.
term editor: Anna Dunn

mathematical constant
type: Class
subclass of: data item
textual definition: A fixed and well-defined number or other non-varying mathematical object.
definition source: [Wikipedia]

kinetic order
type: Class
subclass of: kinetic constant
textual definition: A constant representing the concentration driving force
term editor: Anna Dunn
alternative term: order

antisolvent role
type: Class
subclass of: chemical role
textual definition: The role of a solvent in a precipitation or crystallization in which the solute of a solution is sparingly soluble to induce its solidification.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

seed role
type: Class
subclass of: chemical role
textual definition: The role of a crystalline solid material input in a crystallization to promote nucleation or crystal growth.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]
comment: A seed crystal is a small piece of single crystal or polycrystal material from which a large crystal of typically the same material is to be grown in a laboratory. Used to replicate material, the use of seed crystal to promote growth avoids the otherwise slow randomness of natural crystal growth and allows manufacture on a scale suitable for industry [wikipedia].

precipitate role
type: Class
subclass of: chemical role
textual definition: The role of solids in a slurry
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

slurry
type: Class
subclass of: material entity
textual definition: A suspension (AFM_0000442) that is a mix of solids in a liquid
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

crystalline state
type: Class
subclass of: chemical substance quality
textual definition: A physical quality indicating the structural order of a solid in which its atoms or molecules are arranged in a regular, periodic manner.[wikipedia]
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

purge factor
type: Class
subclass of: process chemistry datum
textual definition: A process chemistry datum that quantifies the ratio of the amount of an impurity in the waste stream of a process to that retained in the product stream.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

crystallization yield
type: Class
subclass of: process chemistry datum
textual definition: A process chemistry datum quantifying the ratio of the mass of desired compound recovered as crystalline material from a crystallization to mass of compound input into the crystallization.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

mother liquor role
type: Class
subclass of: chemical role
textual definition: A debris role of the solution in a slurry resulting from a crystallization
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

crystalline solid
type: Class
subclass of: chemical entity
textual definition: A solid with at least one crystalline phase
definition source: [PROCO]

process environmental factor
type: Class
subclass of: process chemistry datum
textual definition: A process chemistry datum quantifying the environmental impact of a synthetic reaction, and is computed by the ratio of the total mass of waste generated in the synthetic scheme to the mass of product isolated.
alternative term: E-factor
alternative term: environmental factor
definition source: https://en.wikipedia.org/wiki/Process_chemistry

process excellence index
type: Class
subclass of: process chemistry datum
textual definition: The process excellence index (PEI) is a measure of process reproducibility where the robustness of the procedure is evaluated in terms of yield and cycle time of various operations.
alternative term: PEI
definition source: [wikipedia]
definition source: https://en.wikipedia.org/wiki/Process_chemistry

quality service level
type: Class
subclass of: process chemistry datum
textual definition: The quality service level (QSL) is a measure of the reproducibility of the quality of the isolated intermediate or final API, and its calculation involves the ratio of satisfactory quality batches to the total number of batches. A reasonable QSL target is 98 to 100 percent.
alternative term: QSL
definition source: https://en.wikipedia.org/wiki/Process_chemistry

chemical process development
type: Class
subclass of: planned process
textual definition: A planned process with data output of commercial synthetic chemical route.
term editor: Wes, Oliver
definition source: [PROCO]

drug product filing milestone
type: Class
subclass of: product filing milestone
textual definition: A process boundary that represents a milestone of filing the documentation required to obtain regulatory approval to sell a new drug product.
term editor: Wes, Oliver
definition source: [PROCO]

route development optimization
type: Class
subclass of: route related process
subclass of: Restriction
  on property: is about
  some values from: route specification
textual definition: A planned process that is about optimizing a synthetic route.
term editor: Wes, Oliver
alternative term: development optimization
alternative term: process optimization
definition source: [PROCO]

route validation
type: Class
subclass of: process validation
subclass of: route related process
textual definition: A planned process producing data to demonstrate that a commercial route meets regulatory requirements.
term editor: Wes, Oliver
definition source: [PROCO]

reaction screening design
type: Class
subclass of: screening design
subclass of: Restriction
  on property: SIO_000338
  some values from: Class
    intersection of: multi-parallel experimentation
    intersection of: Restriction
      on property: SIO_000229
      some values from: synthetic chemical process
textual definition: A screening design to evaluate possible chemical reactions
term editor: Wes, Oliver
definition source: [PROCO]

route selection
type: Class
subclass of: route related process
subclass of: Restriction
  on property: RO_0002230
  some values from: route selection milestone
textual definition: A process that ends with a milestone where a selection will be made on route process.
term editor: Wes, Oliver
definition source: [PROCO]

mechanistic and kinetic determination
type: Class
subclass of: process chemistry workflow plan
textual definition: Chemical kinetics includes investigations of how experimental conditions influence the speed of a chemical reaction and yield information about the reaction's mechanism and transition states, as well as the construction of mathematical models that also can describe the characteristics of a chemical reaction.
term editor: Wes, Oliver
definition source: [wikipedia]

process validation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: SIO_000229
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: part of
      some values from: Class
        union of: design space
        union of: risk assessment
textual definition: A planned process of demonstrating that a process produces product of adequate quality and yield through the definition of the design space or risk assessments.
term editor: Wes, Oliver
definition source: [PROCO]

polymorph and solvate screening design
type: Class
subclass of: screening design
textual definition: A screening design to discover polymorphs and solvates of a compound
term editor: Wes, Oliver
definition source: [PROCO]

screening design
type: Class
subclass of: process chemistry workflow plan
subclass of: Restriction
  on property: SIO_000338
  some values from: multi-parallel experimentation
textual definition: A process chemistry workflow plan that specifies how a multi-parallel screening study should be conducted.
term editor: Wes, Oliver
definition source: [PROCO]

batch campaign
type: Class
subclass of: planned process
textual definition: A planned process of manufacturing one or more batches of a product in unbroken succession. It includes equipment turnover and cleaning can include dry-runs before committing the starting materials.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

process chemistry workflow plan
type: Class
subclass of: plan specification
textual definition: A plan specification that specifies a process chemistry workflow consisting of a series of unit operations.
term editor: Wes, Oliver
definition source: [PROCO]

review of prior art
type: Class
subclass of: investigation
textual definition: An investigation of published material to find prior art related to a synthetic route
term editor: Wes, Oliver
definition source: [PROCO]

product filing documentation
type: Class
subclass of: document
textual definition: A document to secure permission or continuing permission to market a product from a regulatory body.
definition source: [PROCO]

route related process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: is about
  some values from: route specification
textual definition: A planned process about a synthetic route
term editor: Wes, Oliver
definition source: [PROCO]

process monitoring
type: Class
subclass of: planned process
textual definition: A planned process of measuring a quality of a material associated with a process.
term editor: Wes, Oliver
definition source: [PROCO]

pressure measurement
type: Class
subclass of: process monitoring
textual definition: A process measurement of the pressure in a process
term editor: Wes, Oliver
definition source: [PROCO]

end reaction monitoring
type: Class
subclass of: process monitoring
textual definition: A process monitoring to determine when a chemical reaction has ended.
term editor: Wes, Oliver
definition source: [PROCO]

product approval milestone
type: Class
subclass of: process boundary
textual definition: A process boundary that represents a milestone of obtaining regulatory approval to sell a new product.
term editor: Wes, Oliver
definition source: [PROCO]

drug product approval milestone
type: Class
subclass of: product approval milestone
textual definition: A process boundary that represents a milestone of obtaining regulatory approval to sell a new drug product.
term editor: Wes, Oliver
definition source: [PROCO]

method of flooding
type: Class
subclass of: integral kinetic measurement
textual definition: A kinetic determination method to determine the partial order of a reactant by measuring the concentration of that reactant with all other reactants in large excess
alternative term: Ostwald kinetic method
alternative term: isolation kinetic method
definition source: [PROCO]

induction period
type: Class
subclass of: temporal region
textual definition: A temporal region of initial kinetics of a chemical reaction after which the reaction accelerates.
definition source: [Wikipedia]
note: In some catalytic reactions, a pre-catalyst needs to undergo a transformation to form the active catalyst, before the catalyst can take effect. Time is required for this transformation, hence the induction period. Similarly, for an autocatalytic reaction, where one of the reaction products catalyzes the reaction itself, the rate of reaction is low initially until sufficient products have formed to catalyze the reaction. Reactions generally accelerate when heat is applied. Where a reaction is exothermic, the rate of the reaction may initially be low. As the reaction proceeds, heat is generated, and the rate of reaction increases. This type of reaction often exhibits an induction period as well. The reactions to form Grignard reagents are notorious for having induction periods. This is usually due to two reasons: Firstly, the thin film of oxide on the magnesium reagent must be removed before the bulk magnesium can react. Secondly, Grignard reactions, while exothermic, are typically conducted at low temperature for better selectivity. For these two reasons, Grignard reactions often can have a long induction period, followed by a thermal runaway, even causing the reaction solvent to boil-off.

assessed reactivity purge factor
type: Class
subclass of: process profile
subclass of: purge factor
textual definition: The assessed reactivity of the mutagenic impurity in the processing conditions
definition source: [PROCO]

assessed solubility purge factor
type: Class
subclass of: purge factor
subclass of: Restriction
  on property: is about
  some values from: solubility
textual definition: An assessed purge factor based on the solubility of the impurity in the reaction solvent and therefore its propensity to be purged in the mother liquors of steps that involve an isolation of the solid intermediate/product in that step.
definition source: [PROCO]

unit cell quality
type: Class
subclass of: quality
textual definition: A molecular quality that describes the unit cell of the crystal lattice
term editor: W Schafer
definition source: [PROCO]

space group
type: Class
subclass of: symmetry
subclass of: unit cell quality
textual definition: a symmetry quality of a unit cell in three-dimensional space.
editor note: similar to http://purl.enanomapper.org/onto/ENM_9000037
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

point symmetry
type: Class
subclass of: symmetry
textual definition: a geometric symmetry that keeps at least one point fixed
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

polar point symmetry
type: Class
subclass of: point symmetry
textual definition: a point symmetry that contains a polar axis.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

centrosymmetric point symmetry
type: Class
subclass of: point symmetry
textual definition: a point symmetry in which the original structure can be obtained by reflecting all lattice points through a single point.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

non-centrosymmetric point symmetry
type: Class
subclass of: point symmetry
textual definition: a point symmetry of a structure that is not identical to any inversion of that structure created by reflecting all of its points through a single point.
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

enantiomorphic point symmetry
type: Class
subclass of: non-centrosymmetric point symmetry
textual definition: a non-centrosymmetric point symmetry that cannot be rotated to align with the original structure (chiral).
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

non-centrosymmetric achiral symmetry
type: Class
subclass of: non-centrosymmetric point symmetry
textual definition: a non-centrosymmetric point symmetry that can be rotated to align with the original structure (achiral).
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

unit cell a-axis length
type: Class
subclass of: unit cell quality
textual definition: the length of the a-axis of a unit cell
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

unit cell b-axis length
type: Class
subclass of: unit cell quality
textual definition: the length of the b-axis of a unit cell
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

unit cell c-axis length
type: Class
subclass of: unit cell quality
textual definition: the length of the c-axis of a unit cell
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

unit cell
type: Class
subclass of: portion of material
textual definition: The smallest, regularly repeating material portion of a crystalline lattice
term editor: Wes Schafer, Oliver He
definition source: [PROCO]

cubic unit cell
type: Class
subclass of: unit cell
textual definition: A unit cell that has three perpendicular axes of equal lengths. equivalent to ENM:9000035
alternative term: isometric unit cell
definition source: [PROCO]

tetragonal unit cell
type: Class
subclass of: unit cell
textual definition: A unit cell that has three perpendicular axes, two of equal length
definition source: [PROCO]

orthorhombic unit cell
type: Class
subclass of: unit cell
textual definition: A unit cell that has three perpendicular axes, all of different lengths
definition source: [PROCO]

hexagonal unit cell
type: Class
subclass of: unit cell
textual definition: A unit cell of three equal lateral axes intersecting at angles of 60 degrees and a vertical axis of variable length at right angles
definition source: [PROCO]

trigonal unit cell
type: Class
subclass of: unit cell
textual definition: A unit cell of three equal lateral axes intersecting at the same angle but not perpendicularly
definition source: [PROCO]

monoclinic unit cell
type: Class
subclass of: unit cell
textual definition: A unit cell that has three axes of unequal length, two of which are perpendicular
definition source: [PROCO]

triclinic unit cell
type: Class
subclass of: unit cell
textual definition: A unit cell in which all axes are of different length and no angle is perpendicular nor equal to any other angles.
definition source: [PROCO]

unit cell alpha internal angle
type: Class
subclass of: unit cell quality
textual definition: A unit cell quality describing the angle between the b and c axes.
definition source: [PROCO]

unit cell beta internal angle
type: Class
subclass of: unit cell quality
textual definition: A unit cell quality describing the angle between the a and c axes.
definition source: [PROCO]

unit cell gamma internal angle
type: Class
subclass of: unit cell quality
textual definition: A unit cell quality describing the angle between the a and b axes.
definition source: [PROCO]

unit cell volume
type: Class
subclass of: unit cell quality
textual definition: The volume of the unit cell
definition source: [PROCO]

unit cell Z value
type: Class
subclass of: unit cell quality
textual definition: A unit cell quality indicating the number of formula units (molecules) in the unit cell
definition source: [PROCO]

unit cell Z' value
type: Class
subclass of: unit cell quality
textual definition: A unit cell quality indicating the number of asymmetric units in the unit cell. It is equal to the Z value divided by the lowest Wycoff position multiplicity
definition source: [PROCO]

unit cell crystal density
type: Class
subclass of: unit cell quality
textual definition: A unit cell quality indicating the density of the compound in the unit cell
definition source: [PROCO]

ICH Guideline
type: Class
subclass of: directive information entity
textual definition: A directive information entity issued by the International Conference on Harmonization of Technical Requirements for the Registration of Pharmaceuticals for Human Use with the objective of achieving greater harmonisation worldwide to ensure that safe, effective and high quality medicines are developed, and registered and maintained across the world in the most resource efficient manner whilst meeting high standards. [ICH]
definition source: [PROCO]

habit
type: Class
subclass of: morphology
textual definition: A description of one of the characteristic external shapes (crystal class / point group) of an individual crystal family / system. Factors that impact growth rates on the various crystal faces produce different shapes but possess the same set of symmetry elements as parent crystal class.
definition source: [PROCO]

thermodynamic phase
type: Class
subclass of: portion of material
textual definition: A portion of material within a a region of space in a system throughout which all physical properties of the material are essentially uniform.
definition source: [Wikipedia]

crystalline solid thermodynamic phase
type: Class
subclass of: thermodynamic phase
textual definition: A crystalline phase is a single solid crystalline thermodynamic phase
definition source: [PROCO]

solid solution
type: Class
subclass of: portion of material
textual definition: A solid in solid solution is a solution where the continuous phase is a solid and the dispersed phase is a solid. [Allotrope]
definition source: [Allotrope]

molecular complex
type: Class
subclass of: object aggregate
textual definition: An object aggregate of two or more molecular entities that does not include covalent or ionic interactions
definition source: [PROCO]

co-crystal
type: Class
subclass of: molecular complex
textual definition: A co-crystal is a solid solution and a molecular complex with two or more non-solvent molecules incorporated into the unit cell in a stoichiometric amount.
definition source: [PROCO]

solvate
type: Class
subclass of: molecular complex
textual definition: A solvate is a crystalline material that has solvent molecules incorporated into the crystal lattice in a stoichiometric amount. [Allotrope]
definition source: [Allotrope]

hydrate
type: Class
subclass of: solvate
textual definition: A hydrate is a solvate that has water as the solvent adduct.
definition source: [PROCO]

ionic salt
type: Class
subclass of: solid solution
textual definition: A chemical substance composed of ions held together by electrostatic forces termed ionic bonding.
definition source: [Wikipedia]

anhydrous phase
type: Class
subclass of: crystalline solid thermodynamic phase
textual definition: A crystalline phase without solvent in the unit cell
definition source: [PROCO]

isomorphic desolvate
type: Class
subclass of: anhydrous phase
textual definition: An anhydrous crystalline phase formed experimentally by removing the solvent from a solvate
definition source: [PROCO]

eutectic
type: Class
subclass of: heterogeneous mixture
subclass of: crystalline solid
textual definition: A heterogeneous ensemble of individual components whose crystal structures are like discontinuous solid solutions (phase separated).
definition source: [PROCO] Chem. Commun., 2014, 50, 906

concomitant polymorphs
type: Class
subclass of: heterogeneous mixture
subclass of: crystalline solid
textual definition: A heterogeneous solid solution consisting of two or more polymorphs of the same chemical entity
definition source: [PROCO]

solid dispersion
type: Class
subclass of: heterogeneous mixture
textual definition: A heterogenous mixture in which one or more components is dispersed in a solid matrix
definition source: [PROCO]

point group symmetry
type: Class
subclass of: symmetry
textual definition: A group of geometric symmetries (isometries) that keep at least one point fixed.
definition source: [wikipedia]

pedial
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: Class
    intersection of: polar point symmetry
    intersection of: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: triclinic unit cell
textual definition: An open,one faced triclinic form with enantiomorphic and polar point symmetries
definition source: [PROCO]

pinacoidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: triclinic unit cell
textual definition: 2-faced triclinic form with centrosymmetric point symmetry
definition source: [PROCO]

sphenoidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: Class
    intersection of: polar point symmetry
    intersection of: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: monoclinic unit cell
textual definition: A monoclinic crystal class with two nonparallel faces symmetrical to a 2- or 4-fold axis of symmetry that has enantiomorphic and polar point symmetry.
definition source: [PROCO]

hexoctahedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: cubic unit cell
textual definition: A cubic system crystal class with 48 equal triangular faces and three identical crystallographic axes with four fold rotational axes and centrosymmetric point symmetry
definition source: [PROCO]

hextetrahedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: non-centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: cubic unit cell
textual definition: A cubic system crystal class with 24-faces and four fold rotoinversion axes and non-centrosymmetric point symmetry
definition source: [PROCO]

gyroidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: cubic unit cell
textual definition: A cubic form with no mirror planes and enantiomorphic point symmetry
definition source: [PROCO]

in-silico modeling
type: Class
subclass of: planned process
textual definition: An experiment performed on computer or via computer simulation
definition source: [wikipedia]

Powder Indexing
type: Class
subclass of: in-silico modeling
textual definition: An in-silico modeling to predict the unit cell of the crystal lattice based on the powder x-ray diffractogram
term editor: W. Schafer
definition source: [PROCO]

crystal structure predictions
type: Class
subclass of: in-silico modeling
subclass of: Restriction
  on property: SIO_000229
  some values from: chemical structure
textual definition: An in-silico modeling to calculate calculation of the crystal structures by simulated annealing, evolutionary algorithms, distributed multipole analysis, random sampling, basin-hopping, data mining, density functional theory and molecular mechanics.
definition source: [Wikipedia]

ICH Q11 Guidance for Development and Manufacture of Drug Substances
type: Class
subclass of: ICH Guideline
textual definition: An ICH Guidance for developing and understanding the manufacturing process of the drug substance.
definition source: [ICH]

assessed volatility purge factor
type: Class
subclass of: purge factor
textual definition: An assessed purge factor based on the relative boiling point of the impurity to the reaction solvent and therefore its propensity to be purged in the headspace of steps to which the impurity is subjected..
definition source: [PROCO]

assessed ionisability purge factor
type: Class
subclass of: purge factor
textual definition: An assessed purge factor based on the ionisability of the impurity relative to desired compound and therefore its propensity to be purged in the waste layer of a biphasic system in steps that involve such an extraction.
definition source: [PROCO]

overall assessed purge factor
type: Class
subclass of: purge factor
textual definition: The assessed ratio of maximum possible concentration before purging to its concentration after purging (the final product). It is simply the product of all the assessed purge factors of each reaction step to which the impurity is subjected.
definition source: [PROCO]

common technical document
type: Class
subclass of: directive information entity
subclass of: document
textual definition: A set of specifications maintained by the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). for an application dossier for the registration of Medicines and designed to be used across Europe, Japan and the United States.
definition source: [ICH]

X-Ray diffractivity
type: Class
subclass of: chemical substance quality
subclass of: Restriction
  on property: is about
  some values from: unit cell
textual definition: A chemical substance quality of a crystalline phase that manifests itself as a set of allowed and unallowed peaks corresponding to the diffraction of incident x-ray radiation as a function of the substance's unit cell and its space group.
definition source: [PROCO]

beaker
type: Class
subclass of: container
textual definition: A beaker is a simple container for stirring, mixing and heating liquids commonly used in many laboratories. Beakers are generally cylindrical in shape, with a flat bottom. Most also have a small spout (or "beak") to aid pouring.
definition source: [Wikipedia]

Bunsen burner
type: Class
subclass of: heating device
textual definition: A heating device (environmental control device) that utilizes an open flame for heating.
definition source: [wikipedia]

crucible
type: Class
subclass of: container
textual definition: A crucible is a ceramic or metal container in which metals or other substances may be melted or subjected to very high temperatures. [Wikipedia]
definition source: [Wikipedia]

fractionating column
type: Class
subclass of: device
textual definition: A device to separate vaporized mixtures of liquid compounds with close volatility.
definition source: [wikipedia]

Vigreux column
type: Class
subclass of: fractionating column
textual definition: A fractionating column made of a wide glass tube with multiple internal glass "fingers" that point downwards so that the vapor that enters from the lower opening condenses on the fingers and drips down from them.
definition source: [Wikipedia]

Snyder column
type: Class
subclass of: fractionating column
textual definition: A fractionating column divided into sections (usually 3 to 6) by horizontal glass partitions or constrictions each of which seats a hollow glass bead with an inverted "teardrop" shape acting as check valves, closing and opening with vapor flow, and enhancing vapor-condensate mixing.
definition source: [Wikipedia]

Widmer column
type: Class
subclass of: fractionating column
textual definition: A fractionating column consisting of four concentric glass tubes and a central glass rod, with a thinner glass rod coiled around it to increase the surface area.
definition source: [Wikipedia]

condensor
type: Class
subclass of: device
textual definition: A device used to condense vapors into liquid by cooling.
definition source: [wikipedia]

Liebig condenser
type: Class
subclass of: condensor
textual definition: A condensor consisting of a simple tube surrounded by a jacket of cooling water
definition source: [wikipedia]

Allihn condenser
type: Class
subclass of: condensor
textual definition: A condensor consisting of a jacketed long glass tube with a series of bulbs on the tube to increase the surface area upon which the vapor constituents may condense.
alternative term: bulb condensor
alternative term: reflux condensor
definition source: [Wikipedia]

Graham condensor
type: Class
subclass of: condensor
disjoint with: coil condenser
textual definition: A condensor with a coolant-jacketed spiral coil running the length of the condenser serving as the vapor–condensate path, providing more surface area for cooling.
alternative term: Inland Revenue condenser
definition source: [Wikipedia]

Davies condenser
type: Class
subclass of: condensor
textual definition: A condensor with three concentric glass tubes where coolant circulates in both the outer jacket and the central tube to increase the cooling surface,
alternative term: double surface condenser
definition source: [Wikipedia]

coil condenser
type: Class
subclass of: condensor
textual definition: A condensor consisting of a straight tube containing an internal spiral coil through which coolant flows.
definition source: [Wikipedia]

Dimroth condenser
type: Class
subclass of: condensor
textual definition: A condensor with an internal double spiral through which coolant flows such that the coolant inlet and outlet are both at the top
definition source: [Wikipedia]

cold finger
type: Class
subclass of: condensor
textual definition: A condensor consisting of a vertical rod that is flow-cooled from the inside that is to be immersed in the vapor to provide a condensing surface. This condensor is also used for sublimation.
definition source: [Wikipedia]

Frederichs condensor
type: Class
subclass of: condensor
textual definition: A condensor consisting of a large water-cooled finger tightly fitted inside a wide cylindrical housing. The finger has a helical ridge along its length, so as to leave a narrow helical path for the vapor.
definition source: [Wikipedia]

bulk substance quality
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: portion of material
textual definition: A quality associated with a portion of material
definition source: [PROCO]

environmental control device
type: Class
subclass of: device
textual definition: A device for controlling the environment of a particular space
definition source: [PROCO]

heating mantle
type: Class
subclass of: environmental control device
textual definition: An environmental control device used to apply heat directly to containers.
alternative term: isomantel
definition source: [wikipedia]

round bottom flask
type: Class
subclass of: flask
textual definition: A round-bottom flask is a flask with a spherical body and one or more necks with ground glass joints.
definition source: [Wikipedia]

flask
type: Class
subclass of: container
textual definition: Flasks are narrow-necked glass containers, typically conical or spherical, used in a laboratory to hold reagents or samples.
definition source: [Wikipedia]

volumetric flask
type: Class
subclass of: flask
textual definition: A flask for preparing liquids with volumes of high precision. It is a flask with an approximately pear-shaped body and a long neck with a circumferential fill line.
definition source: [Wikipedia]

syringe pump
type: Class
subclass of: transferring device
textual definition: A syringe which has the function of pumping material into an experiment.
definition source: [PROCO]
comment: [CHMO] term exists

Erlenmeyer flask
type: Class
subclass of: flask
textual definition: An Erlenmeyer flask or conical flask is a type of laboratory flask which features a flat bottom, a conical body, and a cylindrical neck.
definition source: [Wikipedia]

laboratory notebook
type: Class
subclass of: document
textual definition: A document that is a primary record of research used to document their hypotheses, experiments and initial analysis or interpretation of these experiments serving as an organizational tool, a memory aid, and can also have a role in protecting any intellectual property that comes from the research.
alternative term: lab notebook
definition source: [Wikipedia]

evaporation device
type: Class
subclass of: device
textual definition: A device that evaporates
definition source: [PROCO]

international nonproprietary name
type: Class
subclass of: centrally registered identifier
subclass of: written name
textual definition: A centrally registered identifier given to a pharmaceutical drug or an active ingredient coordinated by the World Health Organization (WHO) that is unique generic and non-proprietary.
definition source: [Wikipedia]

chemical structure
type: Class
subclass of: molecular quality
textual definition: The structure of a chemical entity in terms of its molecular geometry and electronic structure.
definition source: [PROCO]

flocculant
type: Class
subclass of: chemical role
textual definition: A synthesis role used to remove suspended solids from liquids by inducing flocculation (the solids begin to aggregate forming flakes, which either precipitate to the bottom or float to the surface of the liquid, and then they can be removed or collected). Flocculants, or flocculating agents (also known as flocking agents), are chemicals that promote flocculation by causing colloids and other suspended particles in liquids to aggregate, forming a floc.
alternative term: clarifying agent
definition source: [Wikipedia]

CTA Section 3.2.S.1.1 Nomenclature
type: Class
subclass of: document part
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: international nonproprietary name
  intersection of: Restriction
    on property: has part
    some values from: preferred IUPAC name
  intersection of: Restriction
    on property: has part
    some values from: chemical abstracts name
  intersection of: Restriction
    on property: has part
    some values from: chemical abstracts number
textual definition: The drug substance nomenclature section of the CTA
definition source: [PROCO]

preferred IUPAC name
type: Class
subclass of: written name
textual definition: A unique name, assigned to a chemical substance and preferred among the possible names generated by IUPAC nomenclature. The "preferred IUPAC nomenclature" provides a set of rules for choosing between multiple possibilities in situations where it is important to decide on a unique name. It is intended for use in legal and regulatory situations.
definition source: [Wikipedia]

chemical abstracts name
type: Class
subclass of: written name
textual definition: The name assigned to a chemical substance by the Chemical Abstracts Service of the American Chemical Society
definition source: [PROCO]

chemical abstracts number
type: Class
subclass of: centrally registered identifier
textual definition: A centrally registered identifier assigned by the Chemical Abstracts Service (CAS) to every chemical substance described in the open scientific literature.
definition source: [Wikipedia]

CTA Section 3.2.S.1.2 Structure
type: Class
subclass of: document part
textual definition: The drug substance structure section of the CTA
definition source: [PROCO]

chemical drawing
type: Class
subclass of: representation form
textual definition: A two or three dimensional representation of a chemical structure.
definition source: [PROCO]

molecular formula
type: Class
subclass of: molecular quality
textual definition: A molecular entity quality which identifies each constituent element by its chemical symbol and indicates the number of atoms of each element found in each discrete molecular entity of that compound.
definition source: [CHEMINF]

CTA Section 3.2.S.1.3 General Properties
type: Class
subclass of: document part
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: international nonproprietary name
  intersection of: Restriction
    on property: has part
    some values from: preferred IUPAC name
  intersection of: Restriction
    on property: has part
    some values from: chemical abstracts name
  intersection of: Restriction
    on property: has part
    some values from: chemical abstracts number
textual definition: The drug substance general properties section of the CTA that includes appearance, thermal behaviour, solubility, chirality /specific rotation, crystallinity / polymorphism, hygroscopicity, solution pH and acid/base diassociation constants.
definition source: [PROCO]

certificate of analysis
type: Class
subclass of: document
textual definition: A document certified by a vendor summarizing test results and specifications for a particular batch of its product.
definition source: [PROCO]

appearance datum
type: Class
subclass of: data item
textual definition: A data item that is about a material entity based on a visual inspection.
definition source: [PROCO]

CTA Section 3.2.S.2.1 Manufacturers
type: Class
subclass of: document part
textual definition: The document part of the common technical document regarding manufacturers
definition source: [PROCO]

synthesis flow chart
type: Class
subclass of: representation form
textual definition: A 2-D representation of a step-by-step progression through a synthesis or part of a synthesis showing reagents, intermediates and reaction conditions.
definition source: [PROCO]

CTA Section 3.2.S.2.2 Description of Manufacturing Process and Process Controls
type: Class
subclass of: document part
textual definition: The description of the drug substance manufacturing process represents the applicant’s commitment for the manufacture of the drug substance. Reference ICH guidances Q5A, Q5B, and Q6B.
definition source: [PROCO]

solution pH datum
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that quantifies the measured pH of a saturated solution of a material at a specified temperature.
definition source: [PROCO]

specific rotation datum
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that quantifies the measured change in orientation of monochromatic plane-polarized light, per unit distance–concentration product, as the light passes through a sample of a compound in solution.
definition source: [wikipedia]

CTA Section 3.2.S.2.3 Control of Materials
type: Class
subclass of: document part
textual definition: Materials used in the manufacture of the drug substance (e.g., raw materials, starting materials, solvents, reagents, catalysts) should be listed, identifying where each material is used in the process. Information on the quality and control of these materials should be provided. Reference ICH guidances Q6A and Q6B.
definition source: [PROCO]

CTA Section 3.2.S.2.4 Controls of Critical Steps and Intermediates
type: Class
subclass of: document part
textual definition: The document part of the common technical document that specifies tests and acceptance criteria (with justification including experimental data) performed at critical steps identified in 3.2.S.2.2 of the manufacturing process to ensure that the process is controlled. Information on the quality and control of intermediates isolated during the process is also provided. Reference ICH guidances Q6A and Q6B.
definition source: [PROCO]

CTA Section 3.2.S.3.1 Elucidation of Structure and other Characteristics
type: Class
subclass of: document part
textual definition: The document part of the common technical document that provides confirmation of structure based on, for example, synthetic route and spectral analyses should be provided. Information such as the potential for isomerism, the identification of stereochemistry, or the potential for forming polymorphs. Reference ICH guidance Q6A.
definition source: [PROCO]

CTA Section 3.2.S.3.2 Impurities
type: Class
subclass of: document part
textual definition: The document part of the common technical document that provides Information on impurities. Reference ICH guidances Q3A, Q3C, Q5C, Q6A, and Q6B.
definition source: [PROCO]

ICH M7 Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals To Limit Potential Carcinogenic Risk
type: Class
subclass of: ICH Guideline
textual definition: An ICH guideline and objective specification for the identification, categorization, qualification, and control of these mutagenic impurities in pahrmaceutical products to limit potential carcinogenic risk.
definition source: [ICH]

DEREK Mutagen Prediction
type: Class
subclass of: in-silico modeling
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: mutagenic impurity
  intersection of: Restriction
    on property: SIO_000229
    some values from: risk assessment
textual definition: An is-silico modeling based on DEREK that determines the risk of a chemical being a mutagenic impurity
definition source: [PROCO]

MCASE Mutagen Prediction
type: Class
subclass of: in-silico modeling
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: mutagenic impurity
  intersection of: Restriction
    on property: SIO_000229
    some values from: risk assessment
textual definition: An is-silico modeling based on MCASE that determines the risk of a chemical being a mutagenic impurity
definition source: [PROCO]

rate equation
type: Class
subclass of: equation
subclass of: Restriction
  on property: has facet
  some values from: Class
    intersection of: molar concentration (quality)
    intersection of: partial rate order
textual definition: An equation that links the initial or forward reaction rate with the molar concentrations or pressures of the reactants and constant parameters (normally rate coefficients and partial reaction orders).
editor note: close match to http://purl.obolibrary.org/obo/STATO_0000071 but derived class is being developed wrt to rate constant and rate orders.
alternative term: rate law
definition source: [Wikipedia]

Reaction Progress Kinetic Analysis
type: Class
subclass of: mechanistic and kinetic determination
textual definition: Kinetic techniques utilized to determine the rate laws of chemical reactions and to aid in elucidation of reaction mechanisms. While the concepts guiding reaction progress kinetic analysis are not new, the process was formalized by Professor Donna Blackmond (currently at Scripps Research Institute) in the late 1990s and has since seen increasingly widespread use. Unlike more common pseudo-first-order analysis, in which an overwhelming excess of one or more reagents is used relative to a species of interest, RPKA probes reactions at synthetically relevant conditions (i.e. with concentrations and reagent ratios resembling those used in the reaction when not exploring the rate law.) Generally, this analysis involves a system in which the concentrations of multiple reactants are changing measurably over the course of the reaction. As the mechanism can vary depending on the relative and absolute concentrations of the species involved, this approach obtains results that are much more representative of reaction behavior under commonly utilized conditions than do traditional tactics. Furthermore, information obtained by observation of the reaction over time may provide insight regarding unexpected behavior such as induction periods, catalyst deactivation, or changes in mechanism.
textual definition: Mechanistic and kinetic determinations utilized to determine the rate laws of chemical reactions and to aid in elucidation of reaction mechanisms. While the concepts guiding reaction progress kinetic analysis are not new, the process was formalized by Professor Donna Blackmond (currently at Scripps Research Institute) in the late 1990s and has since seen increasingly widespread use. Unlike more common pseudo-first-order analysis, in which an overwhelming excess of one or more reagents is used relative to a species of interest, RPKA probes reactions at synthetically relevant conditions (i.e. with concentrations and reagent ratios resembling those used in the reaction when not exploring the rate law.) Generally, this analysis involves a system in which the concentrations of multiple reactants are changing measurably over the course of the reaction. As the mechanism can vary depending on the relative and absolute concentrations of the species involved, this approach obtains results that are much more representative of reaction behavior under commonly utilized conditions than do traditional tactics. Furthermore, information obtained by observation of the reaction over time may provide insight regarding unexpected behavior such as induction periods, catalyst deactivation, or changes in mechanism.
alternative term: RPKA
definition source: [Wikipedia]

process analytical technology
type: Class
subclass of: process chemistry workflow plan
textual definition: A process chemistry workflow plan that utilizes online and at-line measurements to understand chemical processes by defining and monitoring ...
alternative term: PAT
definition source: [PROCO]

steady-state approximation analysis
type: Class
subclass of: mechanistic and kinetic determination
textual definition: A mechanistic and kinetic determination that involves setting the rate of change of a reaction intermediate in a reaction mechanism equal to zero so that the kinetic equations can be simplified by setting the rate of formation of the intermediate equal to the rate of its destruction.
editor note: shouldn't this be a data transformation process?
alternative term: Bodenstein's quasi-steady state approximation
alternative term: stationary-state approximation
definition source: [Wikipedia]

partial rate order
type: Class
subclass of: kinetic order
textual definition: The exponent terms within the rate equation. For elementary (single step) reactions, the reactant order is equal to the stoichiometric coefficient of the reactant.
term editor: Anna Dunn
alternative term: Partial order of reaction
alternative term: Reactant Rate Order
alternative term: Reactant order
definition source: [wikipedia]

overall reaction order
type: Class
subclass of: kinetic order
textual definition: The sum of stoichiometric coefficients of reactants, is always equal to the molecularity of the elementary reaction. However, complex (multi-step) reactions may or may not have reaction orders equal to their stoichiometric coefficients.
definition source: [Wikipedia]

concentration profile
type: Class
subclass of: quality process profile
textual definition: A quality process profile that tracks the concentration changes of a species
definition source: [PROCO]

reaction rate
type: Class
subclass of: measurement datum
textual definition: A measurement datum about the speed at which a chemical reaction takes place, defined as proportional to the increase in the concentration of a product per unit time and to the decrease in the concentration of a reactant per unit time.
editor note: http://purl.obolibrary.org/obo/STATO_0000071 reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval Term IRI: http://purl.obolibrary.org/obo/PATO_0000161 Definition: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. [database_cross_reference: PATOC:melissa]
definition source: [Wikipedia]

integral kinetic measurement
type: Class
subclass of: mechanistic and kinetic determination
textual definition: A kinetic determination method that measures the concentration of reaction species which is proportional to the integral of the reaction rate.
definition source: [wikipedia]

differential kinetic measurement
type: Class
subclass of: mechanistic and kinetic determination
textual definition: A kinetic determination method that measures reaction rate directly. (d[]/dt)
definition source: [wikipedia]

method of initial rates
type: Class
subclass of: differential kinetic measurement
textual definition: A series of experiments whereby the initial concentration of each reactant is varied while the other reactant concentrations are kept constant, allowing the determination of the rate order of the reactant.
definition source: [PROCO]

graphical rate equation
type: Class
subclass of: representation form
textual definition: A plot of the differential kinetic measurement as the y-axis vs. the integral measurement as the x-axis.
definition source: [PROCO]

Variable Time Normalisation Analysis
type: Class
subclass of: mechanistic and kinetic determination
textual definition: A mechanistic and kinetic determination that compares concentration vs. time profiles in a series of experiments to identify product inhibition, catalyst deactivation and the order of components including catalysts.
definition source: [PROCO]

mutagenic impurity
type: Class
subclass of: impurity role
textual definition: An impurity role of DNA reactive material that have significant carcinogenic risk
definition source: [ICH]

domatic
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: polar point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: monoclinic unit cell
textual definition: A 2- faced open form monoclinic crystal with polar point symmetry.
definition source: [PROCO]

prismatic
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: monoclinic unit cell
textual definition: 3, 4, 6, 8, or 12 faced monoclinic crystal with centrosymmetric point symmetry.
definition source: [PROCO]

rhombic-disphenoidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: orthorhombic unit cell
textual definition: Four-faced closed orthorhombic form with enantiomorphic point symmetry
definition source: [PROCO]

rhombic-pyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: polar point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: orthorhombic unit cell
textual definition: 3, 4, 6, 8, or 12 nonparallel faced orthorhombic system with polar point symmetry.
definition source: [PROCO]

rhombic-dipyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: orthorhombic unit cell
textual definition: 8-faced form orthorhombic crystal class with centrosymmetric point symmetry
definition source: [PROCO]

diploidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: cubic unit cell
textual definition: Isometric form with no 4 fold axes and centrosymmetric point symmetry
definition source: [PROCO]

tetartoidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: cubic unit cell
textual definition: General cubic forms which only has 3-fold axes and 2-fold axes with no mirror plane with enantiomorphic point symmetry.
definition source: [PROCO]

tetragonal-pyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: Class
    intersection of: polar point symmetry
    intersection of: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: tetragonal unit cell
textual definition: 4-faced tetragonal form with polar point and enantiomorphic point symmetry.
definition source: [PROCO]

tetragonal-disphenoidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: non-centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: tetragonal unit cell
textual definition: 4-faced closed orthorhombic form with non-centrosymmetric point symmetry.
definition source: [PROCO]

tetragonal-dipyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: tetragonal unit cell
textual definition: 8-faced form with centrosymmetric point symmetry.
definition source: [PROCO]

tetragonal-trapezohedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: tetragonal unit cell
textual definition: 6-, 8-, 12-, or 24-trapezium faced closed tetragonal form with enantiomorphic point symmetry
definition source: [PROCO]

ditetragonal-pyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: polar point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: tetragonal unit cell
textual definition: 8-faced tetragonal form with polar point and enantiomorphic point symmetry
definition source: [PROCO]

tetragonal-scalenohedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: non-centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: tetragonal unit cell
textual definition: 8-faced (tetragonal) or 12-faced (hexagonal) closed tetragonal form with non-centrosymmetric point symmetry
definition source: [PROCO]

ditetragonal-dipyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: tetragonal unit cell
textual definition: 16-faced form tetragonal crystal form with centrosymmetric point symmetry
definition source: [PROCO]

trigonal-pyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: Class
    intersection of: polar point symmetry
    intersection of: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: trigonal unit cell
textual definition: 3-faced form where all faces are related by a 3-fold rotation axis with polar point and enantiomorphic point symmetry.
definition source: [PROCO]

rhombohedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: trigonal unit cell
textual definition: 6 faced closed rhombohedral form of six identical faces in which none of the intersection edges is perpendicular and having centrosymmetric point symmetry
definition source: [PROCO]

trigonal-trapezohedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: trigonal unit cell
textual definition: 6-, 8-, 12-, or 24-trapezohedral faced closed trigonal form with enantiomorphic point symmetry
definition source: [PROCO]

ditrigonal-pyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: polar point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: trigonal unit cell
textual definition: 6-faced trigonal form where all faces are related by a 3-fold rotational axis with polar point symmetry.
definition source: [PROCO]

ditrigonal-scalenohedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: trigonal unit cell
textual definition: 8-faced (tetragonal) or 12-faced (hexagonal) closed form in which the faces are grouped in symmetrical pairs with centrosymmetric point symmetry
definition source: [PROCO]

hexagonal-pyrimidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: Class
    intersection of: polar point symmetry
    intersection of: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: hexagonal unit cell
textual definition: 6-faced form where all faces are related by a 6 axis having polar point and enantiomorphic point symmetry.
definition source: [PROCO]

trigonal-dipyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: non-centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: hexagonal unit cell
textual definition: 6-faced hexagonal form with faces related by a 3-fold axis with a perpendicular mirror plane having non-centrosymmetric point symmetry
definition source: [PROCO]

hexagonal-dipyrimidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: hexagonal unit cell
textual definition: 12-faced hexagonal form with faces related by a 6-fold axis with a perpendicular mirror with a centrosymmetric point symmetry
definition source: [PROCO]

hexagonal-trapezohedral
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: enantiomorphic point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: hexagonal unit cell
textual definition: 6-faced closed hexagonal form with enantiomorphic point symmetry.
definition source: [PROCO]

dihexagonal-pyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: polar point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: hexagonal unit cell
textual definition: 12-faced hexagonal crystal where all faces are related by a 6-fold axis. It has polar point symmetry
definition source: [PROCO]

ditrigonal-dipyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: non-centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: hexagonal unit cell
textual definition: 12-faced form tetragonal crystal class with non-centrosymmetric point symmetry
definition source: [PROCO]

dihexagonal-dipyramidal
type: Class
subclass of: point group symmetry
subclass of: Restriction
  on property: quality influenced by
  some values from: centrosymmetric point symmetry
subclass of: Restriction
  on property: inheres in
  some values from: hexagonal unit cell
textual definition: 24-faced form with faces related by a 6-fold axis with a perpendicular mirror plane and centrosymmetric point symmetry
definition source: [PROCO]

ICH Q3A Impurities in New Drug Substances
type: Class
subclass of: ICH Guideline
textual definition: An ICH guideline about identifying, qualifying and specifying impurities in drug substance.
definition source: [ICH]

ICH Q3C Residual Solvents
type: Class
subclass of: ICH Guideline
textual definition: An ICH guideline for the use residual solvents (organic volatile impurities) in the manufacture of drug substances and dosage forms, and sets pharmaceutical limits for in drug products.
definition source: [ICH]

ICH Q3D Guidance for Elemental Impurities
type: Class
subclass of: ICH Guideline
textual definition: An ICH guideline for the control of elemental impurities in new drug products (medicinal products), establishing Permitted Daily Exposures (PDEs) for 24 Elemental Impurities (EIs) for drug products administered by the oral, parenteral and inhalation routes of administration.
definition source: [ICH]

ICH Q6A Specifications: Test Procedures and Acceptance Criteria for Chemical Substances
type: Class
subclass of: ICH Guideline
textual definition: An ICH guidance on the setting and justification of acceptance criteria and the selection of test procedures for new drug substances of synthetic chemical origin, and new drug products produced from them, which have not been registered previously in the ICH regions.
definition source: [ICH]

Q7 Good Manufacturing Practice Guide for Active Pharmaceutical Ingredients
type: Class
subclass of: ICH Guideline
textual definition: An ICH Guideline for the manufacture of APIs for use in human drug (medicinal) products.
definition source: [ICH]

residual solvent impurity
type: Class
subclass of: impurity role
textual definition: Residual solvents in pharmaceuticals are defined here as organic volatile chemicals that are used or produced in the manufacture of drug substances or excipients, or in the preparation of drug products. The solvents are not completely removed by practical manufacturing techniques.
definition source: [FDA]

ICH Q6A Class 1 Solvent
type: Class
subclass of: residual solvent impurity
textual definition: Solvents to be avoided and with strict low limits as they are human carcinogens, strongly suspected human carcinogens, and environmental hazards.
definition source: [ICH]

ICH Q6A Class 2 Solvent
type: Class
subclass of: residual solvent impurity
textual definition: Solvents to be limited non-genotoxic animal carcinogens or possible causative agents of other irreversible toxicity such as neurotoxicity or teratogenicity. Solvents suspected of other significant but reversible toxicities
definition source: [ICH]

ICH Q6A Class 3 Solvent
type: Class
subclass of: residual solvent impurity
textual definition: Class 3 solvents: Solvents with low toxic potential Solvents with low toxic potential to man; no health-based exposure limit is needed. Class 3 solvents have PDEs of 50 mg or more per day.
definition source: [ICH]

Permitted Daily Exposure
type: Class
subclass of: objective specification
textual definition: The maximum acceptable intake per day of residual solvent in pharmaceutical products
definition source: [ICH]

one-factor-at-a-time experimental design
type: Class
subclass of: experimental design
textual definition: An experimental design involving the testing of factors, or causes, one at a time instead of multiple factors simultaneously.
definition source: [Wikipedia]

experimental design
type: Class
subclass of: plan specification
textual definition: The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions.
definition source: http://edamontology.org/topic_3678

explosion
type: Class
subclass of: process
textual definition: A process during which a material entity undergoes a rapid increase in volume, releasing gasses and various forms of energy, often including thermal, light and sound energy.
definition source: [Wikipedia]

process safety
type: Class
subclass of: planned process
textual definition: A planned process of understanding of the hazards of a chemical process and developing methods to safely manage and minimize the risks of the process.
definition source: [PROCO]

Box–Behnken design
type: Class
subclass of: experimental design
textual definition: An experimental design to produce a response curve sufficient to fit quadratic models of the individual factors
definition source: George Box, Donald Behnken, "Some new three level designs for the study of quantitative variables", Technometrics, Volume 2, pages 455–475, 1960
definition source: [Wikipedia]

Central Composite Design
type: Class
subclass of: experimental design
textual definition: An experimental design consisting of three distinct sets of experimental runs: A factorial (perhaps fractional) design in the factors studied, each having two levels; A set of center points, experimental runs whose values of each factor are the medians of the values used in the factorial portion. This point is often replicated in order to improve the precision of the experiment; A set of axial points, experimental runs identical to the centre points except for one factor, which will take on values both below and above the median of the two factorial levels, and typically both outside their range. All factors are varied in this way.
definition source: [wikipedia]

laboratory notebook experiment identifier
type: Class
subclass of: document part
subclass of: centrally registered identifier
subclass of: Restriction
  on property: part of
  some values from: laboratory notebook
subclass of: Restriction
  on property: is about
  some values from: experiment
textual definition: A centrally registered identifier assigned to a laboratory notebook experiment
term editor: W Schafer
definition source: [PROCO]

batch manufacturing record
type: Class
subclass of: document
textual definition: A document that contemporaneously records when, how, by whom each step to produce a specific batch is executed as well as the specific equipment and the specific materials including exact weights and lot numbers.
term editor: Wes Schafer
alternative term: batch sheet
definition source: [PROCO]

master formula record
type: Class
subclass of: process chemistry workflow plan
textual definition: A plan specification of manufacturing instructions for a specific (unique) batch and includes: specific instructions for each step, the equipment used in each step, sampling and testing procedures for each step, the amount of each component needed to manufacture the batch (Bill of Materials) and the theoretical yield and expected yield of each intermediate as well as the product. .
alternative term: master manufacturing formula
alternative term: master production record
definition source: FDA 21CFR226

bill of materials
type: Class
subclass of: document
textual definition: A document that lists the raw materials, sub-assemblies, intermediate assemblies, sub-components, parts, and the quantities of each needed to manufacture an end product.
alternative term: BOM
alternative term: associated list
alternative term: bill of material
definition source: wikipedia

solubility screening design
type: Class
subclass of: screening design
subclass of: Restriction
  on property: SIO_000338
  some values from: Class
    intersection of: multi-parallel experimentation
    intersection of: Restriction
      on property: SIO_000229
      some values from: Class
        intersection of: measurement datum
        intersection of: Restriction
textual definition: A screening design to determine to solubility of a compound
definition source: [PROCO]

competency question
type: Class
subclass of: objective specification
subclass of: data about an ontology part
textual definition: An objective specification for an ontology in the form of a user-focused question / query that identifies key concepts and their relationships that are normally formalized in first order logic of the ontology. They are also used to test the ontology by querying known instance data or by entailment on its axioms.
term editor: Wes Schafer
definition source: [PROCO]

material costs
type: Class
subclass of: process chemistry datum
textual definition: A process chemistry datum quantifying the sum of the costs of all raw materials, intermediates, reagents, solvents and catalysts procured from external vendor.
definition source: [Wikipedia]

waste stream
type: Class
subclass of: portion of material
textual definition: A portion of material with a debris role that is a material output of a process.
term editor: Wes Schafer
definition source: [PROCO]

product stream
type: Class
subclass of: portion of material
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: product role
textual definition: A portion of material to be further processed that has an ingredient a material with the role of product.
editor note: waste stream can also have the product as an ingredient. Need to convey that it is portion of material that will be further processed.
term editor: W Schafer
definition source: [PROCO]

Control Strategy
type: Class
subclass of: directive information entity
textual definition: A planned set of controls, derived from current product and process understanding that ensures process performance and product quality. The controls can include parameters and attributes related to drug substance and drug product materials and components, facility and equipment operating conditions, in-process controls, finished product specifications, and the associated methods and frequency of monitoring and control.
definition source: [ICH Q10]

risk assessment
type: Class
subclass of: document
textual definition: A document identifying and analyzing potential (future) events that may negatively impact individuals, assets, and/or the environment (i.e. hazard analysis); and making judgments "on the tolerability of the risk on the basis of a risk analysis" while considering influencing factors (i.e. risk evaluation).
definition source: [Wikipedia]

calculation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: SIO_000132
  some values from: information content entity
textual definition: A planned process that converts input data into output data based on some equation or set of equations
editor note: close to AFP_0003282
term editor: W Schafer
definition source: [PROCO]

calculated datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: participates in
  some values from: calculation
textual definition: A data item that is a recording of the output of a calculation.
definition source: [PROCO]

process chemistry datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: chemical process development
textual definition: A data item about process chemistry
definition source: [PROCO]

chemometrics
type: Class
subclass of: in-silico modeling
textual definition: A planned process of extracting information from chemical systems by data-driven means.
definition source: [Wikipedia]

factorial analysis
type: Class
subclass of: chemometrics
subclass of: Restriction
  on property: SIO_000229
  some values from: factor
textual definition: Chemometric method used to describe variability among observed, correlated variables in terms of a potentially lower number of unobserved variables called factors. . The observed variables are modelled as linear combinations of the potential factors, plus "error" terms.
definition source: [Wikipedia]

critical process parameter
type: Class
subclass of: process profile
subclass of: Restriction
  on property: is about
  some values from: critical quality attribute
textual definition: A process profile whose variability has an impact on a critical quality attribute and therefore should be monitored or controlled to ensure the process produces the desired quality.
definition source: [ICH Q8(R2)]

multi-parallel experimentation
type: Class
subclass of: investigation
textual definition: A form of experimentation in which many related experiments (different conditions on the same compound or the same conditions on multiple compounds) are done simultaneously, typically in a well-plate platform.
term editor: W Schafer
definition source: [PROCO]

Arhennius equation
type: Class
subclass of: equation
textual definition: An equation for the temperature dependence of reaction rates used in determining rate of chemical reactions and for calculation of energy of activation.
definition source: [Wikipedia]

pre-exponential factor
type: Class
subclass of: kinetic constant
textual definition: The pre-exponential factor or A factor is the pre-exponential constant in the Arrhenius equation, an empirical relationship between temperature and rate coefficient. It is usually designated by A when determined from experiment, while Z is usually left for collision frequency.
alternative term: A factor
definition source: [Wikipedia]

protein
type: Class
subclass of: peptide
editor preferred label: protein
example of usage: antithrombin III is a protein
textual definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
imported from: Ontology for Biomedical Investigations
imported from: pr.owl

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

failed exploratory term
type: Thing
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: failed exploratory term
textual 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
editor preferred label: metadata complete
textual 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
editor preferred label: organizational term
textual 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
editor preferred label: ready for release
textual 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
editor preferred label: metadata incomplete
textual 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
editor preferred label: uncurated
textual 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
editor preferred label: pending final vetting
textual definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

placeholder removed
type: Thing
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: placeholder removed

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

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

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

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

requires discussion
type: NamedIndividual
type: curation status specification
editor preferred label: requires discussion
textual 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

axiom holds for all times
type: NamedIndividual
textual 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

Information Artifact Ontology (IAO)
type: NamedIndividual
default language: en
Contributor: Adam Goldstein
Contributor: Alan Ruttenberg
Contributor: Albert Goldfain
Contributor: Barry Smith
Contributor: Bjoern Peters
Contributor: Carlo Torniai
Contributor: Chris Mungall
Contributor: Chris Stoeckert
Contributor: Christian A. Boelling
Contributor: Darren Natale
Contributor: David Osumi-Sutherland
Contributor: Gwen Frishkoff
Contributor: Holger Stenzhorn
Contributor: James A. Overton
Contributor: James Malone
Contributor: Jennifer Fostel
Contributor: Jie Zheng
Contributor: Jonathan Rees
Contributor: Larisa Soldatova
Contributor: Lawrence Hunter
Contributor: Mathias Brochhausen
Contributor: Matt Brush
Contributor: Melanie Courtot
Contributor: Michel Dumontier
Contributor: Paolo Ciccarese
Contributor: Pat Hayes
Contributor: Philippe Rocca-Serra
Contributor: Randy Dipert
Contributor: Ron Rudnicki
Contributor: Satya Sahoo
Contributor: Sivaram Arabandi
Contributor: Werner Ceusters
Contributor: William Duncan
Contributor: William Hogan
Contributor: Yongqun (Oliver) He
description: The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.
license: http://creativecommons.org/licenses/by/4.0/
comment: An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
comment: IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
comment: IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
version info: 2020-12-09

Ontology for Biomedical Investigations
type: NamedIndividual
default language: en
OBO foundry unique label: Ontology for Biomedical Investigations
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
subject: An ontology for the annotation of biomedical and functional genomics experiments.
license: http://creativecommons.org/licenses/by/4.0/
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: 2021-04-06

bfo.owl
Contributor: Janna Hastings
Contributor: Leonard Jacuzzo
Contributor: Barry Smith
comment: The BSD license on the BFO project site refers to code used to build BFO.
Contributor: David Osumi-Sutherland
Contributor: Pierre Grenon
Contributor: Werner Ceusters
Contributor: Selja Seppälä
Contributor: Jie Zheng
Contributor: Thomas Bittner
Contributor: Mathias Brochhausen
comment: This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version.
Contributor: Mauricio Almeida
comment: Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif.
Contributor: Melanie Courtot
Contributor: Bjoern Peters
license: http://creativecommons.org/licenses/by/4.0/
Contributor: Yongqun "Oliver" He
Contributor: James A. Overton
Contributor: Jonathan Bona
Contributor: Holger Stenzhorn
Contributor: Fabian Neuhaus
Contributor: Randall Dipert
Contributor: Larry Hunter
Contributor: Stefan Schulz
editor note: BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science.
Contributor: Chris Mungall
Contributor: Ron Rudnicki
editor note: BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation.
Contributor: Mark Ressler
Contributor: Albert Goldfain
editor note: BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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.
Contributor: Alan Ruttenberg
Contributor: Ludger Jansen
Contributor: Bill Duncan

chebi.owl
comment: For any queries contact chebi-help@ebi.ac.uk
has_obo_format_version: 1.2
comment: Author: ChEBI curation team
comment: developed by Michael Ashburner & Pankaj Jaiswal.
date: 26:05:2021 18:56
comment: ChEBI subsumes and replaces the Chemical Ontology first
comment: ChEBI Release version 200

chmo.owl
has_obo_format_version: 1.2
license: http://creativecommons.org/licenses/by/4.0/

fix.owl
comment: saved-by: kirill
has_obo_format_version: 1.0
comment: autogenerated-by: DAG-Edit version 1.419 rev 3
comment: version: $Revision: 1.2 $
comment: date: Mon Apr 04 14:05:41 BST 2005
date: 25:05:2005 12:37

CHEMINF_000193
textual definition: The equilibrium state is characterized by a constant, designated K, which provides quantitative information of the extent of a reaction and is related to the ratio of the concentrations of reactants and products