diff --git "a/proco/proco.owl" "b/proco/proco.owl" new file mode 100755--- /dev/null +++ "b/proco/proco.owl" @@ -0,0 +1,19609 @@ + + + + + Anna Dunn + Wes A. Schafer + Yongqun "Oliver" He (YH) + Zachary Dance + PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry. + OWL-DL + PROCO: a formal ontology in the domain of process chemistry. + PROCO: PROcess Chemistry Ontology + http://creativecommons.org/licenses/by/4.0/ + 04-14-2022 + 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. + PROCO release 20220414 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + Really of interest to developers only + BFO OWL specification label + + + + + + + + + Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 + Person:Alan Ruttenberg + Really of interest to developers only + BFO CLIF specification label + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + example of usage + + 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. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + + + + + + + + definition + definition + 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. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 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. + 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. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + + + + + + + + editor note + + 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. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + + editor note + + + + + + + + term editor + + 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 + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + definition source + + 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 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + 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. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + 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 . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + 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 + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + ISA alternative term + + An alternative term used by the ISA tools project (http://isa-tools.org). + Requested by Alejandra Gonzalez-Beltran +https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 + Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail aid=3603413 group_id=177891 atid=886178 + Person: Alejandra Gonzalez-Beltran + Person: Philippe Rocca-Serra + ISA tools project (http://isa-tools.org) + ISA alternative term + + + + + + + + + IEDB alternative term + + An alternative term used by the IEDB. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IEDB alternative term + + + + + + + + + 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. + temporal interpretation + https://github.com/oborel/obo-relations/wiki/ROAndTime + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + 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. + An entity responsible for making contributions to the + content of the resource. + An entity responsible for making contributions to the content of the resource. + + Contributor + Contributor + + + + + + + + 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. + 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. + An entity primarily responsible for making the content + of the resource. + An entity primarily responsible for making the content of the resource. + + Creator + Creator + + + + + + + + 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. + 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. + A date associated with an event in the life cycle of the + resource. + A date associated with an event in the life cycle of the resource. + + Date + Date + + + + + + + + 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. + 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. + An account of the content of the resource. + + Description + 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). + 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). + The physical or digital manifestation of the resource. + + Format + Format + + + + + + + + + + + + + + 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. + 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. + A reference to a resource from which the present resource + is derived. + A reference to a resource from which the present resource is derived. + + Source + Source + + + + + + + + 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. + 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. + The topic of the content of the resource. + + Subject and Keywords + Subject and Keywords + + + + + + + + + + + + + + creator + + + + + + + + description + + + + + + + + issued + + + + + + + + Mark Miller + 2018-05-11T13:47:29Z + license + + + + + + + + modified + + + + + + + + rights + + + + + + + + + + + + + + title + + + + + + + + citesAsAuthority + + + + + + + + preferredNamespacePrefix + + + + + + + + preferredNamespaceUri + + + + + + + + + + + + + + comment + + + + + + + + subset + + + + + + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_obo_namespace + + + + + + + + has_related_synonym + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + shorthand + + + + + + + + + + + + + + + + + + + + label + label + + + + + + + + + + + + + + The property that identifies the version IRI of an ontology. + + versionIRI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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] + contains + + + + + + + + + + + + Inverse of contains. [Allotrope] + contained in + + + + + + + + + + + influenced by + Inverse of quality influences. [Allotrope] + quality influenced by + + + + + + + + + + + + + Has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part. [SIO] + An atom has subatomic particles as its proper parts. + has proper part + + + + + + + + + + + + is facet of + Facet of relates two information content entities where one information content entity is an aspect of the other one. [Allotrope] + facet of + + + + + + + + + + + + + Relation between an information content entity and some part of it called a facet that is covers some general aspect of information context. [Allotrope] + a timestamp + a title + an ordering + has facet + + + + + + + + + + is proper part of + Inverse of has proper part. [Allotrope] + proper part of + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + 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. + 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 + 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'. + 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'. + part_of + + + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + 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. + 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 + 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'. + 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'. + has_part + + + + + BFO:0000051 + chebi_ontology + has_part + false + has_part + has part + has part + + + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + + [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]) + [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]) + 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 + + realized in + + + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + + 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]) + 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]) + 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 + + realizes + + + + + + + + + + BFO:0000057 + has participant + + + + + + + + + + + + + has measurement unit label + + + + + + + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 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. + 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. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + + is about + + + + + + + + + + + + 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. + 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 + 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 + 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 + person:Alan Ruttenberg + Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan + + + + denotes + + + + + + + + + + inverse of the relation 'denotes' + Person: Jie Zheng, Chris Stoeckert, Mike Conlon + + + + denoted by + + + + + + + + + + is_supported_by_data + 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. + + 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 + OBI + OBI + Philly 2011 workshop + + is_supported_by_data + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + 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. + 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. + 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. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + + has_specified_input + + + + + + + + + + is_specified_input_of + 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 + + 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. + 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. + Alan Ruttenberg + PERSON:Bjoern Peters + + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + 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. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + + has_specified_output + + + + + + + + + + + + + + + is_specified_output_of + is_specified_output_of + + 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. + Alan Ruttenberg + PERSON:Bjoern Peters + + is_specified_output_of + + + + + + + + + has_role + + A relation between a continuant C and a role R. The reciprocal relation of role_of. + replaced by: http://purl.obolibrary.org/obo/BFO_0000087 + GROUP:OBI:<http://obi.sourceforge.net> + PERSON:Chris Mungal + + + obsolete_has_role + true + + + + + + + + + + + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + + 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. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch + + + OBI:0000417 + achieves_planned_objective + + + + + + + + + + objective_achieved_by + + 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. + OBI + OBI + + objective_achieved_by + + + + + + + + + + + + + + + + + + is thermodynically preferred at all temperatures + [PROCO] + monotropically related to + + + + + + + + + a relationship indicating that the process profile quantitates some aspect of the process (e.g. a quality of a material participant) + [PROCO] + profile of + + + + + + + + a relationship between polymorphs that has a cross-over temperature at which one form becomes more thermodynamically favored than the other. + [PROCO] + enantiotropically related to + + + + + + + + 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. + https://en.wikipedia.org/wiki/Solvation + https://en.wikipedia.org/wiki/Solvent + is solvate of + + + + + + + + + + an object property that represents a relation between polymorphs, i.e. different physical forms of the same chemical moiety. + Wes Schafer, Oliver He + https://en.wikipedia.org/wiki/Polymorphism_(materials_science) + is polymorph of + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + 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 + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + 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 + 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. + bearer_of + is bearer of + + + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + + participates in + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + 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. + has_participant + + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + 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). + 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). + 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. + + concretizes + + + + + + + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + 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. + has_function + + has function + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + 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. + has_role + + + RO:0000087 + chebi_ontology + has_role + false + false + has_role + has role + has role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + chebi_ontology + has_functional_parent + false + false + has functional parent + + + + + + + + + chebi_ontology + has_parent_hydride + false + false + has parent hydride + + + + + + + + + + chebi_ontology + is_conjugate_acid_of + true + false + is conjugate acid of + + + + + + + + + chebi_ontology + is_conjugate_base_of + true + false + is conjugate base of + + + + + + + + + chebi_ontology + is_substituent_group_from + false + false + is substituent group from + + + + + + + + + + chebi_ontology + is_tautomer_of + true + is tautomer of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has measurement value + + + + + + + + + + + has specified numeric value + + A relation between a value specification and a number that quantifies it. + 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. + PERSON: James A. Overton + OBI + + has specified numeric value + + + + + + + + + + + + + + + has specified value + + A relation between a value specification and a literal. + 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. + OBI + + has specified value + + + + + + + + + + + + + + + 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. + quantitative systems description parameter + + + + + + + + + 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. + Anna Dunn + + Synonym: reaction rate constant + kinetic constant + + + + + + + + + + + Time interval over which a quantified entity is reduced to half its original value. + half-life + + + + + + + + + + Time taken by a quantity decreasing according to a mono-exponential decay to be divided by two. Sometimes called t1/2. + half-life of an exponential decay + <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> + + + + + + + + + + + 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. + temporal measure + + + + + + + + + + + Synonym: mean lifetime + exponential time constant + <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> + + + + + + + + + + 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. + mass diffusivity + [Wikipedia] + + Synonym: diffusivity + diffusion coefficient + + + + + + + + + + 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. + effective catalytic rate + + + + + + + + + true + + + + engineered artifact + A device is an artifact that is designed to perform a function primarily by means of its mechanical or electrical nature. [Allotrope] + 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] + device + + + + + + + + + + + + + + + + + + + + + + + + true + + vessel + A device that has the function to contain material. [Allotrope] + box, can, plate, rack + tray, flask, vial + container + + + + + + + + + + + + + + + true + + heater + heating equipment + A device used for heating something. [Allotrope] + heating device + + + + + + + + + + + + + + + true + + transferring device + A transferring device is a device that is designed to transfer material. [Allotrope] + transferring device + + + + + + + + + + + + + + + + + + + + true + + controlling function + To alter or govern the size or amplitude of a flow (material, energy, signal). [NIST] + to control + + + + + + + + + + heating function + A function that gives thermal energy to a recipient. [Allotrope] + to heat + + + + + + + + + + + + + + + + + + + + + storing function + To accumulate a flow. [NIST] + A DC electrical battery stores the energy in a flashlight. [NIST] + to store + + + + + + + + + + + + + + + + + + + + true + + channeling function + localizing function + to channel + To cause a flow (material, energy, signal) to move from one location to another location. [NIST] + to localize + + + + + + + + + + + + + + + + + + + + + true + + adjusting function + changing function + to adjust + To adjust the flow of energy, signal, or material in a predetermined and fixed manner. [NIST] + to change + + + + + + + + + + enlarging function + incrementing function + to enlarge + To enlarge a flow in a predetermined and fixed manner. [NIST] + to increment + + + + + + + + + + + + + + + + + + + + + provisioning function + To accumulate or provide a material or energy flow. [NIST] + to provision + + + + + + + + + + + + + + + + + + + + + containing function + To keep a flow within limits. [NIST] + A vacuum bag contains debris vacuumed from a house. [NIST] + to contain + + + + + + + + + + + + + + + + + + + + + conveying function + shifting function + to convey + to shift + transferring function + To shift, or convey, a flow (material, energy, signal) from one place to another. [NIST] + to transfer + + + + + + + + + + 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] + sea water with sand + heterogeneous mixture + + + + + + + + + + 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] + air + sea water + homogeneous mixture + + + + + + + + + + blend + mixture + portion of mixture + 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] + portion of milk + sand + sea water + sea water with sand + portion of mixed material + + + + + + + + + + + IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). + + 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] + chemical substance + + + + + + + + + + being contained + The state of keeping a flow within spatial limits. [Allotrope] + A vacuum bag contains debris vacuumed from a house. [NIST] + containing state + + + + + + + + + + + + + + + + + + + + true + + deliver + transmitting + Transferring is channeling a flow (material, energy, signal) from one place to another. [NIST] + transferring + + + + + + + + + + + + + + + true + true + + channeling + localization + spatial process + A processing that affects the spatial location or orientation of some participants. [Allotrope] + localizing + + + + + + + + + true + + Controlling is changing or regulating a flow in its magnitude. [NIST, Allotrope] + controlling + + + + + + + + + true + http://www.loa.istc.cnr.it/old/Papers/D18.pdf + + state + A state is a homomeric, cumulative process in which all the temporal parts are described by the same expression used for the whole. [Allotrope] + corroding + state + + + + + + + + + true + + modifying + 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] + changing + + + + + + + + + + storing + Storing is containing or collecting flows to accumulate. [NIST] + storing state + + + + + + + + + + providing + Providing is the state of accumulating or supplying a material or energy flow. [NIST] + providing state + + + + + + + + + true + + An activity is a process that is cumulative but not homomeric. [Allotrope, DOLCE] + Same as process in DOLCE. [Allotrope] + activity + + + + + + + + + true + + material state + 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] + state of matter + + + + + + + + + true + + solid state of matter + 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] + solid + + + + + + + + + true + + liquid state of matter + 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] + liquid + + + + + + + + + true + + gaseous + gaseous state of matter + 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] + gas + + + + + + + + + true + + plasma state of matter + 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] + plasma + + + + + + + + + true + Green Book, 2nd ed.: IUPAC Quantities, Units and Symbols in Physical Chemistry. Second Edition, Blackwell Scientific Publications, Oxford, 1993. + + amount concentration + amount concentration (quality) + amount of substance concentration + molar concentration + molarity + molarity (quality) + substance concentration + substance concentration (quality) + 2019-08-19 Changed pref label. [Allotrope] + 2020-05-11 Changed pref label to molar concentration. [Allotrope] + 2020-06-18 Added alt labels. [Allotrope] + Molar concentration is the ratio of molar amount of a substance divided by volume of mixture containing the amount of substance. [Allotrope] + molar concentration (quality) + + + + + + + + + + + + + + + + + A chemical substance quality is a quality that inheres in some portion of chemical substance. [Allotrope] + chemical substance quality + + + + + + + + + + + atomic mass + molecular mass + 2020-03-16 Changed pref label. [Allotrope] + 2020-03-16 Subclassed under pato:mass. [Allotrope] + 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] + molecular mass (molecular quality) + + + + + + + + + + + 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] + hygroscopicity + + + + + + + + + true + + A classification is a proposition that categorizes things into classes or collections of things differentiated by some criteria. [Allotrope] + classification + + + + + + + + + true + + + + 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] + facet + + + + + + + + + true + + + A representation form is a type of information content entity that represents an entity in a certain way. [Allotrope] + plot as representation form of a temperature profile + representation form + + + + + + + + + + + material cleaned + part cleaned + part cleaned role + 2019-10-02 Changed pref label. [Allotrope] + Material that is undergoing a cleaning process. [Allotrope] + material cleaned role + + + + + + + + + + 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] + 2018-12-05 Moved to AFO to maintain single inheritence [Allotrope] + support role + + + + + + + + + Hubka, Eder, Ernst, Design Science, Springer, 1996 + + operand + The role of a participant that is being changed in the process (passive participant) from an input state to an output state. [Allotrope] + operand role + + + + + + + + + + + additive + Additive is a role of material that is added to a mixture in order to achieve a supportive purpose. [Allotrope] + additive role + + + + + + + + + + + PAC, 1996, 68, 155 (Glossary of terms used in chemical kinetics, including reaction dynamics.) + + catalyst + 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] + catalyst role + + + + + + + + + + debris + Debris is a role of material to be waste. [Allotrope] + debris role + + + + + + + + + + + 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 + + detergent + 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] + detergent role + + + + + + + + + + intermedate reagent role + intermediate + intermediate reagent role + intermediate role + reaction intermediate + 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] + reaction intermediate role + + + + + + + + + + reactant + starting material + Reactant role is a role of a chemical entity that is present at the start of a reaction. [Allotrope] + reactant role + + + + + + + + + + detergent + detergent role + washing agent + washing agent role + Cleaning agent role is a role of material used for cleaning something. [Allotrope] + cleaning agent role + + + + + + + + + + ingredient + Ingredient is a role of material that is used in a material combining process to produce a new material. [Allotrope] + ingredient role + + + + + + + + + + The role of a participant of a cleaning process. [Allotrope] + cleaning role + + + + + + + + + + A synthesis role is a role of a material that is participating in a synthesis (material conversion) process. [Allotrope] + synthesis role + + + + + + + + + + A formulation role is a role of a material that is participating in a formulation process. [Allotrope] + formulation role + + + + + + + + + + API + active pharmaceutical ingredient + drug substance + drug substance role + 2020-06-22 Add alt labels. [Allotrope] + 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] + active pharmaceutical ingredient role + + + + + + + + + + by-product + A material role of an expected but not desired product of a synthesis. [Allotrope] + the leaving group in a de-protection step. + by-product role + + + + + + + + + + chemical product + product + A role of a material that is intended and desired to be produced in a synthesis. [Allotrope] + product role + + + + + + + + + + batch + lot + lot role + 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] + batch role + + + + + + + + + + 2019-08-27 Fixed OWL definition, bug #694. [Allotrope] + A filtration role is a role of a material in a filtration process. [Allotrope] + filtration role + + + + + + + + + + flush + rinse + rinse solution + rinsing agent + rinsing role + rinsing solution + 2019-09-20 Changed definition. [Allotrope] + The rinse solution role is a cleaning agent role of a fluid used to flush something in order to remove contaminants. [Allotrope] + rinse solution role + + + + + + + + + + impurity + 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] + 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. + impurity role + + + + + + + + + + degradation product + 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] + degradation product role + + + + + + + + + + + unidentified degradation product + 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] + unidentified degradation product role + + + + + + + + + + + unspecified degradation product + 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] + unspecified degradation product role + + + + + + + + + + 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] + Starting materials are normally commercially available and of defined chemical and physical properties and structure. [ICH-Q3A] + starting material role + + + + + + + + + + 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] + limiting reagent role + + + + + + + + + + enantiomere + enantiomeric impurity + 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] + enantiomeric impurity role + + + + + + + + + + contaminant + contaminant role + extraneous contaminant + An extraneous contaminant role is an impurity role arising from any source extraneous to the manufacturing process. [ICH-Q3A] + extraneous contaminant role + + + + + + + + + + identified impurity + An impurity for which a structural characterization has been achieved. [ICH-Q3A] + identified impurity role + + + + + + + + + + potential impurity + 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] + potential impurity role + + + + + + + + + + specified impurity + 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] + specified impurity role + + + + + + + + + + unidentified impurity + 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] + unidentified impurity role + + + + + + + + + + unspecified impurity + 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] + unspecified impurity role + + + + + + + + + + identified degradation product + A degradation product role for which a structural characterization has been achieved. [ICH-Q3A] + identified degradation product role + + + + + + + + + + specified degradation product + 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] + specified degradation product role + + + + + + + + + + sample + sample (preparation) + sample role + A sample role (preparation) is a role of a material that is prepared for a bearing the sample role in an experiment. [Allotrope] + sample role (preparation) + + + + + + + + + + + drying additive + A drying additive role is the role of a material in a drying process that supports the drying process. [Allotrope] + drying additive role + + + + + + + + + + A drying role role is a role realized in some drying process. [Allotrope] + drying role + + + + + + + + + + drying agent + drying agent role + drying medium + A drying medium role is a drying role of a material that takes or transports the solvent from the material being dried. [Allotrope] + drying medium role + + + + + + + + + + dried material + dried material role + material dried + Material dried role is the drying role of the material being dried. [Allotrope] + material dried role + + + + + + + + + + reaction mixture + A reaction mixture role is a role of a chemical mixture undergoing some chemical reaction. [Allotrope] + reaction mixture role + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + 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 + 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 + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + + + + + continuant + Continuant + continuant + 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. + 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 + 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 + + + + + + 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]) + 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]) + 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]) + 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]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + BFO:0000002 + + continuant + continuant + + + + + + + + + occurrent + Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. + 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 + 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. + 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. + 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. + + + + 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]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + 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]) + + + 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]) + 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]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (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] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + + + + + t-region + TemporalRegion + 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 + + 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]) + All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) + Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) + (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] + (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] + (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] + + temporal region + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + 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]) + 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) + + + + (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] + BFO:0000015 + + process + process + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + 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. + + + 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]) + 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]) + (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] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + 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. + + + + 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]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (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] + (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] + + realizable entity + + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + + + 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]) + 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]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (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] + + quality + + + + + + + + + sdc + SpecificallyDependentContinuant + specifically dependent continuant + 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 + of one-sided specifically dependent continuants: the mass of this tomato + 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. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + 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. + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; 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]) + 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]) + 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. + + + + + (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] + (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] + + specifically dependent continuant + + + + + + + + + role + Role + 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. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + 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. + 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. + + + 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]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + + + + + fiat-object-part + FiatObjectPart + 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 + the FMA:regional parts of an intact human body. + the Western hemisphere of the Earth + the division of the brain into regions + the division of the planet into hemispheres + the dorsal and ventral surfaces of the body + the upper and lower lobes of the left lung + BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions + + 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]) + (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] + + fiat object part + + + + + + + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + 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) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + 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). + 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. + + 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]) + (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] + + object aggregate + + + + + + + + + gdc + GenericallyDependentContinuant + 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. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + 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. + 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]) + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + BFO:0000031 + + generically dependent continuant + generically dependent continuant + + + + + + + + + function + Function + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + 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. + + + 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]) + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + function + + + + + + + + + p-boundary + ProcessBoundary + the boundary between the 2nd and 3rd year of your life. + 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]) + + Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) + (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] + (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] + + process boundary + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + 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 + 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. + 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. + + + + 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]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (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] + (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] + BFO:0000040 + + material entity + material entity + + + + + + + + + process-profile + ProcessProfile + 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 + 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. + 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. + 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]) + + 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]) + (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] + (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] + + process profile + + + + + + + + + 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. + + -1 + 0.000548579903 + 0.0 + KEGG:C05359 + PMID:21614077 + Wikipedia:Electron + electron + chebi_ontology + Elektron + beta + beta(-) + beta-particle + e + e(-) + e- + negatron + CHEBI:10545 + + electron + + + + + + + + + Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. + + chebi_ontology + Mycoplasma genitalium metabolites + CHEBI:131604 + + Mycoplasma genitalium metabolite + + + + + + + + + A molecular entity that can undergo reduction by the gain of hydrogen atom(s). + + R + * + chebi_ontology + A + CHEBI:13193 + + hydrogen acceptor + + + + + + + + + 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. + + Wikipedia:Volatile_organic_compound + chebi_ontology + VOC + VOCs + volatile organic compounds + CHEBI:134179 + + volatile organic compound + + + + + + + + + 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. + + Wikipedia:Mineral_acid + chebi_ontology + inorganic acids + mineral acid + mineral acids + CHEBI:138103 + + inorganic acid + + + + + + + + + Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). + + Wikipedia:https://en.wikipedia.org/wiki/Gas + chebi_ontology + gas molecular entities + gaseous molecular entities + gaseous molecular entity + CHEBI:138675 + + gas molecular entity + + + + + + + + + + + + + + + + -1 + CH2NO2 + InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 + KXDHJXZQYSOELW-UHFFFAOYSA-M + 60.03212 + 60.00910 + NC([O-])=O + Beilstein:3903503 + CAS:302-11-4 + Gmelin:239604 + carbamate + chebi_ontology + Carbamat + Karbamat + carbamate ion + carbamic acid, ion(1-) + CHEBI:13941 + + carbamate + + + + + + + + + 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. + + Wikipedia:Impurity + impurity + chebi_ontology + contaminant + contaminants + impurities + CHEBI:143130 + + impurity + + + + + + + + + A molecular entity that can transfer an electron to another molecular entity. + + electron donor + chebi_ontology + Elektronendonator + donneur d'electron + CHEBI:15022 + + electron donor + + + + + + + + + A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. + + CHEBI:13699 + CHEBI:2377 + KEGG:C00028 + KEGG:C16722 + Acceptor + chebi_ontology + A + Akzeptor + Hydrogen-acceptor + Oxidized donor + accepteur + CHEBI:15339 + + acceptor + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A methyl ketone that consists of propane bearing an oxo group at C2. + + 0 + C3H6O + InChI=1S/C3H6O/c1-3(2)4/h1-2H3 + CSCPPACGZOOCGX-UHFFFAOYSA-N + 58.07914 + 58.04186 + CC(C)=O + CHEBI:13708 + CHEBI:22182 + CHEBI:2398 + CHEBI:40571 + Beilstein:635680 + CAS:67-64-1 + Gmelin:1466 + HMDB:HMDB0001659 + KEGG:C00207 + KEGG:D02311 + LIPID_MAPS_instance:LMFA12000057 + MetaCyc:ACETONE + PDBeChem:ACN + PMID:17190852 + PMID:17347819 + Reaxys:635680 + UM-BBD_compID:c0556 + Wikipedia:Acetone + ACETONE + Acetone + acetone + propan-2-one + chebi_ontology + 2-Propanone + Aceton + Azeton + Dimethyl ketone + Dimethylketon + Propanon + Pyroacetic ether + beta-Ketopropane + dimethylcetone + dimethylketone + methyl ketone + propanone + CHEBI:15347 + + acetone + + + + + + + + + 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. + + 0 + CH3OR + 31.034 + 31.01839 + *C(O)([H])[H] + CHEBI:13676 + CHEBI:14887 + CHEBI:26262 + CHEBI:57489 + CHEBI:8406 + KEGG:C00226 + Primary alcohol + chebi_ontology + 1-Alcohol + a primary alcohol + primary alcohols + CHEBI:15734 + + primary alcohol + + + + + + + + + + + + + + + + + + + + + + + + + + + A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects. + + -1 + CHO2 + InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)/p-1 + BDAGIHXWWSANSR-UHFFFAOYSA-M + 45.01744 + 44.99820 + [H]C([O-])=O + CHEBI:14276 + CHEBI:24081 + Beilstein:1901205 + CAS:71-47-6 + Gmelin:1006 + HMDB:HMDB0000142 + KEGG:C00058 + MetaCyc:FORMATE + PMID:17190852 + PMID:3946945 + Reaxys:1901205 + UM-BBD_compID:c0106 + Wikipedia:Formate + formate + chebi_ontology + HCO2 anion + aminate + formiate + formic acid, ion(1-) + formylate + hydrogen carboxylate + methanoate + CHEBI:15740 + + formate + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. + + 0 + H3N + InChI=1S/H3N/h1H3 + QGZKDVFQNNGYKY-UHFFFAOYSA-N + 17.03056 + 17.02655 + [H]N([H])[H] + CHEBI:13405 + CHEBI:13406 + CHEBI:13407 + CHEBI:13771 + CHEBI:22533 + CHEBI:44269 + CHEBI:44284 + CHEBI:44404 + CHEBI:7434 + Beilstein:3587154 + CAS:7664-41-7 + Drug_Central:4625 + Gmelin:79 + HMDB:HMDB0000051 + KEGG:C00014 + KEGG:D02916 + KNApSAcK:C00007267 + MetaCyc:AMMONIA + MolBase:930 + PDBeChem:NH3 + PMID:110589 + PMID:11139349 + PMID:11540049 + PMID:11746427 + PMID:11783653 + PMID:13753780 + PMID:14663195 + PMID:15092448 + PMID:15094021 + PMID:15554424 + PMID:15969015 + PMID:16008360 + PMID:16050680 + PMID:16348008 + PMID:16349403 + PMID:16614889 + PMID:16664306 + PMID:16842901 + PMID:17025297 + PMID:17439666 + PMID:17569513 + PMID:17737668 + PMID:18670398 + PMID:22002069 + PMID:22081570 + PMID:22088435 + PMID:22100291 + PMID:22130175 + PMID:22150211 + PMID:22240068 + PMID:22290316 + PMID:22342082 + PMID:22385337 + PMID:22443779 + PMID:22560242 + Reaxys:3587154 + Wikipedia:Ammonia + AMMONIA + Ammonia + ammonia + azane + chebi_ontology + Ammoniak + NH3 + R-717 + [NH3] + ammoniac + amoniaco + spirit of hartshorn + CHEBI:16134 + + ammonia + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The simplest monocarboxylic acid amide, obtained by formal condensation of formic acid with ammonia. The parent of the class of formaldehydes. + + 0 + CH3NO + InChI=1S/CH3NO/c2-1-3/h1H,(H2,2,3) + ZHNUHDYFZUAESO-UHFFFAOYSA-N + 45.04066 + 45.02146 + [H]C(N)=O + CHEBI:14275 + CHEBI:24078 + CHEBI:40895 + CHEBI:5143 + Beilstein:505995 + CAS:75-12-7 + Gmelin:824 + HMDB:HMDB0001536 + KEGG:C00488 + MetaCyc:FORMAMIDE + PDBeChem:ARF + PMID:11282235 + PMID:11545392 + PMID:12115814 + PMID:14750843 + PMID:15082074 + PMID:17184725 + PMID:19334838 + PMID:21215846 + PMID:21229996 + PMID:21573300 + PMID:21647491 + PMID:21647492 + PMID:21769603 + PMID:21932847 + Reaxys:505995 + UM-BBD_compID:c0796 + Wikipedia:Formamide + FORMAMIDE + Formamide + formamide + chebi_ontology + Ameisensaeureamid + Formamid + Methanamid + Methanamide + carbamaldehyde + formimidic acid + CHEBI:16397 + + formamide + + + + + + + + + peptide + 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. + + + peptide + + + + + + + + + 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. + + PMID:24934357 + PMID:29710396 + copper chelator + chebi_ontology + copper chelate + copper chelating agent + copper chelating agents + copper chelators + CHEBI:166831 + + copper chelator + + + + + + + + + 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. + + 0 + CH2OR2 + 30.026 + 30.01056 + *C(O)* + chebi_ontology + a secondary fatty alcohol + CHEBI:167095 + + secondary fatty alcohol + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + 0 + C6H6 + InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H + UHOVQNZJYSORNB-UHFFFAOYSA-N + 78.11184 + 78.04695 + c1ccccc1 + CHEBI:13876 + CHEBI:22703 + CHEBI:3025 + CHEBI:41187 + Beilstein:969212 + CAS:71-43-2 + Gmelin:1671 + HMDB:HMDB0001505 + KEGG:C01407 + PDBeChem:BNZ + PMID:11684179 + PMID:11993966 + PMID:12857942 + PMID:14677922 + PMID:15468289 + PMID:15935818 + PMID:16161967 + PMID:17373369 + PMID:18072742 + PMID:18407866 + PMID:18409691 + PMID:18836923 + PMID:19228219 + PMID:21325737 + PMID:23088855 + PMID:23222815 + PMID:23534829 + PMID:6353911 + PMID:8124204 + Reaxys:969212 + UM-BBD_compID:c0142 + Wikipedia:Benzene + BENZENE + Benzene + benzene + chebi_ontology + Benzen + Benzine + Benzol + Bicarburet of hydrogen + Coal naphtha + Mineral naphtha + Phene + Pyrobenzol + Pyrobenzole + [6]annulene + benzole + cyclohexatriene + phenyl hydride + CHEBI:16716 + + benzene + + + + + + + + + deoxyribonucleic acid + High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. + + + deoxyribonucleic acid + + + + + + + + + A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). + + 0 + COR2 + 28.010 + 27.99491 + [*]C([*])=O + CHEBI:13427 + CHEBI:13646 + CHEBI:24974 + CHEBI:6127 + CHEBI:8742 + KEGG:C01450 + Wikipedia:Ketone + Ketone + ketones + chebi_ontology + Keton + R-CO-R' + a ketone + cetone + ketones + CHEBI:17087 + + ketone + + + + + + + + + A molecular entity that can undergo oxidation by the loss of hydrogen atom(s). + + 0 + RH2 + 2.016 + 2.01565 + *([H])[H] + CHEBI:13233 + CHEBI:15018 + CHEBI:8785 + KEGG:C00030 + chebi_ontology + AH2 + Donor + Hydrogen-donor + Reduced acceptor + CHEBI:17499 + + hydrogen donor + + + + + + + + + + + + + + + + + + + + + + + + + + + A pseudohalide anion that is the conjugate base of hydrogen cyanide. + + -1 + CN + InChI=1S/CN/c1-2/q-1 + XFXPMWWXUTWYJX-UHFFFAOYSA-N + 26.01740 + 26.00362 + [C-]#N + CHEBI:14038 + CHEBI:3969 + CHEBI:41780 + Beilstein:1900509 + CAS:57-12-5 + Gmelin:89 + HMDB:HMDB0002084 + KEGG:C00177 + MetaCyc:CPD-13584 + PDBeChem:CYN + PMID:11386635 + PMID:14871577 + PMID:17554165 + PMID:7839575 + Reaxys:1900509 + Wikipedia:Cyanide + Cyanide + cyanide + nitridocarbonate(1-) + chebi_ontology + CN(-) + CN- + CYANIDE ION + Prussiate + Zyanid + CHEBI:17514 + + cyanide + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The simplest member of the class toluenes consisting of a benzene core which bears a single methyl substituent. + + 0 + C7H8 + InChI=1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3 + YXFVVABEGXRONW-UHFFFAOYSA-N + 92.13842 + 92.06260 + Cc1ccccc1 + CHEBI:15248 + CHEBI:27022 + CHEBI:44023 + CHEBI:9624 + Beilstein:635760 + CAS:108-88-3 + DrugBank:DB01900 + Gmelin:2456 + KEGG:C01455 + PDBeChem:MBN + PMID:11182169 + PMID:11314682 + PMID:11846266 + PMID:11991009 + PMID:12062755 + PMID:12213539 + PMID:12237258 + PMID:12784113 + PMID:12876426 + PMID:14512097 + PMID:14559343 + PMID:14605898 + PMID:15015825 + PMID:15019953 + PMID:15119846 + PMID:15193425 + PMID:15542760 + PMID:15567510 + PMID:15695158 + PMID:15796064 + PMID:16316648 + PMID:16348226 + PMID:16601996 + PMID:17145141 + PMID:17175136 + PMID:17497535 + PMID:17725881 + PMID:18397809 + PMID:18832024 + PMID:19261054 + PMID:19384711 + PMID:19429395 + PMID:19635754 + PMID:19765629 + PMID:19825861 + PMID:19928203 + PMID:19969016 + PMID:20347282 + PMID:20837561 + PMID:21430649 + PMID:21655021 + PMID:21731073 + PMID:21802510 + PMID:21840036 + Reaxys:635760 + UM-BBD_compID:c0114 + Wikipedia:Toluene + TOLUENE + Toluene + toluene + chebi_ontology + Toluen + Toluol + methylbenzene + phenylmethane + CHEBI:17578 + + toluene + + + + + + + + + A substance to which an electron may be transferred. + + CHEBI:14207 + CHEBI:14716 + CHEBI:7835 + KEGG:C02177 + electron acceptor + chebi_ontology + Elektronenakzeptor + Oxidized donor + CHEBI:17654 + + electron acceptor + + + + + + + + + + + + + + + + + + + + + + + + + + + + A member of the class of formamides that is formamide in which the amino hydrogens are replaced by methyl groups. + + 0 + C3H7NO + InChI=1S/C3H7NO/c1-4(2)3-5/h3H,1-2H3 + ZMXDDKWLCZADIW-UHFFFAOYSA-N + 73.09382 + 73.05276 + [H]C(=O)N(C)C + CHEBI:12425 + CHEBI:21454 + CHEBI:42077 + CHEBI:7076 + CAS:68-12-2 + DrugBank:DB01844 + HMDB:HMDB0001888 + KEGG:C03134 + MetaCyc:CPD-581 + PDBeChem:DMF + PMID:18666198 + PMID:19608215 + PMID:3824392 + Reaxys:605365 + Wikipedia:Dimethylformamide + N,N-Dimethylformamide + N,N-dimethylformamide + chebi_ontology + DMF + Dimethylformamide + N,N-Dimethylmethanamide + N-Formyldimethylamine + CHEBI:17741 + + N,N-dimethylformamide + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group. + + 0 + CH4O + InChI=1S/CH4O/c1-2/h2H,1H3 + OKKJLVBELUTLKV-UHFFFAOYSA-N + 32.04186 + 32.02621 + CO + CHEBI:14588 + CHEBI:25227 + CHEBI:44080 + CHEBI:44553 + CHEBI:6816 + Beilstein:1098229 + CAS:67-56-1 + Gmelin:449 + HMDB:HMDB0001875 + KEGG:C00132 + KEGG:D02309 + MetaCyc:METOH + PDBeChem:MOH + PMID:11141607 + PMID:11430978 + PMID:11489599 + PMID:11680737 + PMID:11684179 + PMID:14012711 + PMID:14678513 + PMID:14760634 + PMID:15172721 + PMID:15906011 + PMID:16705261 + PMID:17451998 + PMID:17733096 + PMID:19064074 + PMID:19850112 + PMID:20314698 + Reaxys:1098229 + UM-BBD_compID:c0132 + Wikipedia:Methanol + METHANOL + Methanol + methanol + chebi_ontology + CH3OH + MeOH + Methyl alcohol + Methylalkohol + carbinol + spirit of wood + wood alcohol + wood naphtha + wood spirit + CHEBI:17790 + + methanol + + + + + + + + + + + + + + + + A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group. + + 0 + C3H8O + InChI=1S/C3H8O/c1-3(2)4/h3-4H,1-2H3 + KFZMGEQAYNKOFK-UHFFFAOYSA-N + 60.09502 + 60.05751 + CC(C)O + CHEBI:14897 + CHEBI:26280 + CHEBI:43588 + CHEBI:8467 + Beilstein:635639 + CAS:67-63-0 + DrugBank:DB04402 + Drug_Central:4215 + Gmelin:1464 + HMDB:HMDB0000863 + KEGG:C01845 + KEGG:D00137 + KNApSAcK:C00048438 + MetaCyc:ISO-PROPANOL + PDBeChem:IPA + PMID:24524727 + PMID:24653974 + Reaxys:635639 + UM-BBD_compID:c0519 + Wikipedia:Isopropyl_Alcohol + YMDB:YMDB01718 + Propan-2-ol + propan-2-ol + chebi_ontology + 1-methylethanol + 1-methylethyl alcohol + 2-Propanol + 2-hydroxypropane + IPA + ISOPROPYL ALCOHOL + Isopropanol + Isopropyl alcohol + Isopropylalkohol + i-Propylalkohol + i-propanol + isopropyl alcohol + sec-propanol + CHEBI:17824 + + propan-2-ol + + + + + + + + + A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. + + CHEBI:14202 + CHEBI:4697 + KEGG:C01351 + Donor + chebi_ontology + Donator + donneur + CHEBI:17891 + + donor + + + + + + + + + + 0 + COR2 + 28.01010 + 27.99491 + [*]C([*])=O + CHEBI:14136 + CHEBI:23663 + CHEBI:4485 + KEGG:C02146 + Dialkyl ketone + dialkyl ketone + chebi_ontology + dialkyl ketones + CHEBI:18044 + + dialkyl ketone + + + + + + + + + '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. + + CHEBI:14517 + CHEBI:25054 + CHEBI:6486 + KEGG:C01356 + Lipid + lipids + chebi_ontology + CHEBI:18059 + + lipid + + + + + + + + + + + + + + + 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. + + 0 + CNR + 26.01740 + 26.00307 + [*]C#N + CHEBI:13212 + CHEBI:13426 + CHEBI:13660 + CHEBI:25547 + CHEBI:7584 + KEGG:C00726 + Nitrile + nitrile + nitriles + chebi_ontology + Nitril + R-CN + a nitrile + nitrilos + CHEBI:18379 + + nitrile + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A one-carbon compound consisting of a methine group triple bonded to a nitrogen atom + + 0 + CHN + InChI=1S/CHN/c1-2/h1H + LELOWRISYMNNSU-UHFFFAOYSA-N + 27.02530 + 27.01090 + C#N + CHEBI:13362 + CHEBI:5786 + CAS:74-90-8 + HMDB:HMDB0060292 + KEGG:C01326 + KNApSAcK:C00007569 + MetaCyc:HCN + PMID:19849830 + PMID:26700190 + PMID:26778429 + PMID:26823582 + PMID:26940198 + PMID:27123778 + Reaxys:1718793 + Wikipedia:Hydrogen_cyanide + Hydrogen cyanide + hydridonitridocarbon + hydrogen cyanide + hydrogen(nitridocarbonate) + methanenitrile + chebi_ontology + Blausaeure + Cyanwasserstoff + HCN + [CHN] + formonitrile + hydrocyanic acid + CHEBI:18407 + + hydrogen cyanide + + + + + + + + + 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. + + acyl group + alkanoyl + chebi_ontology + acyl groups + alkanoyl group + groupe acyle + CHEBI:22221 + + acyl group + + + + + + + + + + chebi_ontology + CHEBI:22368 + + alpha-1-microglobulin-Ig alpha complex chromophores + + + + + + + + + A monoatomic or polyatomic species having one or more elementary charges of the electron. + + Anion + anion + chebi_ontology + Anionen + aniones + anions + CHEBI:22563 + + anion + + + + + + + + + A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. + + chebi_ontology + antioxidants + antioxydant + antoxidant + CHEBI:22586 + + antioxidant + + + + + + + + + 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). + + KEGG:C00701 + Base + base + chebi_ontology + Base1 + Base2 + Basen + Nucleobase + bases + CHEBI:22695 + + base + + + + + + + + + Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. + + chebi_ontology + CHEBI:22712 + + benzenes + + + + + + + + + Any ketone that is butane substituted by an oxo group at unspecified position. + + chebi_ontology + butanones + CHEBI:22951 + + butanone + + + + + + + + + + + + + + + The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. + + 0 + CH2NO + 44.03272 + 44.01364 + *C(N)=O + PMID:24168430 + carbamoyl + chebi_ontology + -C(O)NH2 + -CONH2 + aminocarbonyl + carbamyl + carbamyl group + carboxamide + CHEBI:23004 + + carbamoyl group + + + + + + + + + + 0 + CO + 28.01010 + 27.99491 + O=C(*)* + carbonyl + carbonyl group + chebi_ontology + >C=O + CHEBI:23019 + + carbonyl group + + + + + + + + + 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. + + Wikipedia:Chromophore + chromophore + chebi_ontology + chromophores + CHEBI:23240 + + chromophore + + + + + + + + + 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). + + Wikipedia:Cofactor_(biochemistry) + cofactor + cofactors + chebi_ontology + CHEBI:23357 + + cofactor + + + + + + + + + + molecular entity + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + 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 + + + molecular entity + chebi_ontology + entidad molecular + entidades moleculares + entite moleculaire + molecular entities + molekulare Entitaet + CHEBI:23367 + + molecular entity + + + + + + + + + + + + + + + Salts and C-organyl derivatives of hydrogen cyanide, HC#N. + + cyanides + chebi_ontology + CHEBI:23424 + + cyanides + + + + + + + + + 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. + + chebi_ontology + drugs + medicine + CHEBI:23888 + + drug + + + + + + + + + + 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. + + enzyme inhibitor + chebi_ontology + enzyme inhibitors + inhibidor enzimatico + inhibidores enzimaticos + inhibiteur enzymatique + inhibiteurs enzymatiques + CHEBI:23924 + + enzyme inhibitor + + + + + + + + + + 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. + + 0 + HOR + 17.007 + 17.00274 + O[*] + LIPID_MAPS_class:LMFA05 + MetaCyc:Fatty-Alcohols + Wikipedia:Fatty_alcohol + fatty alcohol + chebi_ontology + Fettalkohol + Fettalkohole + alcool gras + fatty alcohols + CHEBI:24026 + + fatty alcohol + + + + + + + + + + chebi_ontology + CHEBI:24028 + + iron(3+) chelator + + + + + + + + + Amides with the general formula R(1)R(2)NCHO (R(1) and R(2) can be H). + + chebi_ontology + CHEBI:24079 + + formamides + + + + + + + + + A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. + + chemical entity + chebi_ontology + CHEBI:24431 + + chemical entity + + + + + + + + + A role played by the molecular entity or part thereof within a biological context. + + chebi_ontology + biological function + CHEBI:24432 + + biological role + + + + + + + + + + + + + + + A defined linked collection of atoms or a single atom within a molecular entity. + + group + chebi_ontology + Gruppe + Rest + groupe + grupo + grupos + CHEBI:24433 + + group + + + + + + + + + + + A cyclic compound having as ring members atoms of carbon and at least of one other element. + + chebi_ontology + organic heterocycle + organic heterocyclic compounds + CHEBI:24532 + + organic heterocyclic compound + + + + + + + + + A compound consisting of carbon and hydrogen only. + + hydrocarbon + hydrocarbons + chebi_ontology + Kohlenwasserstoff + Kohlenwasserstoffe + hidrocarburo + hidrocarburos + hydrocarbure + CHEBI:24632 + + hydrocarbon + + + + + + + + + + + + + + + + + Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). + + chebi_ontology + CHEBI:24651 + + hydroxides + + + + + + + + + + + + + + + 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). + + oxoacid + oxoacids + chebi_ontology + oxacids + oxiacids + oxo acid + oxy-acids + oxyacids + CHEBI:24833 + + oxoacid + + + + + + + + + + + chebi_ontology + inorganic anions + CHEBI:24834 + + inorganic anion + + + + + + + + + A molecular entity that contains no carbon. + + chebi_ontology + anorganische Verbindungen + inorganic compounds + inorganic entity + inorganic molecular entities + inorganics + CHEBI:24835 + + inorganic molecular entity + + + + + + + + + A compound which can carry specific ions through membranes of cells or organelles. + + Wikipedia:Ionophore + ionophore + chebi_ontology + ionophores + CHEBI:24869 + + ionophore + + + + + + + + + A molecular entity having a net electric charge. + + Ion + ion + chebi_ontology + Ionen + iones + ions + CHEBI:24870 + + ion + + + + + + + + + Any ionophore capable of transportation of iron ions across membranes. + + chebi_ontology + iron ionophores + CHEBI:24874 + + iron ionophore + + + + + + + + + A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. + + chebi_ontology + CHEBI:25078 + + luciferin + + + + + + + + + Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. + + CHEBI:26619 + CHEBI:35220 + metabolite + chebi_ontology + metabolites + primary metabolites + secondary metabolites + CHEBI:25212 + + metabolite + + + + + + + + + + chebi_ontology + mitochondrial electron transport chain inhibitors + mitochondrial electron-transport chain inhibitor + mitochondrial respiratory chain inhibitors + CHEBI:25355 + + mitochondrial respiratory-chain inhibitor + + + + + + + + + Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. + + molecule + chebi_ontology + Molekuel + molecula + molecules + neutral molecular compounds + CHEBI:25367 + + molecule + + + + + + + + + + + + + + + An oxoacid containing a single carboxy group. + + chebi_ontology + monocarboxylic acids + CHEBI:25384 + + monocarboxylic acid + + + + + + + + + + + + + + + + + 0 + N + 14.007 + 14.00307 + WebElements:N + nitrogen + chebi_ontology + 7N + N + Stickstoff + azote + nitrogen + nitrogeno + CHEBI:25555 + + nitrogen atom + + + + + + + + + + nonmetal + chebi_ontology + Nichtmetall + Nichtmetalle + no metal + no metales + non-metal + non-metaux + nonmetal + nonmetals + CHEBI:25585 + + nonmetal atom + + + + + + + + + + + chebi_ontology + organic heteromonocyclic compounds + CHEBI:25693 + + organic heteromonocyclic compound + + + + + + + + + + Any organic ion with a net negative charge. + + chebi_ontology + organic anions + CHEBI:25696 + + organic anion + + + + + + + + + An organooxygen compound with formula ROR, where R is not hydrogen. + + 0 + OR2 + 15.99940 + 15.99491 + [*]O[*] + ether + ethers + chebi_ontology + ethers + CHEBI:25698 + + ether + + + + + + + + + + + chebi_ontology + organic ions + CHEBI:25699 + + organic ion + + + + + + + + + An alcohol derived from an aliphatic compound. + + 0 + HOR + 17.007 + 17.00274 + O* + KEGG:C02525 + Aliphatic alcohol + chebi_ontology + aliphatic alcohols + an aliphatic alcohol + CHEBI:2571 + + aliphatic alcohol + + + + + + + + + + An oxide is a chemical compound of oxygen with other chemical elements. + + oxide + chebi_ontology + oxides + CHEBI:25741 + + oxide + + + + + + + + + + chebi_ontology + CHEBI:25747 + + oxidized luciferins + + + + + + + + + + + + + + + + + 0 + O + InChI=1S/O + QVGXLLKOCUKJST-UHFFFAOYSA-N + 15.99940 + 15.99491 + [O] + KEGG:C00007 + WebElements:O + oxygen + chebi_ontology + 8O + O + Sauerstoff + oxigeno + oxygen + oxygene + CHEBI:25805 + + oxygen atom + + + + + + + + + + + + + + + + oxygen molecular entity + chebi_ontology + oxygen molecular entities + CHEBI:25806 + + oxygen molecular entity + + + + + + + + + A ketone that is propane carrying at least one oxo substituent. + + chebi_ontology + CHEBI:26292 + + propanones + + + + + + + + + + chebi_ontology + CHEBI:26671 + + sideramine + + + + + + + + + + + Any of low-molecular-mass iron(III)-chelating compounds produced by microorganisms for the purpose of the transport and sequestration of iron. + + siderophore + chebi_ontology + ferrioxamine + ferrioxamines + ironophore + siderochrome + siderochromes + siderophores + CHEBI:26672 + + siderophore + + + + + + + + + + + + + + + + + + A cyclic ether that is butane in which one hydrogen from each methyl group is substituted by an oxygen. + + 0 + C4H8O + InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2 + WYURNTSHIVDZCO-UHFFFAOYSA-N + 72.10570 + 72.05751 + C1CCOC1 + Beilstein:102391 + CAS:109-99-9 + Gmelin:1767 + HMDB:HMDB0000246 + PMID:12571688 + PMID:1811956 + PMID:1911404 + PMID:19716170 + PMID:21316415 + PMID:21842397 + PMID:2675957 + Reaxys:102391 + UM-BBD_compID:c0019 + Wikipedia:THF + oxolane + chebi_ontology + 1,4-epoxybutane + THF + butane alpha,delta-oxide + butylene oxide + furanidine + tetrahydrofuran + tetramethylene oxide + CHEBI:26911 + + oxolane + + + + + + + + + + Any oxacycle having an oxolane (tetrahydrofuran) skeleton. + + chebi_ontology + CHEBI:26912 + + oxolanes + + + + + + + + + Any member of the class of benzenes that is a substituted benzene in which the substituents include one (and only one) methyl group. + + chebi_ontology + CHEBI:27024 + + toluenes + + + + + + + + + A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. + + chebi_ontology + univalent acyl group + univalent carboacyl groups + univalent carboxylic acyl groups + CHEBI:27207 + + univalent carboacyl group + + + + + + + + + + + + + + + + + 0 + C + InChI=1S/C + OKTJSMMVPCPJKN-UHFFFAOYSA-N + 12.01070 + 12.00000 + [C] + CHEBI:23009 + CHEBI:3399 + CAS:7440-44-0 + KEGG:C06265 + WebElements:C + carbon + chebi_ontology + 6C + C + Carbon + Kohlenstoff + carbon + carbone + carbonium + carbono + CHEBI:27594 + + carbon atom + + + + + + + + + + A surfactant (or a mixture containing one or more surfactants) having cleaning properties in dilute solutions. + + CHEBI:23648 + CHEBI:4456 + KEGG:C01689 + detergent + chebi_ontology + Detergents + CHEBI:27780 + + detergent + + + + + + + + + + + + + + + + + + + + + + + + A dialkyl ketone that is a four-carbon ketone carrying a single keto- group at position C-2. + + 0 + C4H8O + InChI=1S/C4H8O/c1-3-4(2)5/h3H2,1-2H3 + ZWEHNKRNPOVVGH-UHFFFAOYSA-N + 72.10572 + 72.05751 + CCC(C)=O + CHEBI:25249 + CHEBI:6858 + Beilstein:741880 + CAS:78-93-3 + Gmelin:25656 + HMDB:HMDB0000474 + KEGG:C02845 + LIPID_MAPS_instance:LMFA12000043 + MetaCyc:MEK + PMID:20403429 + PMID:23050457 + Reaxys:741880 + UM-BBD_compID:c0020 + Wikipedia:Butanone + butan-2-one + chebi_ontology + 2-Butanon + 2-Butanone + 3-butanone + Aethylmethylketon + C2H5COCH3 + Ethyl methyl ketone + Ethylmethylketon + MEK + Methyl ethyl ketone + Methylethylketon + butanone + butanone 2 + ethyl methyl cetone + ethyl(methyl) ketone + ethylmethyl ketone + meetco + methyl acetone + methyl ethyl cetone + methyl(ethyl) ketone + methylacetone + methylethyl ketone + oxobutane + CHEBI:28398 + + butan-2-one + + + + + + + + + + + + + + + + + + + + + + + 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. + + 0 + CH3NO2 + InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4) + KXDHJXZQYSOELW-UHFFFAOYSA-N + 61.04006 + 61.01638 + NC(O)=O + CHEBI:22504 + CHEBI:23002 + CHEBI:3386 + CHEBI:44573 + Beilstein:1734754 + CAS:463-77-4 + DrugBank:DB04261 + Gmelin:130345 + KEGG:C01563 + PDBeChem:OUT + Wikipedia:Carbamic_acid + CARBAMIC ACID + Carbamic acid + carbamic acid + chebi_ontology + Aminoameisensaeure + Aminoformic acid + Carbamate + Carbamidsaeure + CHEBI:28616 + + carbamic acid + + + + + + + + + + + + + + + + The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid. + + -1 + CO2R + 44.00950 + 43.98983 + [O-]C([*])=O + CHEBI:13634 + CHEBI:24022 + CHEBI:4985 + KEGG:C02403 + PMID:18628202 + Fatty acid anion + chebi_ontology + Alkanate + Fettsaeureanion + Fettsaeureanionen + a fatty acid + acido graso anionico + acidos grasos anionicos + anion de l'acide gras + fatty acid anions + CHEBI:28868 + + fatty acid anion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An onium cation obtained by protonation of ammonia. + + +1 + H4N + InChI=1S/H3N/h1H3/p+1 + QGZKDVFQNNGYKY-UHFFFAOYSA-O + 18.03850 + 18.03383 + [H][N+]([H])([H])[H] + CHEBI:22534 + CHEBI:49783 + CHEBI:7435 + CAS:14798-03-9 + Gmelin:84 + KEGG:C01342 + MetaCyc:AMMONIUM + MolBase:929 + PDBeChem:NH4 + PMID:11319011 + PMID:11341317 + PMID:12096804 + PMID:14512268 + PMID:14879753 + PMID:16345391 + PMID:16903292 + PMID:17392693 + PMID:18515490 + PMID:19199063 + PMID:19596600 + PMID:19682559 + PMID:19716251 + PMID:21993530 + PMID:22265469 + PMID:22524020 + PMID:22562341 + PMID:22631217 + Reaxys:16093784 + Wikipedia:Ammonium + ammonium + azanium + chebi_ontology + Ammonium(1+) + NH4(+) + NH4+ + [NH4](+) + ammonium cation + ammonium ion + CHEBI:28938 + + ammonium + + + + + + + + + + + + + + + + The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. + + -1 + CO2R + 44.00950 + 43.98983 + [O-]C([*])=O + CHEBI:13626 + CHEBI:13945 + CHEBI:23026 + CHEBI:58657 + chebi_ontology + a carboxylate + carboxylic acid anions + carboxylic anions + CHEBI:29067 + + carboxylic acid anion + + + + + + + + + + + + + + + + + + + + + + + -1 + H2N + InChI=1S/H2N/h1H2/q-1 + HYGWNUKOUCZBND-UHFFFAOYSA-N + 16.02262 + 16.01927 + [H][N-][H] + amide + azanide + dihydridonitrate(1-) + chebi_ontology + NH2(-) + CHEBI:29337 + + azanide + + + + + + + + + + + + + + + + A divalent inorganic anion resulting from the removal of two protons from ammonia. + + -2 + HN + InChI=1S/HN/h1H/q-2 + DZQYTNGKSBCIOE-UHFFFAOYSA-N + 15.01468 + 15.01200 + [N--][H] + azanediide + hydridonitrate(2-) + chebi_ontology + NH(2-) + imide + CHEBI:29340 + + hydridonitrate(2-) + + + + + + + + + A carboxamide derived from a monocarboxylic acid. + + 0 + CNOR3 + 42.01680 + 41.99799 + [*]N([*])C([*])=O + CHEBI:13211 + CHEBI:22207 + CHEBI:25383 + CHEBI:6977 + chebi_ontology + monocarboxylic acid amides + CHEBI:29347 + + monocarboxylic acid amide + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + 0 + CH2O2 + InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3) + BDAGIHXWWSANSR-UHFFFAOYSA-N + 46.02538 + 46.00548 + [H]C(O)=O + CHEBI:24082 + CHEBI:42460 + CHEBI:5145 + BPDB:1749 + Beilstein:1209246 + CAS:64-18-6 + DrugBank:DB01942 + Gmelin:1008 + HMDB:HMDB0000142 + KEGG:C00058 + KNApSAcK:C00001182 + LIPID_MAPS_instance:LMFA01010040 + MetaCyc:FORMATE + PDBeChem:FMT + PMID:12591956 + PMID:14637377 + PMID:15811469 + PMID:16120414 + PMID:16185830 + PMID:16222862 + PMID:16230297 + PMID:16445901 + PMID:16465784 + PMID:18034701 + PMID:18397576 + PMID:22080171 + PMID:22280475 + PMID:22304812 + PMID:22385261 + PMID:22447125 + PMID:22483350 + PMID:22499553 + PMID:22540994 + PMID:22606986 + PMID:22622393 + PMID:3946945 + PMID:7361809 + Patent:CN101481304 + Reaxys:1209246 + Wikipedia:Formic_acid + FORMIC ACID + Formic acid + formic acid + chebi_ontology + Acide formique + Ameisensaeure + H-COOH + HCO2H + HCOOH + Methanoic acid + aminic acid + bilorin + formylic acid + hydrogen carboxylic acid + methoic acid + CHEBI:30751 + + formic acid + + + + + + + + + A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. + + 0 + HOR + 17.007 + 17.00274 + O[*] + CHEBI:13804 + CHEBI:22288 + CHEBI:2553 + KEGG:C00069 + Alcohol + alcohols + chebi_ontology + an alcohol + CHEBI:30879 + + alcohol + + + + + + + + + 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. + + CHEBI:22473 + CHEBI:2633 + KEGG:C00241 + Amide + amides + chebi_ontology + CHEBI:32988 + + amide + + + + + + + + + Intended use of the molecular entity or part thereof by humans. + + chebi_ontology + CHEBI:33232 + + application + + + + + + + + + A particle not known to have substructure. + + elementary particle + chebi_ontology + elementary particles + CHEBI:33233 + + fundamental particle + + + + + + + + + + + + + + + + chebi_ontology + oxoacid derivatives + CHEBI:33241 + + oxoacid derivative + + + + + + + + + + + chebi_ontology + inorganic hydrides + CHEBI:33242 + + inorganic hydride + + + + + + + + + + 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. + + chebi_ontology + organic fundamental parents + organic parent hydrides + CHEBI:33245 + + organic fundamental parent + + + + + + + + + Any substituent group which does not contain carbon. + + chebi_ontology + inorganic groups + CHEBI:33246 + + inorganic group + + + + + + + + + + + + + + + Any substituent group or skeleton containing carbon. + + chebi_ontology + organic groups + CHEBI:33247 + + organic group + + + + + + + + + Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. + + organyl group + organyl groups + chebi_ontology + groupe organyle + grupo organilo + grupos organilo + CHEBI:33249 + + organyl group + + + + + + + + + + + + + + + + + + + + + A chemical entity constituting the smallest component of an element having the chemical properties of the element. + + CHEBI:22671 + CHEBI:23907 + atom + chebi_ontology + atome + atomo + atoms + atomus + element + elements + CHEBI:33250 + + atom + + + + + + + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + + nucleus + chebi_ontology + Atomkern + Kern + noyau + noyau atomique + nuclei + nucleo + nucleo atomico + nucleus atomi + CHEBI:33252 + + atomic nucleus + + + + + + + + + + Heavy nuclear particle: proton or neutron. + + nucleon + chebi_ontology + Nukleon + Nukleonen + nucleons + CHEBI:33253 + + nucleon + + + + + + + + + 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. + + primary amide + primary amides + chebi_ontology + CHEBI:33256 + + primary amide + + + + + + + + + + An anion consisting of more than one atom. + + chebi_ontology + polyatomic anions + CHEBI:33273 + + polyatomic anion + + + + + + + + + A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. + + CHEBI:22582 + PMID:12964249 + PMID:22117953 + PMID:22439833 + PMID:22849268 + PMID:22849276 + PMID:22958833 + chebi_ontology + Antibiotika + Antibiotikum + antibiotic + antibiotics + antibiotique + antimicrobial + antimicrobial agents + antimicrobials + microbicide + microbicides + CHEBI:33281 + + antimicrobial agent + + + + + + + + + A substance (or active part thereof) that kills or slows the growth of bacteria. + + chebi_ontology + antibacterial agents + antibacterials + bactericide + bactericides + CHEBI:33282 + + antibacterial agent + + + + + + + + + A nutrient is a food component that an organism uses to survive and grow. + + chebi_ontology + nutrients + CHEBI:33284 + + nutrient + + + + + + + + + A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. + + chebi_ontology + heteroorganic entities + organoelement compounds + CHEBI:33285 + + heteroorganic entity + + + + + + + + + An energy-rich substance that can be transformed with release of usable energy. + + chebi_ontology + CHEBI:33292 + + fuel + + + + + + + + + Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. + + pnictogens + chebi_ontology + group 15 elements + group V elements + nitrogenoideos + nitrogenoides + pnictogene + pnictogenes + CHEBI:33300 + + pnictogen + + + + + + + + + + + + + + + A p-block molecular entity containing any pnictogen. + + pnictogen molecular entity + chebi_ontology + pnictogen molecular entities + CHEBI:33302 + + pnictogen molecular entity + + + + + + + + + Any p-block element belonging to the group 16 family of the periodic table. + + PMID:17084588 + chalcogen + chalcogens + chebi_ontology + Chalkogen + Chalkogene + anfigeno + anfigenos + calcogeno + calcogenos + chalcogene + chalcogenes + group 16 elements + group VI elements + CHEBI:33303 + + chalcogen + + + + + + + + + + + + + + + Any p-block molecular entity containing a chalcogen. + + chalcogen molecular entity + chebi_ontology + chalcogen compounds + chalcogen molecular entities + CHEBI:33304 + + chalcogen molecular entity + + + + + + + + + + group 14 elements + chebi_ontology + carbon group element + carbon group elements + carbonoides + cristallogene + cristallogenes + group IV elements + CHEBI:33306 + + carbon group element atom + + + + + + + + + An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. + + main group elements + chebi_ontology + Hauptgruppenelement + Hauptgruppenelemente + main group element + CHEBI:33318 + + main group element atom + + + + + + + + + + + + + + + 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). + + hydracid + chebi_ontology + hydracids + CHEBI:33405 + + hydracid + + + + + + + + + + chebi_ontology + s-block element + s-block elements + CHEBI:33559 + + s-block element atom + + + + + + + + + Any main group element atom belonging to the p-block of the periodic table. + + chebi_ontology + p-block element + p-block elements + CHEBI:33560 + + p-block element atom + + + + + + + + + + + + + + + + + + + + + + + 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. + + 0 + CHO2R + 45.01740 + 44.99765 + OC([*])=O + CHEBI:13428 + CHEBI:13627 + CHEBI:23027 + PMID:17147560 + PMID:18433345 + Wikipedia:Carboxylic_acid + carboxylic acid + carboxylic acids + chebi_ontology + Carbonsaeure + Carbonsaeuren + Karbonsaeure + RC(=O)OH + acide carboxylique + acides carboxyliques + acido carboxilico + acidos carboxilicos + CHEBI:33575 + + carboxylic acid + + + + + + + + + + + + + + + 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. + + chebi_ontology + main group compounds + main group molecular entities + CHEBI:33579 + + main group molecular entity + + + + + + + + + + + + + + + + carbon group molecular entity + chebi_ontology + carbon group molecular entities + CHEBI:33582 + + carbon group molecular entity + + + + + + + + + Any molecule that consists of a series of atoms joined together to form a ring. + + Wikipedia:Cyclic_compound + chebi_ontology + cyclic compounds + CHEBI:33595 + + cyclic compound + + + + + + + + + A cyclic compound having as ring members atoms of the same element only. + + homocyclic compound + homocyclic compounds + chebi_ontology + isocyclic compounds + CHEBI:33597 + + homocyclic compound + + + + + + + + + + A homocyclic compound in which all of the ring members are carbon atoms. + + carbocyclic compound + carbocyclic compounds + chebi_ontology + carbocycle + CHEBI:33598 + + carbocyclic compound + + + + + + + + + + + + + + + + chebi_ontology + hydrogen compounds + hydrogen molecular entities + CHEBI:33608 + + hydrogen molecular entity + + + + + + + + + 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. + + aromatic compounds + aromatic molecular entity + chebi_ontology + aromatics + aromatische Verbindungen + CHEBI:33655 + + aromatic compound + + + + + + + + + + Any monocyclic or polycyclic aromatic hydrocarbon. + + arene + arenes + chebi_ontology + aromatic hydrocarbons + CHEBI:33658 + + arene + + + + + + + + + + + chebi_ontology + organic aromatic compounds + CHEBI:33659 + + organic aromatic compound + + + + + + + + + + chebi_ontology + monocyclic compounds + CHEBI:33661 + + monocyclic compound + + + + + + + + + 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. + + annulene + annulenes + chebi_ontology + CHEBI:33662 + + annulene + + + + + + + + + + + cyclic hydrocarbon + chebi_ontology + cyclic hydrocarbons + CHEBI:33663 + + cyclic hydrocarbon + + + + + + + + + + monocyclic hydrocarbon + monocyclic hydrocarbons + chebi_ontology + monocyclic hydrocarbons + CHEBI:33664 + + monocyclic hydrocarbon + + + + + + + + + + + heteromonocyclic compound + heteromonocyclic compounds + chebi_ontology + CHEBI:33670 + + heteromonocyclic compound + + + + + + + + + + + + + + + An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. + + s-block molecular entity + chebi_ontology + s-block compounds + s-block molecular entities + CHEBI:33674 + + s-block molecular entity + + + + + + + + + + + + + + + A main group molecular entity that contains one or more atoms of a p-block element. + + chebi_ontology + p-block compounds + p-block molecular entities + p-block molecular entitiy + CHEBI:33675 + + p-block molecular entity + + + + + + + + + + Hydrides are chemical compounds of hydrogen with other chemical elements. + + chebi_ontology + CHEBI:33692 + + hydrides + + + + + + + + + nucleic acid + 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. + + + nucleic acid + + + + + + + + + ribonucleic acid + High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. + + + ribonucleic acid + + + + + + + + + + + + + + + + A carboxylic acid containing one or more amino groups. + + CHEBI:13815 + CHEBI:22477 + Wikipedia:Amino_acid + chebi_ontology + Aminocarbonsaeure + Aminokarbonsaeure + Aminosaeure + amino acids + CHEBI:33709 + + amino acid + + + + + + + + + + An organic compound having at least one hydroxy group attached to a carbon atom. + + CHEBI:64710 + hydroxy compounds + chebi_ontology + organic alcohol + organic hydroxy compounds + CHEBI:33822 + + organic hydroxy compound + + + + + + + + + + Any organic molecule that consists of atoms connected in the form of a ring. + + chebi_ontology + organic cyclic compounds + CHEBI:33832 + + organic cyclic compound + + + + + + + + + + + chebi_ontology + benzenoid aromatic compounds + benzenoid compound + CHEBI:33836 + + benzenoid aromatic compound + + + + + + + + + macromolecule + 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. + polymer + + + macromolecule + + + + + + + + + + + chebi_ontology + aromatic annulenes + CHEBI:33842 + + aromatic annulene + + + + + + + + + A monocyclic aromatic hydrocarbon. + + chebi_ontology + monocyclic arenes + CHEBI:33847 + + monocyclic arene + + + + + + + + + A substance used in a chemical reaction to detect, measure, examine, or produce other substances. + + reagent + chebi_ontology + reactif + reactivo + reagents + CHEBI:33893 + + reagent + + + + + + + + + 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. + + chebi_ontology + macronutrients + CHEBI:33937 + + macronutrient + + + + + + + + + + + chebi_ontology + nitrogen hydrides + CHEBI:35106 + + nitrogen hydride + + + + + + + + + Saturated acyclic nitrogen hydrides having the general formula NnHn+2. + + chebi_ontology + azanes + CHEBI:35107 + + azane + + + + + + + + + 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. + + surfactant + chebi_ontology + surface active agent + surfactants + CHEBI:35195 + + surfactant + + + + + + + + + A part of a molecular entity (atom or group of atoms) in which electronic excitation associated with a given emission band is approximately localized. + + lumiphore + chebi_ontology + luminophore + CHEBI:35197 + + lumiphore + + + + + + + + + A substance that diminishes the rate of a chemical reaction. + + inhibitor + chebi_ontology + inhibidor + inhibiteur + inhibitors + CHEBI:35222 + + inhibitor + + + + + + + + + A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction. + + catalyst + chebi_ontology + Katalysator + catalizador + catalyseur + CHEBI:35223 + + catalyst + + + + + + + + + Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base. + + chebi_ontology + buffer compound + buffer compounds + CHEBI:35225 + + buffer + + + + + + + + + + Any heteroorganic entity containing at least one carbon-nitrogen bond. + + organonitrogen compounds + chebi_ontology + organonitrogens + CHEBI:35352 + + organonitrogen compound + + + + + + + + + + + + + + + + Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. + + 0 + CHO2R + 45.01740 + 44.99765 + OC([*])=O + CHEBI:13633 + CHEBI:24024 + CHEBI:4984 + KEGG:C00162 + PMID:14287444 + PMID:14300208 + PMID:14328676 + Wikipedia:Fatty_acid + Fatty acid + fatty acids + chebi_ontology + Fettsaeure + Fettsaeuren + acide gras + acides gras + acido graso + acidos grasos + fatty acids + CHEBI:35366 + + fatty acid + + + + + + + + + + An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. + + CHEBI:33274 + CHEBI:33436 + oxoanion + chebi_ontology + oxoacid anions + oxoanions + CHEBI:35406 + + oxoanion + + + + + + + + + + heterocyclic parent hydrides + chebi_ontology + heterocyclic fundamental parent + heterocyclic organic fundamental parents + organic heterocyclic fundamental parents + CHEBI:35552 + + heterocyclic organic fundamental parent + + + + + + + + + + + chebi_ontology + carbon oxoacids + oxoacids of carbon + CHEBI:35605 + + carbon oxoacid + + + + + + + + + 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. + + 0 + CH2OR2 + 30.026 + 30.01056 + *C(*)O + CHEBI:13425 + CHEBI:13686 + CHEBI:26617 + CHEBI:58662 + CHEBI:8741 + CHEBI:9077 + KEGG:C00432 + KEGG:C01612 + Secondary alcohol + chebi_ontology + R-CHOH-R' + a secondary alcohol + secondary alcohols + CHEBI:35681 + + secondary alcohol + + + + + + + + + + + + + + + A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated. + + -1 + CO2R + 44.01000 + 43.98983 + [O-]C([*])=O + CHEBI:13657 + CHEBI:25382 + CHEBI:3407 + KEGG:C00060 + chebi_ontology + Carboxylate + Monocarboxylate + a monocarboxylate + monocarboxylates + monocarboxylic acid anions + CHEBI:35757 + + monocarboxylic acid anion + + + + + + + + + + + pnictogen hydride + chebi_ontology + pnictogen hydrides + CHEBI:35881 + + pnictogen hydride + + + + + + + + + + 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. + + chebi_ontology + neurotransmitter agents + CHEBI:35942 + + neurotransmitter agent + + + + + + + + + + Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). + + chebi_ontology + leptons + CHEBI:36338 + + lepton + + + + + + + + + + Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). + + chebi_ontology + baryons + CHEBI:36339 + + baryon + + + + + + + + + Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. + + fermion + chebi_ontology + fermions + CHEBI:36340 + + fermion + + + + + + + + + A particle smaller than an atom. + + Wikipedia:Subatomic_particle + chebi_ontology + subatomic particles + CHEBI:36342 + + subatomic particle + + + + + + + + + A subatomic particle known to have substructure (i.e. consisting of smaller particles). + + chebi_ontology + composite particles + CHEBI:36343 + + composite particle + + + + + + + + + Hadron is a subatomic particle which experiences the strong force. + + chebi_ontology + hadrons + CHEBI:36344 + + hadron + + + + + + + + + A nucleus or any of its constituents in any of their energy states. + + nuclear particle + chebi_ontology + CHEBI:36347 + + nuclear particle + + + + + + + + + + + + + + + Any molecular entity consisting of more than one atom. + + chebi_ontology + polyatomic entities + CHEBI:36357 + + polyatomic entity + + + + + + + + + + An ion consisting of more than one atom. + + chebi_ontology + polyatomic ions + CHEBI:36358 + + polyatomic ion + + + + + + + + + + chebi_ontology + saturated heterocyclic parent hydride + saturated heterocyclic parent hydrides + saturated organic heterocyclic parents + CHEBI:36388 + + saturated organic heterocyclic parent + + + + + + + + + + + chebi_ontology + saturated heteromonocyclic parent hydride + saturated heteromonocyclic parent hydrides + saturated organic heteromonocyclic parents + CHEBI:36389 + + saturated organic heteromonocyclic parent + + + + + + + + + + + + + + + + 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. + + carbonyl compounds + chebi_ontology + CHEBI:36586 + + carbonyl compound + + + + + + + + + + + + + + + Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. + + oxo compounds + chebi_ontology + organic oxo compounds + CHEBI:36587 + + organic oxo compound + + + + + + + + + + pseudohalide group + chebi_ontology + halogenoid group + pseudohalido group + pseudohalo groups + pseudohalogen group + CHEBI:36823 + + pseudohalo group + + + + + + + + + + pseudohalide ions + chebi_ontology + pseudohalide anions + pseudohalides + pseudohalogen anion + pseudohalogen ion + CHEBI:36828 + + pseudohalide anion + + + + + + + + + + + chebi_ontology + polyatomic monoanions + CHEBI:36829 + + polyatomic monoanion + + + + + + + + + + -1 + chebi_ontology + monoanions + CHEBI:36830 + + monoanion + + + + + + + + + + + + + + + + + + + + + + 0 + CHN + InChI=1S/CHN/c1-2/h2H + QIUBLANJVAOHHY-UHFFFAOYSA-N + 27.02538 + 27.01090 + [C-]#[NH+] + Beilstein:2069401 + CAS:6914-07-4 + Gmelin:113 + hydrogen isocyanide + nitriliomethanide + chebi_ontology + CNH + HN(+)#C(-) + HNC + hydroisocyanic acid + CHEBI:36856 + + hydrogen isocyanide + + + + + + + + + + + chebi_ontology + inorganic ions + CHEBI:36914 + + inorganic ion + + + + + + + + + + + chebi_ontology + inorganic cations + CHEBI:36915 + + inorganic cation + + + + + + + + + A monoatomic or polyatomic species having one or more elementary charges of the proton. + + CHEBI:23058 + CHEBI:3473 + KEGG:C01373 + Cation + cation + chebi_ontology + Kation + Kationen + cationes + cations + CHEBI:36916 + + cation + + + + + + + + + + An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. + + organochalcogen compound + chebi_ontology + organochalcogen compounds + CHEBI:36962 + + organochalcogen compound + + + + + + + + + + An organochalcogen compound containing at least one carbon-oxygen bond. + + PMID:17586126 + organooxygen compound + chebi_ontology + organooxygen compounds + CHEBI:36963 + + organooxygen compound + + + + + + + + + + + + + + + + + amino-acid anion + chebi_ontology + amino acid anions + amino-acid anions + CHEBI:37022 + + amino-acid anion + + + + + + + + + + chebi_ontology + organic hydrides + CHEBI:37175 + + organic hydride + + + + + + + + + + mononuclear parent hydrides + chebi_ontology + mononuclear hydride + mononuclear hydrides + CHEBI:37176 + + mononuclear parent hydride + + + + + + + + + + Any ether in which the oxygen atom forms part of a ring. + + CHEBI:37406 + cyclic ether + cyclic ethers + epoxy compounds + chebi_ontology + cyclic ethers + epoxy compounds + CHEBI:37407 + + cyclic ether + + + + + + + + + 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). + + CHEBI:13800 + CHEBI:13801 + CHEBI:22209 + CHEBI:2426 + KEGG:C00174 + Acid + acid + chebi_ontology + Saeure + Saeuren + acide + acido + acids + CHEBI:37527 + + acid + + + + + + + + + A molecular entity consisting of two or more chemical elements. + + chebi_ontology + chemical compound + heteroatomic molecular entities + CHEBI:37577 + + heteroatomic molecular entity + + + + + + + + + + + + + + + + + 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. + + 0 + CNOR3 + 42.01680 + 41.99799 + [*]C(=O)N([*])[*] + CHEBI:35354 + CHEBI:35355 + carboxamides + chebi_ontology + carboxamides + primary carboxamide + CHEBI:37622 + + carboxamide + + + + + + + + + + + + + + + A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid. + + carboacyl groups + carboxylic acyl group + chebi_ontology + carboxylic acyl groups + CHEBI:37838 + + carboacyl group + + + + + + + + + + Any organic heterocyclic compound containing at least one ring oxygen atom. + + PMID:17134300 + chebi_ontology + heterocyclic organooxygen compounds + organooxygen heterocyclic compounds + oxacycles + CHEBI:38104 + + oxacycle + + + + + + + + + + Any of low-molecular-mass iron(III)-chelating compounds produced by plants for the purpose of the transport and sequestration of iron. + + CHEBI:26122 + CHEBI:38117 + chebi_ontology + Phytosiderophor + phytosiderophores + CHEBI:38155 + + phytosiderophore + + + + + + + + + + chebi_ontology + iron chelating agents + iron chelators + CHEBI:38157 + + iron chelator + + + + + + + + + A ligand with two or more separate binding sites that can bind to a single metallic central atom, forming a chelate. + + CHEBI:23090 + CHEBI:3585 + CHEBI:6789 + KEGG:C00917 + KEGG:C02169 + chebi_ontology + Chelating agent + Metal chelator + chelating agents + chelators + complexon + CHEBI:38161 + + chelator + + + + + + + + + + chebi_ontology + CHEBI:38162 + + iron(2+) chelator + + + + + + + + + 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. + + chebi_ontology + cholinergic agent + cholinergic drugs + cholinomimetic + CHEBI:38323 + + cholinergic drug + + + + + + + + + + + + + + + + + + + + + + A nitrile that is hydrogen cyanide in which the hydrogen has been replaced by a methyl group. + + 0 + C2H3N + InChI=1S/C2H3N/c1-2-3/h1H3 + WEVYAHXRMPXWCK-UHFFFAOYSA-N + 41.05196 + 41.02655 + CC#N + CHEBI:22185 + CHEBI:30972 + CHEBI:41432 + Beilstein:741857 + CAS:75-05-8 + Gmelin:895 + PDBeChem:CCN + PMID:17347819 + PMID:19100763 + PMID:20370615 + PMID:985423 + PPDB:1349 + Reaxys:741857 + Wikipedia:Acetonitrile + ACETONITRILE + acetonitrile + chebi_ontology + CH3-C#N + MeCN + NCMe + cyanomethane + ethanenitrile + methyl cyanide + CHEBI:38472 + + acetonitrile + + + + + + + + + + chebi_ontology + CHEBI:38496 + + electron-transport chain inhibitor + + + + + + + + + + chebi_ontology + CHEBI:38497 + + respiratory-chain inhibitor + + + + + + + + + + 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). + + CHEBI:38501 + CHEBI:62966 + PMID:12969439 + Wikipedia:Cytochrome_c_oxidase + chebi_ontology + CcO inhibitor + EC 1.9.3.1 (cytochrome c oxidase) inhibitors + EC 1.9.3.1 inhibitor + EC 1.9.3.1 inhibitors + NADH cytochrome c oxidase inhibitor + NADH cytochrome c oxidase inhibitors + Warburg's respiratory enzyme inhibitor + Warburg's respiratory enzyme inhibitors + complex IV (mitochondrial electron transport) inhibitor + complex IV (mitochondrial electron transport) inhibitors + cytochrome a3 inhibitor + cytochrome a3 inhibitors + cytochrome aa3 inhibitor + cytochrome aa3 inhibitors + cytochrome c oxidase (EC 1.9.3.1) inhibitor + cytochrome c oxidase (EC 1.9.3.1) inhibitors + cytochrome c oxidase inhibitor + cytochrome c oxidase inhibitors + cytochrome oxidase inhibitor + cytochrome oxidase inhibitors + cytochrome-c oxidase inhibitor + cytochrome-c oxidase inhibitors + ferrocytochrome c oxidase inhibitor + ferrocytochrome c oxidase inhibitors + ferrocytochrome-c:oxygen oxidoreductase inhibitor + ferrocytochrome-c:oxygen oxidoreductase inhibitors + indophenol oxidase inhibitor + indophenol oxidase inhibitors + indophenolase inhibitor + indophenolase inhibitors + mitochondrial complex IV inhibitor + mitochondrial complex IV inhibitors + mitochondrial cytochrome-c oxidase inhibitors + CHEBI:38500 + + EC 1.9.3.1 (cytochrome c oxidase) inhibitor + + + + + + + + + Any agent that affects the transport of molecular entities across a biological membrane. + + chebi_ontology + membrane transport modulators + CHEBI:38632 + + membrane transport modulator + + + + + + + + + A surfactant with an uncharged hydrophilic headgroup. + + chebi_ontology + non-ionic surfactant + nonionic surfactants + CHEBI:38828 + + nonionic surfactant + + + + + + + + + Any alkylbenzene that is benzene substituted with one or more methyl groups. + + chebi_ontology + methylbenzenes + CHEBI:38975 + + methylbenzene + + + + + + + + + + + + + + + + A monocyclic arene that is benzene substituted with one or more alkyl groups. + + alkylbenzene + chebi_ontology + Alkylbenzol + alkylbenzenes + CHEBI:38976 + + alkylbenzene + + + + + + + + + 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. + + Wikipedia:Good's_buffers + chebi_ontology + Good buffer substance + Good's buffer + Good's buffers + CHEBI:39011 + + Good's buffer substance + + + + + + + + + + A molecular entity capable of donating a hydron to an acceptor (Bronsted base). + + Bronsted acid + chebi_ontology + Bronsted-Saeure + acide de Bronsted + donneur d'hydron + hydron donor + CHEBI:39141 + + Bronsted acid + + + + + + + + + + A molecular entity capable of accepting a hydron from a donor (Bronsted acid). + + Bronsted base + chebi_ontology + Bronsted-Base + accepteur d'hydron + base de Bronsted + hydron acceptor + CHEBI:39142 + + Bronsted base + + + + + + + + + + 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. + + Lewis acid + chebi_ontology + Lewis-Saeure + accepteur d'une paire d'electrons + acide de Lewis + electron acceptor + electron-pair acceptor + CHEBI:39143 + + Lewis acid + + + + + + + + + + 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. + + Lewis base + chebi_ontology + Lewis-Base + base de Lewis + donneur d'une paire d'electrons + electron donor + CHEBI:39144 + + Lewis base + + + + + + + + + + 0 + HO + 17.00734 + 17.00274 + *O[H] + CHEBI:24706 + CHEBI:43171 + PDBeChem:OH + HYDROXY GROUP + hydroxy + hydroxy group + chebi_ontology + -OH + hydroxyl + hydroxyl group + CHEBI:43176 + + hydroxy group + + + + + + + + + + 0 + O + 15.99940 + 15.99491 + O=* + CHEBI:29353 + CHEBI:44607 + PDBeChem:O + OXO GROUP + oxo + chebi_ontology + =O + CHEBI:46629 + + oxo group + + + + + + + + + + A liquid that can dissolve other substances (solutes) without any change in their chemical composition. + + Wikipedia:Solvent + chebi_ontology + Loesungsmittel + solvant + solvents + CHEBI:46787 + + solvent + + + + + + + + + + 0 + CHO2 + 45.01744 + 44.99765 + *C(=O)O + CHEBI:23025 + CHEBI:41420 + PDBeChem:FMT + CARBOXY GROUP + carboxy + chebi_ontology + -C(O)OH + -CO2H + -COOH + carboxyl group + CHEBI:46883 + + carboxy group + + + + + + + + + + Any member of the class of dioxanes that is a cyclohexane in which two carbon atoms are replaced by oxygen atoms. + + 0 + C4H8O2 + 88.105 + 88.05243 + dioxane + chebi_ontology + CHEBI:46923 + + dioxane + + + + + + + + + + + chebi_ontology + CHEBI:46926 + + dioxanes + + + + + + + + + + + + + + + + + + + + + + + + + + + + A dioxane with oxygen atoms at positions 1 and 4. + + 0 + C4H8O2 + InChI=1S/C4H8O2/c1-2-6-4-3-5-1/h1-4H2 + RYHBNJHYFVUHQT-UHFFFAOYSA-N + 88.10512 + 88.05243 + C1COCCO1 + CHEBI:34064 + CHEBI:41951 + CHEBI:46925 + Beilstein:102551 + CAS:123-91-1 + DrugBank:DB03316 + KEGG:C14440 + LINCS:LSM-37087 + PDBeChem:DIO + PMID:14550759 + PMID:18044507 + PMID:20598439 + PPDB:1638 + Reaxys:102551 + Wikipedia:1,4-Dioxane + 1,4-Dioxane + 1,4-dioxane + chebi_ontology + 1,4-DIETHYLENE DIOXIDE + 1,4-Dioxan + 1,4-dioxacyclohexane + Dioxan-1,4 + di(ethylene oxide) + dioxane-1,4 + glycol ethylene ether + p-Dioxane + tetrahydro-1,4-dioxin + tetrahydro-p-dioxin + tetrahydro-para-dioxin + CHEBI:47032 + + 1,4-dioxane + + + + + + + + + double-stranded DNA + + + double-stranded DNA + + + + + + + + + A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds. + + polar solvent + chebi_ontology + polar solvents + CHEBI:48354 + + polar solvent + + + + + + + + + + chebi_ontology + CHEBI:48355 + + non-polar solvent + + + + + + + + + + A polar solvent that is capable of acting as a hydron (proton) donor. + + protogenic solvent + chebi_ontology + CHEBI:48356 + + protic solvent + + + + + + + + + + chebi_ontology + CHEBI:48357 + + aprotic solvent + + + + + + + + + + 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. + + dipolar aprotic solvent + chebi_ontology + CHEBI:48358 + + polar aprotic solvent + + + + + + + + + + Solvent that is capable of acting as a hydron (proton) acceptor. + + protophilic solvent + chebi_ontology + HBA solvent + hydrogen bond acceptor solvent + CHEBI:48359 + + protophilic solvent + + + + + + + + + + Self-ionizing solvent possessing both characteristics of Bronsted acids and bases. + + amphiprotic solvent + chebi_ontology + CHEBI:48360 + + amphiprotic solvent + + + + + + + + + + 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). + + imidic acid + imidic acids + chebi_ontology + imidic acids + imino acids + CHEBI:48377 + + imidic acid + + + + + + + + + + + carboximidic acid + carboximidic acids + chebi_ontology + carboximidic acids + CHEBI:48378 + + carboximidic acid + + + + + + + + + + + + + + + + + + + + + + A carboximidic acid that is formic acid in which the carbonyl oxygen is replaced by an imino group. + + 0 + CH3NO + InChI=1S/CH3NO/c2-1-3/h1H,(H2,2,3) + ZHNUHDYFZUAESO-UHFFFAOYSA-N + 45.04066 + 45.02146 + [H]C(O)=N + Beilstein:1918433 + PMID:16331898 + Reaxys:1918433 + imidoformic acid + chebi_ontology + CHEBI:48431 + + formimidic acid + + + + + + + + + A role played by a substance that can react readily with, and thereby eliminate, radicals. + + chebi_ontology + free radical scavengers + free-radical scavenger + CHEBI:48578 + + radical scavenger + + + + + + + + + + + + + + + + 0 + CN + 26.017 + 26.00307 + C(#N)* + CHEBI:36824 + CHEBI:48818 + PDBeChem:CYN + cyanido + cyano + chebi_ontology + -C#N + -CN + CYANIDE GROUP + NC- + carbonitrile group + CHEBI:48819 + + cyano group + + + + + + + + + Any drug that binds to but does not activate cholinergic receptors, thereby blocking the actions of acetylcholine or cholinergic agonists. + + chebi_ontology + Anticholinergika + Anticholinergikum + acetylcholine antagonists + acetylcholine receptor antagonist + agent anticholinergique + agente anticolinergico + agentes anticolinergicos + anticholinergic agents + anticholinergics + anticholinergiques + anticolinergicos + cholinergic-blocking agents + CHEBI:48873 + + cholinergic antagonist + + + + + + + + + + + + + + + + + + 0 + H + InChI=1S/H + YZCKVEUIGOORGS-UHFFFAOYSA-N + 1.00794 + 1.00783 + [H] + CHEBI:24634 + CHEBI:49636 + WebElements:H + hydrogen + chebi_ontology + 1H + H + Wasserstoff + hidrogeno + hydrogen + hydrogene + CHEBI:49637 + + hydrogen atom + + + + + + + + + + + + + + + + + + + + + + A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. + + chebi_ontology + organic amino compounds + CHEBI:50047 + + organic amino compound + + + + + + + + + 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. + + chebi_ontology + chemoprotectant + chemoprotectants + chemoprotective agent + chemoprotective agents + protective agents + CHEBI:50267 + + protective agent + + + + + + + + + + chebi_ontology + CHEBI:50312 + + onium compound + + + + + + + + + Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. + + onium cations + chebi_ontology + onium cations + onium ion + onium ions + CHEBI:50313 + + onium cation + + + + + + + + + An agent, with unique chemical structure and biochemical requirements, which generates nitric oxide. + + CHEBI:77704 + chebi_ontology + NO donor + NO donors + NO generator + NO generators + NO releasing agent + NO releasing agents + nitric oxide donors + nitric oxide generators + nitric oxide releasing agent + nitric oxide releasing agents + CHEBI:50566 + + nitric oxide donor + + + + + + + + + An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position. + + CHEBI:22937 + CHEBI:50581 + chebi_ontology + alkyl alcohols + hydroxyalkane + hydroxyalkanes + CHEBI:50584 + + alkyl alcohol + + + + + + + + + + + + + + + Any molecular entity that contains carbon. + + CHEBI:25700 + CHEBI:33244 + chebi_ontology + organic compounds + organic entity + organic molecular entities + CHEBI:50860 + + organic molecular entity + + + + + + + + + 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. + + chebi_ontology + agente carcinogeno + cancerigene + cancerogene + carcinogen + carcinogene + carcinogenic agents + carcinogeno + carcinogens + CHEBI:50903 + + carcinogenic agent + + + + + + + + + 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). + + chebi_ontology + CHEBI:50907 + + deaminating agent + + + + + + + + + A role played by a chemical compound exihibiting itself through the ability to induce damage to the liver in animals. + + chebi_ontology + agente hepatotoxico + hepatotoxic agents + hepatotoxicant + hepatotoxicants + hepatotoxin + hepatotoxins + hepatoxic agent + hepatoxicant + CHEBI:50908 + + hepatotoxic agent + + + + + + + + + + A poison that interferes with the functions of the nervous system. + + CHEBI:50911 + Wikipedia:Neurotoxin + chebi_ontology + agente neurotoxico + nerve poison + nerve poisons + neurotoxic agent + neurotoxic agents + neurotoxicant + neurotoxins + CHEBI:50910 + + neurotoxin + + + + + + + + + A role played by the molecular entity or part thereof within a chemical context. + + chebi_ontology + CHEBI:51086 + + chemical role + + + + + + + + + + + + + + + + CHEBI:25556 + CHEBI:7594 + KEGG:C06061 + chebi_ontology + Nitrogenous compounds + nitrogen compounds + nitrogen molecular entities + CHEBI:51143 + + nitrogen molecular entity + + + + + + + + + A role played by a compound that facilitates the rapid drying of gels without their cracking. + + chebi_ontology + CHEBI:51268 + + drying control chemical additive + + + + + + + + + Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s). + + chebi_ontology + organodiyl groups + CHEBI:51422 + + organodiyl group + + + + + + + + + + chebi_ontology + CHEBI:51446 + + organic divalent group + + + + + + + + + + chebi_ontology + CHEBI:51447 + + organic univalent group + + + + + + + + + A ketone of formula RC(=O)CH3 (R =/= H). + + chebi_ontology + methyl ketones + CHEBI:51867 + + methyl ketone + + + + + + + + + + + + + + + + + + + + + An organic anion that is the conjugate base of methanol. + + -1 + CH3O + InChI=1S/CH3O/c1-2/h1H3/q-1 + NBTOZLQBSIZIKS-UHFFFAOYSA-N + 31.03390 + 31.01894 + C[O-] + Reaxys:1839368 + chebi_ontology + methoxide ion + CHEBI:52090 + + methoxide + + + + + + + + + A biological role played by the molecular entity or part thereof within a biochemical context. + + chebi_ontology + CHEBI:52206 + + biochemical role + + + + + + + + + + chebi_ontology + CHEBI:52208 + + biophysical role + + + + + + + + + A role played by the molecular entity or part thereof which causes the development of a pathological process. + + chebi_ontology + etiopathogenetic agent + etiopathogenetic role + CHEBI:52209 + + aetiopathogenetic role + + + + + + + + + A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties. + + chebi_ontology + CHEBI:52210 + + pharmacological role + + + + + + + + + + chebi_ontology + CHEBI:52211 + + physiological role + + + + + + + + + Any molecule or ion capable of binding to a central metal atom to form coordination complexes. + + Wikipedia:Ligand + chebi_ontology + ligands + CHEBI:52214 + + ligand + + + + + + + + + A chemical role played by the molecular entity or part thereof in a photochemical process. + + chebi_ontology + photochemical roles + CHEBI:52215 + + photochemical role + + + + + + + + + + A role played by a molecular entity or part thereof in a photobiochemical process. + + chebi_ontology + CHEBI:52216 + + photobiochemical role + + + + + + + + + Any substance introduced into a living organism with therapeutic or diagnostic purpose. + + CHEBI:33293 + CHEBI:33294 + chebi_ontology + farmaco + medicament + pharmaceuticals + CHEBI:52217 + + pharmaceutical + + + + + + + + + The role played by a molecular entity, such as an atom or free radical, which is involved in chain-propagating reactions. + + chebi_ontology + chain carriers + CHEBI:53431 + + chain carrier + + + + + + + + + A cyclic compound having as ring members atoms of at least two different elements. + + Heterocyclic compound + chebi_ontology + compuesto heterociclico + compuestos heterociclicos + heterocycle + heterocyclic compounds + CHEBI:5686 + + heterocyclic compound + + + + + + + + + + A reagent that forms a bond to its reaction partner (the nucleophile) by accepting both bonding electrons from that reaction partner. + + chebi_ontology + electrophile + electrophiles + electrophilic reagents + CHEBI:59739 + + electrophilic reagent + + + + + + + + + + A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. + + chebi_ontology + nucleophile + nucleophiles + nucleophilic reagents + CHEBI:59740 + + nucleophilic reagent + + + + + + + + + A surfactant molecule with hydrophilic groups at both ends of a hydrophobic hydrocarbon chain + + chebi_ontology + alpha-omega-type surfactant + bolaamphiphiles + bolaform surfactant + bolaphile + CHEBI:59752 + + bolaamphiphile + + + + + + + + + A surfactant molecule possessing both hydrophilic and lipophilic properties. + + chebi_ontology + amphiphiles + CHEBI:59941 + + amphiphile + + + + + + + + + An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. + + chebi_ontology + a monovalent cation + CHEBI:60242 + + monovalent inorganic cation + + + + + + + + + + + + + + + Any organic molecular entity derived from a fatty acid. + + chebi_ontology + FA derivative + FA derivatives + fatty acid derivatives + CHEBI:61697 + + fatty acid derivative + + + + + + + + + Any donor that can transfer acyl groups between molecular entities. + + PMID:16100120 + PMID:19052863 + chebi_ontology + CHEBI:62049 + + acyl donor + + + + + + + + + Any additive that enhances the efficiency of fuel. + + chebi_ontology + fuel additives + fuel enhancer + CHEBI:62803 + + fuel additive + + + + + + + + + The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability. + + chebi_ontology + emulgent + emulgents + emulsifiers + CHEBI:63046 + + emulsifier + + + + + + + + + + A food additive used to form or maintain a uniform emulsion of two (or more) phases in a food. + + chebi_ontology + food emulsifiers + CHEBI:63047 + + food emulsifier + + + + + + + + + A catalyst that facilitates the migration of a reactant from one phase into another phase where reaction occurs. + + Wikipedia:Phase_transfer_catalyst + chebi_ontology + PTC + phase transfer catalyst + phase transfer catalysts + phase-transfer catalysts + CHEBI:63060 + + phase-transfer catalyst + + + + + + + + + Chemical role played by a material when used to promote crystallisation. + + Wikipedia:Crystallization_adjutant + chebi_ontology + crystallisation adjutants + crystallization adjutant + crystallization adjutants + CHEBI:63064 + + crystallisation adjutant + + + + + + + + + The element or compound in a reduction-oxidation (redox) reaction that donates an electron to another species. + + Wikipedia:Reducing_agent + chebi_ontology + reducer + reducers + reducing agents + reductant + reductants + CHEBI:63247 + + reducing agent + + + + + + + + + A substance that removes electrons from another reactant in a redox reaction. + + chebi_ontology + oxidant + oxidants + oxidiser + oxidisers + oxidising agents + oxidizer + oxidizers + oxidizing agent + oxidizing agents + CHEBI:63248 + + oxidising agent + + + + + + + + + A substance capable of undergoing rapid and highly exothermic decomposition. + + Wikipedia:Explosive_material + chebi_ontology + explosive compound + explosive compounds + explosive material + explosives + explosives chemical + explosives chemicals + CHEBI:63490 + + explosive + + + + + + + + + Any compound that can be used for the treatment of neurodegenerative disorders. + + chebi_ontology + neuroprotectant + neuroprotectants + neuroprotective agents + CHEBI:63726 + + neuroprotective agent + + + + + + + + + Any compound that leaves a pliable, cohesive, and continuous covering over a surface when applied to it. + + chebi_ontology + film-forming agent + film-forming agents + film-forming compounds + CHEBI:63908 + + film-forming compound + + + + + + + + + + Any substance which is added to food to preserve or enhance its flavour and/or appearance. + + Wikipedia:Food_additive + chebi_ontology + food additives + CHEBI:64047 + + food additive + + + + + + + + + Any chemical substance produced during the conversion of a reactant to a product. + + Wikipedia:Reaction_intermediate + chebi_ontology + chemical intermediate + CHEBI:64297 + + reaction intermediate + + + + + + + + + An organic molecular entity containing a single carbon atom (C1). + + chebi_ontology + one-carbon compounds + CHEBI:64708 + + one-carbon compound + + + + + + + + + Any organic molecular entity that is acidic and contains carbon in covalent linkage. + + chebi_ontology + organic acids + CHEBI:64709 + + organic acid + + + + + + + + + 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. + + Wikipedia:Poison + chebi_ontology + poisonous agent + poisonous agents + poisonous substance + poisonous substances + poisons + toxic agent + toxic agents + toxic substance + toxic substances + CHEBI:64909 + + poison + + + + + + + + + Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes. + + chebi_ontology + food preservatives + CHEBI:65255 + + food preservative + + + + + + + + + Any entity used to generate reactive oxygen species. + + chebi_ontology + ROS generator + ROS generators + reactive oxygen species generators + CHEBI:70982 + + reactive oxygen species generator + + + + + + + + + + Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. + + chebi_ontology + organic compound + organic compounds + organic molecules + CHEBI:72695 + + organic molecule + + + + + + + + + A photochemical role realized in the absorption of ultraviolet light, for example to protect skin cells from damage. + + Wikipedia:UV_filter + chebi_ontology + UV filter + UV filters + ultraviolet filters + CHEBI:73335 + + ultraviolet filter + + + + + + + + + + + + + + + + + + + + + + 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. + + PMID:10634967 + PMID:19159745 + PMID:22259088 + PMID:22268909 + PMID:22524563 + PMID:22879057 + PMID:23082721 + PMID:23148246 + PMID:23396451 + PMID:23466063 + PMID:23557707 + Wikipedia:Ketone_body + chebi_ontology + ketone bodies + CHEBI:73693 + + ketone body + + + + + + + + + Any compound used as a monomer for a polymerisation process. The term is generally used in relation to industrial polymerisation processes. + + chebi_ontology + polymerization monomer + CHEBI:74236 + + polymerisation monomer + + + + + + + + + A compound that causes the contraction of body tissues, typically used to reduce bleeding from minor abrasions. + + Wikipedia:Astringent + chebi_ontology + adstringent + adstringents + astringents + CHEBI:74783 + + astringent + + + + + + + + + Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. + + chebi_ontology + eukaryotic metabolites + CHEBI:75763 + + eukaryotic metabolite + + + + + + + + + Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. + + CHEBI:77721 + CHEBI:77743 + chebi_ontology + animal metabolites + CHEBI:75767 + + animal metabolite + + + + + + + + + Any animal metabolite produced during a metabolic reaction in mammals. + + CHEBI:77464 + CHEBI:77744 + chebi_ontology + mammalian metabolites + CHEBI:75768 + + mammalian metabolite + + + + + + + + + Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). + + chebi_ontology + Mus musculus metabolite + Mus musculus metabolites + mouse metabolites + CHEBI:75771 + + mouse metabolite + + + + + + + + + Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). + + CHEBI:76949 + CHEBI:76951 + chebi_ontology + S. cerevisiae metabolite + S. cerevisiae metabolites + S. cerevisiae secondary metabolite + S. cerevisiae secondary metabolites + Saccharomyces cerevisiae metabolites + Saccharomyces cerevisiae secondary metabolites + baker's yeast metabolite + baker's yeast metabolites + baker's yeast secondary metabolite + baker's yeast secondary metabolites + CHEBI:75772 + + Saccharomyces cerevisiae metabolite + + + + + + + + + Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. + + chebi_ontology + prokaryotic metabolites + CHEBI:75787 + + prokaryotic metabolite + + + + + + + + + A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'. + + Wikipedia:Greenhouse_gas + chebi_ontology + greenhouse gases + CHEBI:76413 + + greenhouse gas + + + + + + + + + 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. + + chebi_ontology + fluorescence quenchers + CHEBI:76648 + + fluorescence quencher + + + + + + + + + An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*). + + Wikipedia:Oxidoreductase + chebi_ontology + EC 1.* (oxidoreductase) inhibitors + EC 1.* inhibitor + EC 1.* inhibitors + oxidoreductase (EC 1.*) inhibitor + oxidoreductase (EC 1.*) inhibitors + oxidoreductase inhibitor + oxidoreductase inhibitors + CHEBI:76725 + + EC 1.* (oxidoreductase) inhibitor + + + + + + + + + An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on a heme group of donors (EC 1.9.*.*). + + chebi_ontology + EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitor + EC 1.9.* (oxidoreductase acting on a heme group of donors) inhibitors + EC 1.9.* (oxidoreductase acting on donor heme group) inhibitors + EC 1.9.* inhibitor + EC 1.9.* inhibitors + oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitor + oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitors + CHEBI:76736 + + EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor + + + + + + + + + Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). + + Wikipedia:Hydrolase + chebi_ontology + EC 3.* (hydrolase) inhibitors + EC 3.* inhibitor + EC 3.* inhibitors + EC 3.*.*.* inhibitor + EC 3.*.*.* inhibitors + hydrolase (EC 3.*) inhibitor + hydrolase (EC 3.*) inhibitors + hydrolase inhibitor + hydrolase inhibitors + CHEBI:76759 + + EC 3.* (hydrolase) inhibitor + + + + + + + + + Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*). + + chebi_ontology + EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor + EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors + EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor + EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors + EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors + EC 3.5.* inhibitor + EC 3.5.* inhibitors + CHEBI:76764 + + EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor + + + + + + + + + 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.*). + + chebi_ontology + EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors + EC 3.5.1.* inhibitor + EC 3.5.1.* inhibitors + non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor + non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors + CHEBI:76807 + + EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor + + + + + + + + + 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.*). + + chebi_ontology + EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitors + EC 1.9.3.* inhibitor + EC 1.9.3.* inhibitors + oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitor + oxidoreductase acting on donor heme group, oxygen as acceptor (EC 1.9.3.*) inhibitors + CHEBI:76870 + + EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor + + + + + + + + + An enzyme inhibitor that interferes with one or more steps in a metabolic pathway. + + chebi_ontology + metabolic pathway inhibitor + metabolic pathway inhibitors + pathway inhibitors + CHEBI:76932 + + pathway inhibitor + + + + + + + + + Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. + + CHEBI:75765 + CHEBI:76947 + chebi_ontology + fungal metabolites + CHEBI:76946 + + fungal metabolite + + + + + + + + + Any prokaryotic metabolite produced during a metabolic reaction in bacteria. + + CHEBI:75760 + CHEBI:76970 + chebi_ontology + CHEBI:76969 + + bacterial metabolite + + + + + + + + + Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. + + chebi_ontology + E.coli metabolite + E.coli metabolites + Escherichia coli metabolites + CHEBI:76971 + + Escherichia coli metabolite + + + + + + + + + Any product obtained as a result of thermally induced non-enzymatic degradation. + + chebi_ontology + thermal artefact + thermal artefacts + thermal degradation products + CHEBI:77521 + + thermal degradation product + + + + + + + + + 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). + + PMID:23588491 + PMID:23612540 + PMID:24246231 + Wikipedia:Maillard_reaction + chebi_ontology + Maillard product + Maillard products + maillard reaction products + CHEBI:77523 + + Maillard reaction product + + + + + + + + + Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). + + CHEBI:75770 + CHEBI:77123 + chebi_ontology + H. sapiens metabolite + H. sapiens metabolites + Homo sapiens metabolite + Homo sapiens metabolites + CHEBI:77746 + + human metabolite + + + + + + + + + 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. + + Wikipedia:Persistant_organic_pollutant + chebi_ontology + POP + POPs + persistent organic pollutants + CHEBI:77853 + + persistent organic pollutant + + + + + + + + + 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). + + Wikipedia:Amidase + chebi_ontology + EC 3.5.1.4 (amidase) inhibitors + EC 3.5.1.4 inhibitor + EC 3.5.1.4 inhibitors + N-acetylaminohydrolase inhibitor + N-acetylaminohydrolase inhibitors + acylamidase inhibitor + acylamidase inhibitors + acylamide amidohydrolase inhibitor + acylamide amidohydrolase inhibitors + amidase (EC 3.5.1.4) inhibitor + amidase (EC 3.5.1.4) inhibitors + amidase inhibitor + amidase inhibitors + amidohydrolase inhibitor + amidohydrolase inhibitors + deaminase inhibitor + deaminase inhibitors + fatty acylamidase inhibitor + fatty acylamidase inhibitors + CHEBI:77941 + + EC 3.5.1.4 (amidase) inhibitor + + + + + + + + + + An antioxidant that used as a food additives to help guard against food deterioration. + + chebi_ontology + food antioxidants + CHEBI:77962 + + food antioxidant + + + + + + + + + + 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. + + Wikipedia:Sequestrant + chebi_ontology + sequestrants + CHEBI:77963 + + sequestrant + + + + + + + + + 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. + + chebi_ontology + dietary component + dietary components + food components + CHEBI:78295 + + food component + + + + + + + + + Any minor or unwanted substance introduced into the environment that can have undesired effects. + + chebi_ontology + environmental contaminants + CHEBI:78298 + + environmental contaminant + + + + + + + + + + Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage. + + chebi_ontology + environmental food contaminants + CHEBI:78299 + + environmental food contaminant + + + + + + + + + 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. + + Wikipedia:Refrigerant + chebi_ontology + refrigerants + CHEBI:78433 + + refrigerant + + + + + + + + + Any inorganic anion with a valency of two. + + chebi_ontology + divalent inorganic anions + CHEBI:79388 + + divalent inorganic anion + + + + + + + + + Any inorganic anion with a valency of one. + + chebi_ontology + monovalent inorganic anions + CHEBI:79389 + + monovalent inorganic anion + + + + + + + + + Any nitrile derived from an aliphatic compound. + + 0 + CNR + 26.017 + 26.00307 + [*]C#N + KEGG:C16072 + chebi_ontology + an aliphatic nitrile + CHEBI:80291 + + aliphatic nitrile + + + + + + + + + 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. + + PMID:2909515 + chebi_ontology + phytochrome chromophores + CHEBI:82632 + + phytochrome chromophore + + + + + + + + + A chemical compound that, when added to a liquid or gas, decreases the corrosion rate of a material, typically a metal or an alloy. + + PMID:23636692 + PMID:25594340 + PMID:25839822 + PMID:25912625 + PMID:25955130 + PMID:26160863 + PMID:26343626 + PMID:26347374 + PMID:26364631 + PMID:26727190 + Wikipedia:Corrosion_inhibitor + chebi_ontology + corrosion inhibitors + CHEBI:91015 + + corrosion inhibitor + + + + + + + + + An independent material continuant that is self-connected and retains its identity over time. + + CHMO:0000993 + portion of material + + + + + + + + + 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. + + CHMO:0000997 + chromatography column + + + + + + + + + + A method that results in the separation of two or more components according to some property. + + FIX:0000002 + partition + CHMO:0000999 + separation method + + + + + + + + + A separation method where the components are distributed between two phases, one of which is stationary, while the other moves in a definite direction. + + FIX:0000053 + analytical chromatography + chromatographic analysis + preparative chromatography + CHMO:0001000 + chromatography + + + + + + + + + + + + + + + + + + + + + + + + + + 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). + + CHMO:0002118 + preparative column chromatography + CHMO:0001001 + column chromatography + + + + + + + + + Chromatography where the separation is caused by differing biological specificity of the analyte-ligand interactions. + + bioaffinity chromatography + CHMO:0001006 + affinity chromatography + + + + + + + + + Chromatography in which separation is based mainly on differences between the adsorption affinities of the sample components for the surface of an active solid. + + batchelorc + 2009-03-06T04:48:25Z + CHMO:0001128 + adsorption chromatography + + + + + + + + + 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. + + batchelorc + 2009-03-06T04:48:37Z + FIX:0000618 + CHMO:0001129 + displacement chromatography + + + + + + + + + A method used to synthesise a sample. + + CHMO:0001301 + synthesis method + + + + + + + + + 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. + + deposition + CHMO:0001310 + sample deposition + + + + + + + + + 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. + + CHMO:0001387 + ionothermal synthesis + + + + + + + + + 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. + + solvothermal method + solvothermal process + solvothermal reaction + solvothermal treatment + CHMO:0001458 + solvothermal synthesis + + + + + + + + + + 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. + + age hardening + aging + dispersion hardening + precipitate ageing + precipitation hardening + CHMO:0001464 + ageing + + + + + + + + + A heat treatment that alters the microstructure of a material causing changes in its properties such as strength and hardness + + CHMO:0001465 + annealing + + + + + + + + + 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. + + crystallization + CHMO:0001477 + crystallisation + + + + + + + + + The simultaneous crystallisation of two different substances or two different structural elements of the same substance. + + co crystallisation + co crystallization + co-crystallisation + co-crystallization + cocrystallization + CHMO:0001478 + cocrystallisation + + + + + + + + + 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. + + fractional crystallization + CHMO:0001479 + fractional crystallisation + + + + + + + + + + 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. + + CHMO:0001532 + distillation + + + + + + + + + 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. + + CHMO:0001533 + batch distillation + + + + + + + + + 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. + + CHMO:0001534 + continuous distillation + + + + + + + + + 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. + + CHMO:0001535 + extractive distillation + + + + + + + + + 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. + + CHMO:0001536 + fractional distillation + + + + + + + + + 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. + + CHMO:0001537 + reactive distillation + + + + + + + + + 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°). + + CHMO:0001538 + simple distillation + + + + + + + + + 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. + + CHMO:0001539 + steam distillation + + + + + + + + + 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. + + low temperature distillation + low-temperature distillation + CHMO:0001540 + vacuum distillation + + + + + + + + + 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. + + CHMO:0001541 + air-sensitive vacuum distillation + + + + + + + + + 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. + + CHMO:0001542 + molecular distillation + + + + + + + + + + The process of removing a solvent from a substance. + + drying + CHMO:0001549 + sample drying + + + + + + + + + The removal of solvent from a sample by the application of radio frequency (3 Hz to 300 GHz) or microwave (1–1000 mm) radiation. + + CHMO:0001550 + dielectric drying + + + + + + + + + The removal of solvent from a sample by the application of heated air. + + CHMO:0001551 + direct drying + + + + + + + + + The removal of solvent from a sample by applying it as a thin layer to the surface of a heated drum. + + CHMO:0001552 + drum drying + + + + + + + + + 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. + + cryodesiccation + freeze-drying + lyophilization + CHMO:0001553 + freeze drying + + + + + + + + + The removal of solvent from a sample by heating in an oven. + + CHMO:0001554 + oven drying + + + + + + + + + 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. + + spray-drying + CHMO:0001555 + spray drying + + + + + + + + + The removal of solvent from a sample without passing through the liquid–gas boundary, by immersion in a supercritical fluid and de-pressurisation. + + critical point drying + critical-point drying + super-critical point drying + CHMO:0001556 + supercritical drying + + + + + + + + + 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. + + CHMO:0001557 + vacuum drying + + + + + + + + + + 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. + + CHMO:0001574 + evaporation + + + + + + + + + The evaporation of solvent from a sample by placing it a centrifuge and spinning it rapidly. + + CHMO:0001575 + centrifugal evaporation + + + + + + + + + The removal of solvent from a sample by applying heat and lowering the pressure above the sample whilst rotating it at 10–300 rpm. + + CHMO:0001576 + rotary evaporation + + + + + + + + + + The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it. + + CHMO:0001577 + extraction + + + + + + + + + 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. + + co-extraction + CHMO:0001578 + coextraction + + + + + + + + + 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). + + liquid-solid extraction + solid phase extraction + solid-phase extraction + sorbent extraction + sorptive extraction + LSE + SPE + CHMO:0001583 + liquid-solid extraction + + + + + + + + + The transfer of a solute from one phase (the 'donor' or 'feed' phase) to another (the 'acceptor' or 'strip' phase) across a nonporous membrane. + + CHMO:0001593 + membrane extraction + + + + + + + + + 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. + + MESI + membrane extraction sorbent interface + membrane extraction with sorbent interface + membrane extraction with trapping on a sorbent interface + CHMO:0001594 + membrane extraction with a sorbent interface + + + + + + + + + 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. + + PME + CHMO:0001595 + polymeric membrane extraction + + + + + + + + + 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. + + SLM extraction + SLME + supported liquid membrane (SLM) extraction + CHMO:0001596 + supported liquid membrane extraction + + + + + + + + + An analytical process that sequentially chemically leaches metals from soils, sludges or sediments. + + sequential chemical extraction + CHMO:0001597 + sequentional extraction + + + + + + + + + The process of transferring a substance from any matrix to an appropriate liquid phase. + + CHMO:0001598 + solvent extraction + + + + + + + + + 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. + + gas-liquid extraction + sublation + CHMO:0001599 + gas–liquid extraction + + + + + + + + + The process of transferring a dissolved substance from one liquid phase to another (immiscible or partially miscible) liquid phase in contact with it. + + LLE + liquid phase extraction + liquid-liquid distribution + liquid-liquid extraction + liquid-liquid partition + liquid-phase extraction + CHMO:0001600 + liquid–liquid extraction + + + + + + + + + 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. + + CPE + cloud point extraction + CHMO:0001601 + cloud-point extraction + + + + + + + + + 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). + + PFE + PLE + PSE + accelerated solvent extraction + accelerated-solvent extraction + pressurised fluid extraction + pressurised liquid extraction + pressurised solvent extraction + pressurised-liquid extraction + pressurised-solvent extraction + pressurized fluid extraction + pressurized liquid extraction + pressurized solvent extraction + pressurized-fluid extraction + pressurized-liquid extraction + pressurized-solvent extraction + CHMO:0001604 + pressurised-fluid extraction + + + + + + + + + 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. + + shake flask extraction + CHMO:0001606 + shake-flask extraction + + + + + + + + + The process of transferring the soluble components of a solid to the liquid phase using a solvent. + + solid-liquid extraction dry extraction + CHMO:0001607 + solid–liquid extraction + + + + + + + + + The process of transferring a substance from any matrix to a liquid phase using a supercritical fluid. + + SCFE + SFE + supercritical extraction + supercritical fluid extraction + CHMO:0001610 + supercritical fluid extraction + + + + + + + + + The process of transferring a substance from any matrix to another where the amount of reagent used is lower than that dictated by stoichiometry. + + CHMO:0001612 + substoichiometric extraction + + + + + + + + + + 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. + + CHMO:0001624 + fermentation + + + + + + + + + + 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. + + CHMO:0001625 + fractionation + + + + + + + + + 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. + + CHMO:0001636 + foam fractionation + + + + + + + + + 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. + + normal freezing + progressive freezing + CHMO:0001637 + freeze distillation + + + + + + + + + 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. + + CHMO:0001640 + filtration + + + + + + + + + A pressure-driven membrane-based separation process in which particles and dissolved macromolecules larger than 0.1 micrometre are rejected. + + microfiltration + CHMO:0001641 + micro-filtration + + + + + + + + + A pressure-driven membrane-based separation process in which particles and dissolved macromolecules larger 200 Da are rejected. + + NF + nanofiltration + CHMO:0001642 + nano-filtration + + + + + + + + + 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.) + + RO + CHMO:0001643 + reverse osmosis + + + + + + + + + The separation of a solid phase from a liquid phase by passing the sample through a porous medium under pressure. + + vacuum filtration + CHMO:0001644 + suction filtration + + + + + + + + + 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. + + UF + ultrafiltration + CHMO:0001645 + ultra-filtration + + + + + + + + + + The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting. + + dry grinding + milling + solid-state grinding + solvent-free grinding + CHMO:0001652 + grinding + + + + + + + + + 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. + + LAG + solvent-drop grinding + CHMO:0001653 + liquid-assisted grinding + + + + + + + + + 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. + + CHMO:0001654 + ball milling + + + + + + + + + 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. + + HSBM + high speed ball milling + CHMO:0001655 + high-speed ball milling + + + + + + + + + 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). + + HEBM + high energy ball milling + CHMO:0001656 + high-energy ball milling + + + + + + + + + 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). + + CHMO:0001657 + wet grinding + + + + + + + + + + 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. + + CHMO:0001685 + mixing + + + + + + + + + + The growth of larger crystals from those of smaller size, which have a higher solubility than the larger ones. + + Ostwald-ripening + CHMO:0001686 + Ostwald ripening + + + + + + + + + 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. + + CHMO:0001688 + precipitation + + + + + + + + + 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+). + + CHMO:0001689 + affinity precipitation + + + + + + + + + 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. + + coprecipitation + CHMO:0001690 + co-precipitation + + + + + + + + + The subsequent precipitation of a chemically different species upon the surface of an initial precipitate usually, but not necessarily, including a common ion. + + CHMO:0001696 + postprecipitation + + + + + + + + + The planned repetition of a precipitation to remove impurities from a precipitate or improve its stoichiometry. + + CHMO:0001697 + reprecipitation + + + + + + + + + + Any material processing method that uses a supercritical fluid. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-03T09:36:47Z + CHMO:0001904 + supercritical fluid method + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-03T09:44:30Z + SAS + SF antisolvent process + supercritical anti-solvent fractionation + supercritical anti-solvent precipitation + supercritical anti-solvent process + supercritical antisolvent fractionation + supercritical antisolvent precipitation + supercritical fluid antisolvent process + CHMO:0001905 + supercritical antisolvent technique + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-10T10:59:22Z + GAS + GAS recrystallisation + GAS recrystallization + GASP + GASR + gas anti-solvent precipitation + gas anti-solvent reaction + gas anti-solvent recrystallisation + gas anti-solvent recrystallization + gas antisolvent precipitation + gas antisolvent reaction + gas antisolvent recrystallisation + gas antisolvent recrystallization + CHMO:0001945 + gas antisolvent technique + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-10T11:02:33Z + precipitation using compressed anti-solvent + precipitation using compressed antisolvent + precipitation with compressed anti-solvent + PCA + CHMO:0001947 + precipitation with compressed antisolvent + + + + + + + + + The removal of solvent from a sample without passing through the liquid–gas boundary, by immersion in supercritical CO2 and de-pressurisation. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-18T10:00:03Z + CO2 critical point drying + CO2 critical-point drying + CO2 super-critical point drying + supercritical CO2 drying + CHMO:0001987 + supercritical carbon dioxide drying + + + + + + + + + The process of transferring a substance from any matrix into ethanol. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-18T10:18:25Z + EtOH extraction + CHMO:0001989 + ethanol extraction + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-19T01:59:21Z + CHMO:0002011 + sequential centrifugation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-19T02:00:33Z + low speed centrifugation + CHMO:0002012 + low-speed centrifugation + + + + + + + + + A method where a sample is purified by removing impurities on the basis of their density in a centrifuge. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-19T02:05:24Z + CHMO:0002014 + preparative centrifugation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-19T02:10:04Z + CHMO:0002015 + differential centrifugation + + + + + + + + + The intensive mixing of μtually insoluble phases (sometimes with addition of surfactants) to obtain a soluble suspension or emulsion. + + https://orcid.org/0000-0001-5985-7429 + 2009-06-19T02:29:46Z + homogenation + homogenization + CHMO:0002020 + homogenisation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-01T02:42:13Z + CHMO:0002066 + trituration + + + + + + + + + The process of making a polymer blend by mechanically mixing different polymers together in the melt. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-06T11:06:28Z + mechanical mixing + CHMO:0002106 + physical blending + + + + + + + + + The removal of solvent from a sample by the application of an inert gas or air. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-08T04:06:02Z + CHMO:0002124 + blow drying + + + + + + + + + + The removal of ions from a solution using an ion-exchange method. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-13T01:17:32Z + deionization + CHMO:0002157 + deionisation method + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-13T01:35:58Z + CHMO:0002158 + Czochralski process + + + + + + + + + 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). + + https://orcid.org/0000-0001-5985-7429 + 2009-07-13T01:37:26Z + flame fusion + CHMO:0002159 + Verneuil process + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-13T01:43:03Z + Bridgman technique + Bridgman-Stockbarger technique + CHMO:0002160 + Bridgeman technique + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-22T09:23:11Z + re-crystallisation + re-crystallization + recrystallization + CHMO:0002198 + recrystallisation + + + + + + + + + The removal of solvent from a sample, usually by the application of heat. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-24T02:31:03Z + drying + CHMO:0002208 + solvent evaporation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T03:22:04Z + CHMO:0002217 + sample sublimation + + + + + + + + + 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). + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T03:22:24Z + CHMO:0002218 + fractional sublimation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T03:23:24Z + vacuum-sublimation method + CHMO:0002219 + vacuum sublimation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T03:23:35Z + high vacuum sublimation + CHMO:0002220 + high-vacuum sublimation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T04:03:12Z + Lely technique + CHMO:0002221 + Lely method + + + + + + + + + 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'). + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T03:25:09Z + modified Lely method + seed sublimation + seeded sublimation method + seeded sublimation technique + seeded-sublimation growth technique + seeded-sublimation method + seeded-sublimation technique + CHMO:0002222 + seeded sublimation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T03:26:30Z + SSM + close space sublimation + close-space sublimation + sandwich sublimation method + sandwich sublimation technique + sandwich-sublimation method + sublimation sandwich method + sublimation-sandwich method + CHMO:0002223 + sandwich sublimation + + + + + + + + + Any synthesis method used to grow crystals. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T04:05:29Z + CHMO:0002224 + crystal growth method + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-28T04:20:26Z + Acheson technique + CHMO:0002225 + Acheson method + + + + + + + + + + + + + + + Any technique used to physically separate an analyte from byproducts, reagents or contaminating substances. + + https://orcid.org/0000-0001-5985-7429 + 2009-07-29T03:59:53Z + CHMO:0002231 + purification + + + + + + + + + The sedimentation of a solid material (a 'precipitate') from a liquid solution caused by the addition of an additional different solvent. + + https://orcid.org/0000-0001-5985-7429 + 2009-09-28T11:52:22Z + CHMO:0002465 + solvent precipitation + + + + + + + + + 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'. + + https://orcid.org/0000-0001-5985-7429 + 2009-09-28T11:55:08Z + CHMO:0002466 + protein precipitation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-10-13T11:06:56Z + vapor phase extraction + vapor-phase extraction + vapour phase extraction + CHMO:0002523 + vapour-phase extraction + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-10-13T11:10:28Z + DPE + bioslurping + dual phase extraction + multi-phase extraction + multiphase extraction + vacuum-enhanced extraction + CHMO:0002524 + dual-phase extraction + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2009-12-07T05:40:30Z + CHMO:0002634 + azeotropic distillation + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2010-01-05T11:46:52Z + CVT + chemical vapor transport + CHMO:0002652 + chemical vapour transport + + + + + + + + + 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. + + https://orcid.org/0000-0001-5985-7429 + 2010-01-05T11:50:07Z + SA-CVT + SACVT + surface assisted CVT + surface assisted chemical vapor transport + surface assisted chemical vapour transport + surface-assisted CVT + surface-assisted chemical vapor transport + surface-assisted chemical-vapor-transport + surface-assisted chemical-vapour-transport + CHMO:0002653 + surface-assisted chemical vapour transport + + + + + + + + + A process wherein one material is extracted from another by interaction with a solvent. + + CHMO:0002742 + elution + + + + + + + + + A sample preparation step involving the increase in temperature of a sample. + + CHMO:0002770 + ought to be in OBI. Will put here pro tem. + sample heating + + + + + + + + + + A preparative step where the concentration of one component is increased. + + CHMO:0002771 + concentrating + + + + + + + + + + A preparative step involving the removal of dissolved gases from a sample. + + http://en.wikipedia.org/wiki/Degasification + degasification + CHMO:0002772 + degassing + + + + + + + + + A mixing step where a soluble component is mixed with a liquid component. + + CHMO:0002773 + dissolving + + + + + + + + + Mixing involving the agitation of a solution through circular motion. + + CHMO:0002774 + stirring + + + + + + + + + Stirring achieved by rotating a magnetic stir bar in a solution. + + CHMO:0002775 + magnetic stirring + + + + + + + + + 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. + + CHMO:0002852 + spiking + + + + + + + + + + dispersive solid-phase extraction + CHMO:0002863 + dispersive solid phase extraction + + + + + + + + + + Material processing in which a liquid or gas transitions into a solid. + + CHMO:0002916 + sample solidification + + + + + + + + + Material processing in which a sample is cooled by immersion in a fluid. + + CHMO:0002917 + sample quenching + + + + + + + + + + fix.ontology + FIX:0000277 + reaction property + + + + + + + + + + fix.ontology + Gibbs energy change + FIX:0000279 + Gibbs free energy change + + + + + + + + + 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. + [Wikipedia] + + fix.ontology + Gibbs energy of activation + FIX:0000280 + Gibbs free energy of activation + + + + + + + + + + fix.ontology + oxidation-reduction reaction property + FIX:0000281 + redox reaction property + + + + + + + + + + + fix.ontology + oxidation-reduction potential change + FIX:0000285 + redox potential change + + + + + + + + + + fix.ontology + FIX:0000368 + kinetic reaction property + + + + + + + + + + fix.ontology + FIX:0000369 + thermodynamic reaction property + + + + + + + + + molecular_function + 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. + + + molecular_function + + + + + + + + + catalytic activity + 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. + + + catalytic activity + + + + + + + + + + + + + + + protein-containing complex + A ribosome is a protein complex. + 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. + protein complex + + + protein-containing complex + + + + + + + + + DNA polymerase activity + 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. + + + DNA polymerase activity + + + + + + + + + + + + + + + + + + + + + DNA polymerase complex + A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. + + + DNA polymerase complex + + + + + + + + + measurement unit label + Examples of measurement unit labels are liters, inches, weight per volume. + + A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. + 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. + 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. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + + + measurement unit label + + + + + + + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + + 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. + 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." + 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. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + + + + IAO:0000005 + objective specification + objective specification + + + + + + + + + Pour the contents of flask 1 into flask 2 + + A directive information entity that describes an action the bearer will take. + Alan Ruttenberg + OBI Plan and Planned Process branch + + + action specification + + + + + + + + + datum label + + 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 + http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n + GROUP: IAO + 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. + + + + datum label + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + 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. + 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. + 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. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + 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 + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + + + data item + + + + + + + + + symbol + a serial number such as "12324X" + a stop sign + a written proper name such as "OBI" + + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 20091104, MC: this needs work and will most probably change + 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). + PERSON: James A. Overton + PERSON: Jonathan Rees + based on Oxford English Dictionary + + + symbol + + + + + + + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 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). + 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. + PERSON: Chris Stoeckert + OBI_0000142 + + + + IAO:0000030 + information content entity + information content entity + + + + + + + + + + + + + + + + + + 1 + + + + + + 1 + + + 10 feet. 3 ml. + + A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. + 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in +this case we explicitly refer to the singular form + 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. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + + + scalar measurement datum + + + + + + + + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + 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. + 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. + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + 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 + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + + + + IAO:0000033 + directive information entity + directive information entity + + + + + + + + + algorithm + PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. + + 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. + Philippe Rocca-Serra + PlanAndPlannedProcess Branch + OBI_0000270 + adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + + algorithm + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + 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. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + + + curation status specification + + + + + + + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + 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. + 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 + 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. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + group:OBI + + + data set + + + + + + + + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + + + data about an ontology part + + + + + + + + + + + + + + + + + + + + + plan specification + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + + 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. + 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. + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + OBI Plan and Planned Process branch + OBI_0000344 + + + 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 + plan specification + + + + + + + + + + + + + + + measurement datum + 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,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + + measurement datum + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + 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. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + + obsolescence reason specification + + + + + + + + + textual entity + Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities + + 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. + 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. + 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. + PERSON: Lawrence Hunter + text + + + textual entity + + + + + + + + + document + A journal article, patent application, laboratory notebook, or a book + + A collection of information content entities intended to be understood together as a whole + PERSON: Lawrence Hunter + + + document + + + + + + + + + + + + + + + document part + An abstract, introduction, method or results section. + + An information content entity that is part of a document. + PERSON: Lawrence Hunter + + + document part + + + + + + + + + + + + + + + + + + + + + Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. + + A planned process in which a document is created or added to by including the specified input in it. + 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 + Bjoern Peters + wikipedia http://en.wikipedia.org/wiki/Documenting + + documenting + + + + + + + + + + + + + + + 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. + + A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID symbol + Original proposal from Bjoern, discussions at IAO calls + + + centrally registered identifier symbol + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. + 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'). + Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. + Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. + + 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. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID + Original proposal from Bjoern, discussions at IAO calls + + + centrally registered identifier + + + + + + + + + PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. + + 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. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID registry + Original proposal from Bjoern, discussions at IAO calls + + + centrally registered identifier registry + + + + + + + + + written name + "Bill Clinton" + "The Eiffel Tower" + "United States of America" + + A textual entity that denotes a particular in reality. + PERSON: Bill Hogan + https://github.com/information-artifact-ontology/IAO/issues/114 + 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. + + + written name + + + + + + + + + identifier + 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. + + + identifier + + + + + + + + + + + + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + '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.) + 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. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + 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) + + + CHMO:0001840 + OBI:0000011 + planned process + planned process + + + + + + + + + + + + + + + reference substance role + 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 + + a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. + Person:Jennifer Fostel + reference substance + OBI + + reference substance role + + + + + + + + + + + + + + + + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + + processed material + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + investigation + Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation + + a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). + Bjoern Peters + OBI branch derived + Could add specific objective specification + 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 + + study + investigation + + + + + + + + + + + + + + + + + + + + + evaluant role + 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. + + 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 + 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) + examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") + GROUP: Role Branch + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + + evaluant role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay + Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. + + A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + 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. + PlanAndPlannedProcess Branch + measuring + scientific observation + OBI branch derived + + study assay + any method + assay + + + + + + + + + + reagent role + Buffer, dye, a catalyst, a solvating agent. + + 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. + PERSON:Matthew Brush + reagent + PERSON:Matthew Brush + 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. + + + (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 that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). + + reagent role + reagent + 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] + reagent role + + + + + + + + + + + + + + + + + + + + + + + + + + + material processing + A cell lysis, production of a cloning vector, creating a buffer. + + A planned process which results in physical changes in a specified input material + A planned process which results in physical changes in a specified input material. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra + material transformation + OBI branch derived + + + CHMO:0001131 + CHMO:0001267 + CHMO:0001461 + FIX:0000258 + material transformations + preparative method + sample preparation + sample preparation step + sample preparative method + OBI:0000094 + material processing + material processing + + + + + + + + + protocol + 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. + + 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. + PlanAndPlannedProcess Branch + OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) + + study protocol + protocol + + + + + + + + + + + + + + + + + + + + + interpreting data + 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. + + 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 + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + Bjoern Peters + + drawing a conclusion based on data + + + + + + + + + + + + + + + + + + + + planning + 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. + + a process of creating or modifying a plan specification + 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'. + Bjoern Peters + Bjoern Peters + Plans and Planned Processes Branch + + planning + + + + + + + + + synthesizing function + + 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. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + + synthesizing function + + + + + + + + + + + + + + + + + + + + + PCR product + PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. + + is double stranded DNA that is the specified output of a polymerase chain reaction + We are using PCR and not the written out words, as this is the most common used. + GROUP: OBI BIomaterial Branch + GROUP: OBI BIomaterial Branch + + PCR product + + + + + + + + + + + + + + + + + + + + + nucleic acid template role + a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 + + 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. + + nucleic acid template role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + polymerase chain reaction + Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 + + 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. + OBI Plan + PCR + adapted from wikipedai + + polymerase chain reaction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + enzyme + + (protein or rna) or has_part (protein or rna) and +has_function some GO:0003824 (catalytic activity) + 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. + person: Melanie Courtot + GROUP:OBI + + enzyme + + + + + + + + + assay objective + the objective to determine the weight of a mouse. + + an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) + PPPB branch + PPPB branch + + assay objective + + + + + + + + + material transformation objective + The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. + + an objective specifiction that creates an specific output object from input materials. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + artifact creation objective + GROUP: OBI PlanAndPlannedProcess Branch + + material transformation objective + + + + + + + + + + + + + + + + + + + + + + + + + study design execution + injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. + + a planned process that carries out a study design + 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. + branch derived + 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. + + study design execution + + + + + + + + + + manufacturer + Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. [OBI] + With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. [OBI] + 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] + 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] + manufacturer role + + + + + + + + + + + + + + + data set of predicted values according to fitted curve + + 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. + PERSON: James Malone + PERSON: Monnie McGee + + data set of predicted values according to fitted curve + + + + + + + + + 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. + + OBI:0000796 + purification objective + + + + + + + + + + + + + + + + + + + + + amplified DNA + Amplied DNA created by PCR + + DNA that has been produced in an enzymatic amplification process + PERSON: Alan Ruttenberg + Alan Ruttenberg + + amplified DNA + + + + + + + + + + + + + + + + + + + + + + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 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 role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + + + CHMO:0000998 + OBI:0000968 + device + + + + + + + + + rate measurement datum + 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. + + A scalar measurement datum that represents the number of events occuring over a time interval + PERSON: Bjoern Peters, Randi Vita + IEDB + + rate measurement datum + + + + + + + + + + + + + + + + + + + + + conclusion based on data + 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". + + An information content entity that is inferred from data. + 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. + Group:2013 Philly Workshop group + Group:2013 Philly Workshop group + + conclusion based on data + + + + + + + + + + + + 1 + + + + + + 1 + + + scalar value specification + + A value specification that consists of two parts: a numeral and a unit label + PERSON:Bjoern Peters + + scalar value specification + + + + + + + + + value specification + The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. + + An information content entity that specifies a value within a classification scheme or on a quantitative scale. + 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. + PERSON:Bjoern Peters + + value specification + + + + + + + + + pipette + + 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. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://en.wikipedia.org/wiki/Pipette + + pipette + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + data transformation + 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. + + A planned process that produces output data from input data. + Elisabetta Manduchi + Helen Parkinson + James Malone + Melanie Courtot + Philippe Rocca-Serra + Richard Scheuermann + Ryan Brinkman + Tina Hernandez-Boussard + data analysis + data processing + Branch editors + + data transformation + + + + + + + + + + + + + + + + + + + + + + + curve fitting data transformation + + 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. + Elisabetta Manduchi + James Malone + Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Curve_fitting + + curve fitting data transformation + + + + + + + + + data transformation objective + normalize objective + + An objective specification to transformation input data into output data + Modified definition in 2013 Philly OBI workshop + James Malone + PERSON: James Malone + + data transformation objective + + + + + + + + + curve fitting objective + + 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. + Elisabetta Manduchi + James Malone + PERSON: Elisabetta Manduchi + + curve fitting objective + + + + + + + + + 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. + + CHMO:0001047 + FIX:0000259 + FIX:0000260 + OBI:0302886 + centrifugation + + + + + + + + + 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. + + rinsing + OBI:0302888 + washing + + + + + + + + + + + + + + + study design + 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. + + 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: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert + experimental design + rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. + + study design + + + + + + + + + A material processing in which components of an input material become segregated in space. + + OBI:0600014 + material component separation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + enzymatic amplification + the use of a polymerase chain reaction to amplify a fragment of DNA + + the use of enzymes to increase the number of molecules of a biomaterial + PERSON:Kevin Clancy + OBI branch derived + + enzymatic amplification + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + quality + + + + + + + + + A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. + + concentration + quality + PATO:0000033 + + + + concentration of + + + + + + + + + + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + + quality + PATO:0000051 + + morphology + + + + + + + + + A 1-D extent quality which is equal to the distance between two points. + + quality + PATO:0000122 + + + + length + + + + + + + + + A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. + + quality + PATO:0000125 + + + + mass + + + + + + + + + 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. + + quality + PATO:0000965 + + symmetry + + + + + + + + + A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid. + + quality + PATO:0001536 + + + + + solubility + + + + + + + + + A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. + + quality + PATO:0001574 + + + flow rate + + + + + + + + + A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. + + George Gkoutos + 2010-03-10T03:18:15Z + PATO:0002061 + relational molecular quality + quality + PATO:0002182 + molecular quality + + + + + + + + + + + + + + + + + + + + + + + + + + + Synthesis is a planned material process that combines, changes or converts material to produce a new material. [Allotrope] + Wes Schafer, Oliver He + [PROCO] + synthetic chemical process + + + + + + + + + An experimental design to limit the number of experiments covering the space by assuming the Interactions between the factors are negligible + [PROCO] + Plackett–Burman design + + + + + + + + + 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. + [wikipedia] + prior art + + + + + + + + + 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. + [ICH Q8(R2)] + design space + + + + + + + + + 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. + W Schafer + [wikipedia] + factor + + + + + + + + + An information content entity that asserts the equality of two expressions. + [Wikipedia] + equation + + + + + + + + + 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. + [wikipedia] + factorial design + + + + + + + + + + + + + + + A process of systematically selecting possible synthetic routes to make a particular product or intermediate. + Wes Schafer, Oliver He + [PROCO] + route scouting + + + + + + + + + A process boundary that represents a milestone decision on route selection. + Wes, Oliver + [PROCO] + route selection milestone + + + + + + + + + + + + + + + A process profile that tracks some aspect of a reaction. + [PROCO] + reaction process profile + + + + + + + + + A temporal region that describes the length of time that a synthesis occurs. + W Schafer + [PROCO] + synthesis reaction time + + + + + + + + + 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. + CQA + [ICH Q8(R2)] + critical quality attribute + + + + + + + + + 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. + [Wikipedia] + experiment + + + + + + + + + + + + + + + A directive information entity that specifies allowed ranges recorded for a process profile. + [PROCO] + process profile specification + + + + + + + + + + + + + + + + + + + + + + + + + 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. + Wes, Oliver + CPP specification + https://en.wikipedia.org/wiki/Critical_process_parameters + CPP 'has facet' some specification +(note: like has part, but it is for info). + critical process parameter specification + + + + + + + + + + + + + + + + + + + + + + + + + A directive information entity that species the acceptable range of values associated with a material quality + W Schafer + [PROCO] + quality specification + + + + + + + + + + + + + + + A quality specification set against a critical quality attribute of a material + [PROCO] + CQA specification + + + + + + + + + + + + + + + + + + + + + + + + + A chemical entity that is the end point product generated from a synthetic chemical process. + Oliver He, Wes Schafer + https://en.wikipedia.org/wiki/Product_(chemistry) + chemical product + + + + + + + + + A chemical product that is used for commercial purpose. + Oliver, Wes + [PROCO] + commercial chemical product + + + + + + + + + A process profile that is about temperature. + Oliver, Wes + [PROCO] + temperature profile in synthesis process + + + + + + + + + + + + + + + A chemcial entity with the role starting material in a synthesis. + [PROCO] + starting material for synthesis + + + + + + + + + + + + + + + A chemical entity that is the product of a chemical reaction but not the last step in a synthesis. + [PROCO] + intermediate material for synthesis + + + + + + + + + + + + + + + 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. + Oliver He, Wes Schafer + [Wikipedia] + https://en.wikipedia.org/wiki/Impurity + chemical impurity + + + + + + + + + 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. + [ICH Q7] + GMP starting material + + + + + + + + + + + + + + + + + + + + + + + + + + A synthetic process governed by the cGMP regulations. + Wes Schafer, Oliver He + commercial synthetic process + [PROCO] + GMP synthetic process + + + + + + + + + A process measurement of the temperature in a process + Wes, Oliver + [PROCO] + temperature measurement + + + + + + + + + A unit operation of adding a reagent or starting material to a chemical reaction + Wes, Oliver + inserting material + [PROCO] + charging material + + + + + + + + + A synthetic process governed by the GLP regulations. + Wes Schafer, Oliver He + [PROCO] + GLP synthetic process + + + + + + + + + A plan specification that specifies the action and objective of a synthetic process, as defined in CFR - Code of Federal Regulations Title 21. + Wes, Oliver + https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=210.1 + GMP specification of synthetic process + + + + + + + + + + + + + + + A process profile that represents the number of revolution of stirs given a specific time period + Wes, Oliver + stirring profile in synthesis process + [PROCO] + stir rate profile + + + + + + + + + + + + + + + + + + + + + + + + + A process profile in synthesis process that is about material flow + Oliver, Wes + [PROCO] + material flow profile in synthesis process + + + + + + + + + + + + + + + A planned process. + Wes, Oliver + [PROCO] + process chemistry filing + + + + + + + + + A process profile that tracks the quality of some process participant. + [PROCO] + quality process profile + + + + + + + + + Reaction rate is the rate of the changing concentration of a product during a reaction process. + Wes, Oliver + https://en.wikipedia.org/wiki/Reaction_rate + reaction rate profile + + + + + + + + + A unit operation to remove portions of material from a synthesis stream by trapping it on a filter. + Wes, Oliver + [PROCO] + filtering + + + + + + + + + A basic and unit step in a process + unit operation + https://en.wikipedia.org/wiki/Unit_operation + 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. + unit operation in chemical processing + + + + + + + + + + + + + + + A process that has as a material output a crystalline solid or a mixture that has as an ingredient a crystalline solid. + Wes Schafer, Oliver He + crystallization + https://en.wikipedia.org/wiki/Crystallization + 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] + 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. + crystallization + + + + + + + + + The process mass intensity (PMI) calculates the ratio of the total mass of materials to the mass of the isolated product + PMI + [wikipedia] + https://en.wikipedia.org/wiki/Process_chemistry + process mass intensity + + + + + + + + + A substance or material consisting of very large molecules, or macromolecules, composed of many repeating subunits. + https://en.wikipedia.org/wiki/Polymer + polymer + + + + + + + + + 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. + Wes, Oliver + fate and purge + fate and purge of impurity + [PROCO] + impurity fate and purge determination + + + + + + + + + A sequenced plan of synthetic steps and defined intermediates to make a specific product from commercially available starting materials + Wes, Oliver + [PROCO] + route specification + + + + + + + + + A sequenced set of unit operations for a single synthetic reaction or simultaneous reactions that are executed in a single equipment train. + Wes, Oliver + [PROCO] + https://www.chemistryworld.com/opinion/what-counts-as-a-step-during-chemical-synthesis/2500261.article#/ + synthetic step specification + + + + + + + + + A process boundary that represents a milestone of filing the documentation required to obtain regulatory approval to sell a new product. + Wes, Oliver + [PROCO] + product filing milestone + + + + + + + + + + A process chemistry datum describing the ultimate final state and location of an impurity in a synthetic process. + [PROCO] + fate of impurity + + + + + + + + + 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. + Anna Dunn + rate constant + + + + + + + + + A fixed and well-defined number or other non-varying mathematical object. + [Wikipedia] + mathematical constant + + + + + + + + + A constant representing the concentration driving force + Anna Dunn + order + kinetic order + + + + + + + + + The role of a solvent in a precipitation or crystallization in which the solute of a solution is sparingly soluble to induce its solidification. + Wes Schafer, Oliver He + [PROCO] + antisolvent role + + + + + + + + + The role of a crystalline solid material input in a crystallization to promote nucleation or crystal growth. + Wes Schafer, Oliver He + [PROCO] + 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]. + seed role + + + + + + + + + The role of solids in a slurry + Wes Schafer, Oliver He + [PROCO] + precipitate role + + + + + + + + + A suspension (AFM_0000442) that is a mix of solids in a liquid + Wes Schafer, Oliver He + [PROCO] + slurry + + + + + + + + + A physical quality indicating the structural order of a solid in which its atoms or molecules are arranged in a regular, periodic manner.[wikipedia] + Wes Schafer, Oliver He + [PROCO] + crystalline state + + + + + + + + + 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. + Wes Schafer, Oliver He + [PROCO] + purge factor + + + + + + + + + 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. + Wes Schafer, Oliver He + [PROCO] + crystallization yield + + + + + + + + + A debris role of the solution in a slurry resulting from a crystallization + Wes Schafer, Oliver He + [PROCO] + mother liquor role + + + + + + + + + A solid with at least one crystalline phase + [PROCO] + crystalline solid + + + + + + + + + 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. + E-factor + environmental factor + https://en.wikipedia.org/wiki/Process_chemistry + process environmental factor + + + + + + + + + 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. + PEI + [wikipedia] + https://en.wikipedia.org/wiki/Process_chemistry + process excellence index + + + + + + + + + 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. + QSL + https://en.wikipedia.org/wiki/Process_chemistry + quality service level + + + + + + + + + A planned process with data output of commercial synthetic chemical route. + Wes, Oliver + [PROCO] + chemical process development + + + + + + + + + A process boundary that represents a milestone of filing the documentation required to obtain regulatory approval to sell a new drug product. + Wes, Oliver + [PROCO] + drug product filing milestone + + + + + + + + + + + + + + + A planned process that is about optimizing a synthetic route. + Wes, Oliver + development optimization + process optimization + [PROCO] + route development optimization + + + + + + + + + + A planned process producing data to demonstrate that a commercial route meets regulatory requirements. + Wes, Oliver + [PROCO] + route validation + + + + + + + + + + + + + + + + + + + + + + + + + A screening design to evaluate possible chemical reactions + Wes, Oliver + [PROCO] + reaction screening design + + + + + + + + + + + + + + + A process that ends with a milestone where a selection will be made on route process. + Wes, Oliver + [PROCO] + route selection + + + + + + + + + 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. + Wes, Oliver + [wikipedia] + mechanistic and kinetic determination + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + Wes, Oliver + [PROCO] + process validation + + + + + + + + + A screening design to discover polymorphs and solvates of a compound + Wes, Oliver + [PROCO] + polymorph and solvate screening design + + + + + + + + + + + + + + + A process chemistry workflow plan that specifies how a multi-parallel screening study should be conducted. + Wes, Oliver + [PROCO] + screening design + + + + + + + + + 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. + Wes Schafer, Oliver He + [PROCO] + batch campaign + + + + + + + + + A plan specification that specifies a process chemistry workflow consisting of a series of unit operations. + Wes, Oliver + [PROCO] + process chemistry workflow plan + + + + + + + + + An investigation of published material to find prior art related to a synthetic route + Wes, Oliver + [PROCO] + review of prior art + + + + + + + + + A document to secure permission or continuing permission to market a product from a regulatory body. + [PROCO] + product filing documentation + + + + + + + + + + + + + + + A planned process about a synthetic route + Wes, Oliver + [PROCO] + route related process + + + + + + + + + A planned process of measuring a quality of a material associated with a process. + Wes, Oliver + [PROCO] + process monitoring + + + + + + + + + A process measurement of the pressure in a process + Wes, Oliver + [PROCO] + pressure measurement + + + + + + + + + A process monitoring to determine when a chemical reaction has ended. + Wes, Oliver + [PROCO] + end reaction monitoring + + + + + + + + + A process boundary that represents a milestone of obtaining regulatory approval to sell a new product. + Wes, Oliver + [PROCO] + product approval milestone + + + + + + + + + A process boundary that represents a milestone of obtaining regulatory approval to sell a new drug product. + Wes, Oliver + [PROCO] + drug product approval milestone + + + + + + + + + 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 + Ostwald kinetic method + isolation kinetic method + [PROCO] + method of flooding + + + + + + + + + A temporal region of initial kinetics of a chemical reaction after which the reaction accelerates. + [Wikipedia] + induction period + 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. + + + + + + + + + + The assessed reactivity of the mutagenic impurity in the processing conditions + [PROCO] + assessed reactivity purge factor + + + + + + + + + + + + + + + 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. + [PROCO] + assessed solubility purge factor + + + + + + + + + A molecular quality that describes the unit cell of the crystal lattice + W Schafer + [PROCO] + unit cell quality + + + + + + + + + + a symmetry quality of a unit cell in three-dimensional space. + similar to http://purl.enanomapper.org/onto/ENM_9000037 + Wes Schafer, Oliver He + [PROCO] + space group + + + + + + + + + a geometric symmetry that keeps at least one point fixed + Wes Schafer, Oliver He + [PROCO] + point symmetry + + + + + + + + + a point symmetry that contains a polar axis. + Wes Schafer, Oliver He + [PROCO] + polar point symmetry + + + + + + + + + a point symmetry in which the original structure can be obtained by reflecting all lattice points through a single point. + Wes Schafer, Oliver He + [PROCO] + centrosymmetric point symmetry + + + + + + + + + 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. + Wes Schafer, Oliver He + [PROCO] + non-centrosymmetric point symmetry + + + + + + + + + a non-centrosymmetric point symmetry that cannot be rotated to align with the original structure (chiral). + Wes Schafer, Oliver He + [PROCO] + enantiomorphic point symmetry + + + + + + + + + a non-centrosymmetric point symmetry that can be rotated to align with the original structure (achiral). + Wes Schafer, Oliver He + [PROCO] + non-centrosymmetric achiral symmetry + + + + + + + + + the length of the a-axis of a unit cell + Wes Schafer, Oliver He + [PROCO] + unit cell a-axis length + + + + + + + + + the length of the b-axis of a unit cell + Wes Schafer, Oliver He + [PROCO] + unit cell b-axis length + + + + + + + + + the length of the c-axis of a unit cell + Wes Schafer, Oliver He + [PROCO] + unit cell c-axis length + + + + + + + + + The smallest, regularly repeating material portion of a crystalline lattice + Wes Schafer, Oliver He + [PROCO] + unit cell + + + + + + + + + A unit cell that has three perpendicular axes of equal lengths. +equivalent to ENM:9000035 + isometric unit cell + [PROCO] + cubic unit cell + + + + + + + + + A unit cell that has three perpendicular axes, two of equal length + [PROCO] + tetragonal unit cell + + + + + + + + + A unit cell that has three perpendicular axes, all of different lengths + [PROCO] + orthorhombic unit cell + + + + + + + + + A unit cell of three equal lateral axes intersecting at angles of 60 degrees and a vertical axis of variable length at right angles + [PROCO] + hexagonal unit cell + + + + + + + + + A unit cell of three equal lateral axes intersecting at the same angle but not perpendicularly + [PROCO] + trigonal unit cell + + + + + + + + + A unit cell that has three axes of unequal length, two of which are perpendicular + [PROCO] + monoclinic unit cell + + + + + + + + + A unit cell in which all axes are of different length and no angle is perpendicular nor equal to any other angles. + [PROCO] + triclinic unit cell + + + + + + + + + A unit cell quality describing the angle between the b and c axes. + [PROCO] + unit cell alpha internal angle + + + + + + + + + A unit cell quality describing the angle between the a and c axes. + [PROCO] + unit cell beta internal angle + + + + + + + + + A unit cell quality describing the angle between the a and b axes. + [PROCO] + unit cell gamma internal angle + + + + + + + + + The volume of the unit cell + [PROCO] + unit cell volume + + + + + + + + + A unit cell quality indicating the number of formula units (molecules) in the unit cell + [PROCO] + unit cell Z value + + + + + + + + + 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 + [PROCO] + unit cell Z' value + + + + + + + + + A unit cell quality indicating the density of the compound in the unit cell + [PROCO] + unit cell crystal density + + + + + + + + + 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] + [PROCO] + ICH Guideline + + + + + + + + + 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. + [PROCO] + habit + + + + + + + + + A portion of material within a a region of space in a system throughout which all physical properties of the material are essentially uniform. + [Wikipedia] + thermodynamic phase + + + + + + + + + A crystalline phase is a single solid crystalline thermodynamic phase + [PROCO] + crystalline solid thermodynamic phase + + + + + + + + + A solid in solid solution is a solution where the continuous phase is a solid and the dispersed phase is a solid. [Allotrope] + [Allotrope] + solid solution + + + + + + + + + An object aggregate of two or more molecular entities that does not include covalent or ionic interactions + [PROCO] + molecular complex + + + + + + + + + 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. + [PROCO] + co-crystal + + + + + + + + + A solvate is a crystalline material that has solvent molecules incorporated into the crystal lattice in a stoichiometric amount. [Allotrope] + [Allotrope] + solvate + + + + + + + + + A hydrate is a solvate that has water as the solvent adduct. + [PROCO] + hydrate + + + + + + + + + A chemical substance composed of ions held together by electrostatic forces termed ionic bonding. + [Wikipedia] + ionic salt + + + + + + + + + A crystalline phase without solvent in the unit cell + [PROCO] + anhydrous phase + + + + + + + + + An anhydrous crystalline phase formed experimentally by removing the solvent from a solvate + [PROCO] + isomorphic desolvate + + + + + + + + + + A heterogeneous ensemble of individual components whose crystal structures are like discontinuous solid solutions (phase separated). + [PROCO] Chem. Commun., 2014, 50, 906 + eutectic + + + + + + + + + + A heterogeneous solid solution consisting of two or more polymorphs of the same chemical entity + [PROCO] + concomitant polymorphs + + + + + + + + + A heterogenous mixture in which one or more components is dispersed in a solid matrix + [PROCO] + solid dispersion + + + + + + + + + A group of geometric symmetries (isometries) that keep at least one point fixed. + [wikipedia] + point group symmetry + + + + + + + + + + + + + + + + + + + + + + + + + + + + An open,one faced triclinic form with enantiomorphic and polar point symmetries + [PROCO] + pedial + + + + + + + + + + + + + + + + + + + + + 2-faced triclinic form with centrosymmetric point symmetry + [PROCO] + pinacoidal + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + [PROCO] + sphenoidal + + + + + + + + + + + + + + + + + + + + + A cubic system crystal class with 48 equal triangular faces + and three identical crystallographic axes with four fold rotational axes and centrosymmetric point symmetry + [PROCO] + hexoctahedral + + + + + + + + + + + + + + + + + + + + + A cubic system crystal class with 24-faces and four fold rotoinversion axes and non-centrosymmetric point symmetry + [PROCO] + hextetrahedral + + + + + + + + + + + + + + + + + + + + + A cubic form with no mirror planes and enantiomorphic point symmetry + [PROCO] + gyroidal + + + + + + + + + An experiment performed on computer or via computer simulation + [wikipedia] + in-silico modeling + + + + + + + + + An in-silico modeling to predict the unit cell of the crystal lattice based on the powder x-ray diffractogram + W. Schafer + [PROCO] + Powder Indexing + + + + + + + + + + + + + + + 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. + [Wikipedia] + crystal structure predictions + + + + + + + + + An ICH Guidance for developing and understanding the manufacturing process of the drug substance. + [ICH] + ICH Q11 Guidance for Development and Manufacture of Drug Substances + + + + + + + + + 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.. + [PROCO] + assessed volatility purge factor + + + + + + + + + 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. + [PROCO] + assessed ionisability purge factor + + + + + + + + + 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. + [PROCO] + overall assessed purge factor + + + + + + + + + + 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. + [ICH] + common technical document + + + + + + + + + + + + + + + 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. + [PROCO] + X-Ray diffractivity + + + + + + + + + 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. + [Wikipedia] + beaker + + + + + + + + + A heating device (environmental control device) that utilizes an open flame for heating. + [wikipedia] + Bunsen burner + + + + + + + + + A crucible is a ceramic or metal container in which metals or other substances may be melted or subjected to very high temperatures. [Wikipedia] + [Wikipedia] + crucible + + + + + + + + + A device to separate vaporized mixtures of liquid compounds with close volatility. + [wikipedia] + fractionating column + + + + + + + + + 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. + [Wikipedia] + Vigreux column + + + + + + + + + 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. + [Wikipedia] + Snyder column + + + + + + + + + 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. + [Wikipedia] + Widmer column + + + + + + + + + A device used to condense vapors into liquid by cooling. + [wikipedia] + condensor + + + + + + + + + A condensor consisting of a simple tube surrounded by a jacket of cooling water + [wikipedia] + Liebig condenser + + + + + + + + + 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. + bulb condensor + reflux condensor + [Wikipedia] + Allihn condenser + + + + + + + + + + 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. + Inland Revenue condenser + [Wikipedia] + Graham condensor + + + + + + + + + A condensor with three concentric glass tubes where coolant circulates in both the outer jacket and the central tube to increase the cooling surface, + double surface condenser + [Wikipedia] + Davies condenser + + + + + + + + + A condensor consisting of a straight tube containing an internal spiral coil through which coolant flows. + [Wikipedia] + coil condenser + + + + + + + + + A condensor with an internal double spiral through which coolant flows such that the coolant inlet and outlet are both at the top + [Wikipedia] + Dimroth condenser + + + + + + + + + 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. + [Wikipedia] + cold finger + + + + + + + + + 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. + [Wikipedia] + Frederichs condensor + + + + + + + + + + + + + + + A quality associated with a portion of material + [PROCO] + bulk substance quality + + + + + + + + + A device for controlling the environment of a particular space + [PROCO] + environmental control device + + + + + + + + + An environmental control device used to apply heat directly to containers. + isomantel + [wikipedia] + heating mantle + + + + + + + + + A round-bottom flask is a flask with a spherical body and one or more necks with ground glass joints. + [Wikipedia] + round bottom flask + + + + + + + + + Flasks are narrow-necked glass containers, typically conical or spherical, used in a laboratory to hold reagents or samples. + [Wikipedia] + flask + + + + + + + + + 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. + [Wikipedia] + volumetric flask + + + + + + + + + A syringe which has the function of pumping material into an experiment. + [PROCO] + [CHMO] term exists + syringe pump + + + + + + + + + An Erlenmeyer flask or conical flask is a type of laboratory flask which features a flat bottom, a conical body, and a cylindrical neck. + [Wikipedia] + Erlenmeyer flask + + + + + + + + + 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. + lab notebook + [Wikipedia] + laboratory notebook + + + + + + + + + A device that evaporates + [PROCO] + evaporation device + + + + + + + + + + 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. + [Wikipedia] + international nonproprietary name + + + + + + + + + The structure of a chemical entity in terms of its molecular geometry and electronic structure. + [PROCO] + chemical structure + + + + + + + + + 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. + clarifying agent + [Wikipedia] + flocculant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The drug substance nomenclature section of the CTA + [PROCO] + CTA Section 3.2.S.1.1 Nomenclature + + + + + + + + + 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. + [Wikipedia] + preferred IUPAC name + + + + + + + + + The name assigned to a chemical substance by the Chemical Abstracts Service of the American Chemical Society + [PROCO] + chemical abstracts name + + + + + + + + + A centrally registered identifier assigned by the Chemical Abstracts Service (CAS) to every chemical substance described in the open scientific literature. + [Wikipedia] + chemical abstracts number + + + + + + + + + The drug substance structure section of the CTA + [PROCO] + CTA Section 3.2.S.1.2 Structure + + + + + + + + + A two or three dimensional representation of a chemical structure. + [PROCO] + chemical drawing + + + + + + + + + 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. + [CHEMINF] + molecular formula + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + [PROCO] + CTA Section 3.2.S.1.3 General Properties + + + + + + + + + A document certified by a vendor summarizing test results and specifications for a particular batch of its product. + [PROCO] + certificate of analysis + + + + + + + + + A data item that is about a material entity based on a visual inspection. + [PROCO] + appearance datum + + + + + + + + + The document part of the common technical document regarding manufacturers + [PROCO] + CTA Section 3.2.S.2.1 Manufacturers + + + + + + + + + A 2-D representation of a step-by-step progression through a synthesis or part of a synthesis showing reagents, intermediates and reaction conditions. + [PROCO] + synthesis flow chart + + + + + + + + + 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. + [PROCO] + CTA Section 3.2.S.2.2 Description of Manufacturing Process and Process Controls + + + + + + + + + A scalar measurement datum that quantifies the measured pH of a saturated solution of a material at a specified temperature. + [PROCO] + solution pH datum + + + + + + + + + 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. + [wikipedia] + specific rotation datum + + + + + + + + + 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. + [PROCO] + CTA Section 3.2.S.2.3 Control of Materials + + + + + + + + + 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. + [PROCO] + CTA Section 3.2.S.2.4 Controls of Critical Steps and Intermediates + + + + + + + + + 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. + [PROCO] + CTA Section 3.2.S.3.1 Elucidation of Structure and other Characteristics + + + + + + + + + The document part of the common technical document that provides Information on impurities. Reference ICH guidances Q3A, Q3C, Q5C, Q6A, and Q6B. + [PROCO] + CTA Section 3.2.S.3.2 Impurities + + + + + + + + + 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. + [ICH] + ICH M7 Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals To Limit Potential Carcinogenic Risk + + + + + + + + + + + + + + + + + + + + + + + An is-silico modeling based on DEREK that determines the risk of a chemical being a mutagenic impurity + [PROCO] + DEREK Mutagen Prediction + + + + + + + + + + + + + + + + + + + + + + + An is-silico modeling based on MCASE that determines the risk of a chemical being a mutagenic impurity + [PROCO] + MCASE Mutagen Prediction + + + + + + + + + + + + + + + + + + + + + + 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). + close match to http://purl.obolibrary.org/obo/STATO_0000071 but derived class is being developed wrt to rate constant and rate orders. + rate law + [Wikipedia] + rate equation + + + + + + + + + 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. + 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. + RPKA + [Wikipedia] + Reaction Progress Kinetic Analysis + + + + + + + + + A process chemistry workflow plan that utilizes online and at-line measurements to understand chemical processes by defining and monitoring ... + PAT + [PROCO] + process analytical technology + + + + + + + + + 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. + shouldn't this be a data transformation process? + Bodenstein's quasi-steady state approximation + stationary-state approximation + [Wikipedia] + steady-state approximation analysis + + + + + + + + + The exponent terms within the rate equation. For elementary (single step) reactions, the reactant order is equal to the stoichiometric coefficient of the reactant. + Anna Dunn + Partial order of reaction + Reactant Rate Order + Reactant order + [wikipedia] + partial rate order + + + + + + + + + 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. + [Wikipedia] + overall reaction order + + + + + + + + + A quality process profile that tracks the concentration changes of a species + [PROCO] + concentration profile + + + + + + + + + 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. + 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] + [Wikipedia] + reaction rate + + + + + + + + + A kinetic determination method that measures the concentration of reaction species which is proportional to the integral of the reaction rate. + [wikipedia] + integral kinetic measurement + + + + + + + + + A kinetic determination method that measures reaction rate directly. (d[]/dt) + [wikipedia] + differential kinetic measurement + + + + + + + + + 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. + [PROCO] + method of initial rates + + + + + + + + + A plot of the differential kinetic measurement as the y-axis vs. the integral measurement as the x-axis. + [PROCO] + graphical rate equation + + + + + + + + + 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. + [PROCO] + Variable Time Normalisation Analysis + + + + + + + + + An impurity role of DNA reactive material that have significant carcinogenic risk + [ICH] + mutagenic impurity + + + + + + + + + + + + + + + + + + + + + A 2- faced open form monoclinic crystal with polar point symmetry. + [PROCO] + domatic + + + + + + + + + + + + + + + + + + + + + 3, 4, 6, 8, or 12 faced monoclinic crystal with centrosymmetric point symmetry. + [PROCO] + prismatic + + + + + + + + + + + + + + + + + + + + + Four-faced closed orthorhombic form with enantiomorphic point symmetry + [PROCO] + rhombic-disphenoidal + + + + + + + + + + + + + + + + + + + + + 3, 4, 6, 8, or 12 nonparallel faced orthorhombic system with polar point symmetry. + [PROCO] + rhombic-pyramidal + + + + + + + + + + + + + + + + + + + + + 8-faced form orthorhombic crystal class with centrosymmetric point symmetry + [PROCO] + rhombic-dipyramidal + + + + + + + + + + + + + + + + + + + + + Isometric form with no 4 fold axes and centrosymmetric point symmetry + [PROCO] + diploidal + + + + + + + + + + + + + + + + + + + + + General cubic forms which only has 3-fold axes and 2-fold axes with no mirror plane with enantiomorphic point symmetry. + [PROCO] + tetartoidal + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4-faced tetragonal form with polar point and enantiomorphic point symmetry. + [PROCO] + tetragonal-pyramidal + + + + + + + + + + + + + + + + + + + + + 4-faced closed orthorhombic form with non-centrosymmetric point symmetry. + [PROCO] + tetragonal-disphenoidal + + + + + + + + + + + + + + + + + + + + + 8-faced form with centrosymmetric point symmetry. + [PROCO] + tetragonal-dipyramidal + + + + + + + + + + + + + + + + + + + + + 6-, 8-, 12-, or 24-trapezium faced closed tetragonal form with enantiomorphic point symmetry + [PROCO] + tetragonal-trapezohedral + + + + + + + + + + + + + + + + + + + + + 8-faced tetragonal form with polar point and enantiomorphic point symmetry + [PROCO] + ditetragonal-pyramidal + + + + + + + + + + + + + + + + + + + + + 8-faced (tetragonal) or 12-faced (hexagonal) closed tetragonal form with non-centrosymmetric point symmetry + [PROCO] + tetragonal-scalenohedral + + + + + + + + + + + + + + + + + + + + + 16-faced form tetragonal crystal form with centrosymmetric point symmetry + [PROCO] + ditetragonal-dipyramidal + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3-faced form where all faces are related by a 3-fold rotation axis with polar point and enantiomorphic point symmetry. + [PROCO] + trigonal-pyramidal + + + + + + + + + + + + + + + + + + + + + 6 faced closed rhombohedral form of six identical faces in which none of the intersection edges is perpendicular and having centrosymmetric point symmetry + [PROCO] + rhombohedral + + + + + + + + + + + + + + + + + + + + + 6-, 8-, 12-, or 24-trapezohedral faced closed trigonal form with enantiomorphic point symmetry + [PROCO] + trigonal-trapezohedral + + + + + + + + + + + + + + + + + + + + + 6-faced trigonal form where all faces are related by a 3-fold rotational axis with polar point symmetry. + [PROCO] + ditrigonal-pyramidal + + + + + + + + + + + + + + + + + + + + + 8-faced (tetragonal) or 12-faced (hexagonal) closed form in which the faces are grouped in symmetrical pairs with centrosymmetric point symmetry + [PROCO] + ditrigonal-scalenohedral + + + + + + + + + + + + + + + + + + + + + + + + + + + + 6-faced form where all faces are related by a 6 axis having polar point and enantiomorphic point symmetry. + [PROCO] + hexagonal-pyrimidal + + + + + + + + + + + + + + + + + + + + + 6-faced hexagonal form with faces related by a 3-fold axis with a perpendicular mirror plane having non-centrosymmetric point symmetry + [PROCO] + trigonal-dipyramidal + + + + + + + + + + + + + + + + + + + + + 12-faced hexagonal form with faces related by a 6-fold axis with a perpendicular mirror with a centrosymmetric point symmetry + [PROCO] + hexagonal-dipyrimidal + + + + + + + + + + + + + + + + + + + + + 6-faced closed hexagonal form with enantiomorphic point symmetry. + [PROCO] + hexagonal-trapezohedral + + + + + + + + + + + + + + + + + + + + + 12-faced hexagonal crystal where all faces are related by a 6-fold axis. It has polar point symmetry + [PROCO] + dihexagonal-pyramidal + + + + + + + + + + + + + + + + + + + + + 12-faced form tetragonal crystal class with non-centrosymmetric point symmetry + [PROCO] + ditrigonal-dipyramidal + + + + + + + + + + + + + + + + + + + + + 24-faced form with faces related by a 6-fold axis with a perpendicular mirror plane and centrosymmetric point symmetry + [PROCO] + dihexagonal-dipyramidal + + + + + + + + + An ICH guideline about identifying, qualifying and specifying impurities in drug substance. + [ICH] + ICH Q3A Impurities in New Drug Substances + + + + + + + + + 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. + [ICH] + ICH Q3C Residual Solvents + + + + + + + + + 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. + [ICH] + ICH Q3D Guidance for Elemental Impurities + + + + + + + + + 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. + [ICH] + ICH Q6A Specifications: Test Procedures and Acceptance Criteria for Chemical Substances + + + + + + + + + An ICH Guideline for the manufacture of APIs for use in human drug (medicinal) products. + [ICH] + Q7 Good Manufacturing Practice Guide for Active Pharmaceutical Ingredients + + + + + + + + + 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. + [FDA] + residual solvent impurity + + + + + + + + + Solvents to be avoided and with strict low limits as they are human carcinogens, strongly suspected human carcinogens, and environmental hazards. + [ICH] + ICH Q6A Class 1 Solvent + + + + + + + + + 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 + [ICH] + ICH Q6A Class 2 Solvent + + + + + + + + + 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. + [ICH] + ICH Q6A Class 3 Solvent + + + + + + + + + The maximum acceptable intake per day of residual solvent in pharmaceutical products + [ICH] + Permitted Daily Exposure + + + + + + + + + An experimental design involving the testing of factors, or causes, one at a time instead of multiple factors simultaneously. + [Wikipedia] + one-factor-at-a-time experimental design + + + + + + + + + The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions. + http://edamontology.org/topic_3678 + experimental design + + + + + + + + + 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. + [Wikipedia] + explosion + + + + + + + + + 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. + [PROCO] + process safety + + + + + + + + + An experimental design to produce a response curve sufficient to fit quadratic models of the individual factors + George Box, Donald Behnken, "Some new three level designs for the study of quantitative variables", Technometrics, Volume 2, pages 455–475, 1960 + [Wikipedia] + Box–Behnken design + + + + + + + + + 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. + [wikipedia] + Central Composite Design + + + + + + + + + + + + + + + + + + + + + + A centrally registered identifier assigned to a laboratory notebook experiment + W Schafer + [PROCO] + laboratory notebook experiment identifier + + + + + + + + + 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. + Wes Schafer + batch sheet + [PROCO] + batch manufacturing record + + + + + + + + + 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. +. + master manufacturing formula + master production record + FDA 21CFR226 + master formula record + + + + + + + + + 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. + BOM + associated list + bill of material + wikipedia + bill of materials + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A screening design to determine to solubility of a compound + [PROCO] + solubility screening design + + + + + + + + + + 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. + Wes Schafer + [PROCO] + competency question + + + + + + + + + A process chemistry datum quantifying the sum of the costs of all raw materials, intermediates, reagents, solvents and catalysts procured from external vendor. + [Wikipedia] + material costs + + + + + + + + + A portion of material with a debris role that is a material output of a process. + Wes Schafer + [PROCO] + waste stream + + + + + + + + + + + + + + + + + + + + + + + + + A portion of material to be further processed that has an ingredient a material with the role of product. + waste stream can also have the product as an ingredient. Need to convey that it is portion of material that will be further processed. + W Schafer + [PROCO] + product stream + + + + + + + + + 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. + [ICH Q10] + Control Strategy + + + + + + + + + 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). + [Wikipedia] + risk assessment + + + + + + + + + + + + + + + A planned process that converts input data into output data based on some equation or set of equations + close to AFP_0003282 + W Schafer + [PROCO] + calculation + + + + + + + + + + + + + + + A data item that is a recording of the output of a calculation. + [PROCO] + calculated datum + + + + + + + + + + + + + + + A data item about process chemistry + [PROCO] + process chemistry datum + + + + + + + + + A planned process of extracting information from chemical systems by data-driven means. + [Wikipedia] + chemometrics + + + + + + + + + + + + + + + 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. + [Wikipedia] + factorial analysis + + + + + + + + + + + + + + + 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. + [ICH Q8(R2)] + critical process parameter + + + + + + + + + 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. + W Schafer + [PROCO] + multi-parallel experimentation + + + + + + + + + An equation for the temperature dependence of reaction rates used in determining rate of chemical reactions and for calculation of energy of activation. + [Wikipedia] + Arhennius equation + + + + + + + + + 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. + A factor + [Wikipedia] + pre-exponential factor + + + + + + + + + protein + antithrombin III is a protein + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. + + + protein + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + + metadata complete + 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. + metadata complete + + + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + PERSON:Alan Ruttenberg + organizational term + + + + + + + + + + ready for release + 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." + ready for release + + + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + + pending final vetting + 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. + pending final vetting + + + + + + + + + + placeholder removed + placeholder removed + + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + term imported + 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 imported + + + + + + + + + term split + 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. + term split + + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + requires discussion + 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. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + +## 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 + + + axiom holds for all times + + + + + + + + en + Adam Goldstein + Alan Ruttenberg + Albert Goldfain + Barry Smith + Bjoern Peters + Carlo Torniai + Chris Mungall + Chris Stoeckert + Christian A. Boelling + Darren Natale + David Osumi-Sutherland + Gwen Frishkoff + Holger Stenzhorn + James A. Overton + James Malone + Jennifer Fostel + Jie Zheng + Jonathan Rees + Larisa Soldatova + Lawrence Hunter + Mathias Brochhausen + Matt Brush + Melanie Courtot + Michel Dumontier + Paolo Ciccarese + Pat Hayes + Philippe Rocca-Serra + Randy Dipert + Ron Rudnicki + Satya Sahoo + Sivaram Arabandi + Werner Ceusters + William Duncan + William Hogan + Yongqun (Oliver) He + 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. + Information Artifact Ontology (IAO) + + 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 + IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 + IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 + + 2020-12-09 + + + + + + + + en + Ontology for Biomedical Investigations + Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester + Alan Ruttenberg + Allyson Lister + Barry Smith + Bill Bug + Bjoern Peters + Carlo Torniai + Chris Mungall + Chris Stoeckert + Chris Taylor + Christian Bolling + Cristian Cocos + Daniel Rubin + Daniel Schober + Dawn Field + Dirk Derom + Elisabetta Manduchi + Eric Deutsch + Frank Gibson + Gilberto Fragoso + Helen C. Causton + Helen Parkinson + Holger Stenzhorn + James A. Overton + James Malone + Jay Greenbaum + Jeffrey Grethe + Jennifer Fostel + Jessica Turner + Jie Zheng + Joe White + John Westbrook + Kevin Clancy + Larisa Soldatova + Lawrence Hunter + Liju Fan + Luisa Montecchi + Matthew Brush + Matthew Pocock + Melanie Courtot + Melissa Haendel + Mervi Heiskanen + Monnie McGee + Norman Morrison + Philip Lord + Philippe Rocca-Serra + Pierre Grenon + Richard Bruskiewich + Richard Scheuermann + Robert Stevens + Ryan R. Brinkman + Stefan Wiemann + Susanna-Assunta Sansone + Tanya Gray + Tina Hernandez-Boussard + Trish Whetzel + Yongqun He + 2009-07-31 + 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. + OWL-DL + An ontology for the annotation of biomedical and functional genomics experiments. + http://creativecommons.org/licenses/by/4.0/ + Ontology for Biomedical Investigations + 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. + 2021-04-06 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A relation between an information content entity and a value specification that specifies its value. + has value specification + + OBI + has value specification + PERSON: James A. Overton + + + + Janna Hastings + Leonard Jacuzzo + + + Barry Smith + The BSD license on the BFO project site refers to code used to build BFO. + David Osumi-Sutherland + Pierre Grenon + + Werner Ceusters + Selja Seppälä + Jie Zheng + Thomas Bittner + Mathias Brochhausen + 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. + Mauricio Almeida + 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. + Melanie Courtot + + Bjoern Peters + + + Yongqun "Oliver" He + + James A. Overton + Jonathan Bona + Holger Stenzhorn + Fabian Neuhaus + + Randall Dipert + + + Larry Hunter + Stefan Schulz + 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. + Chris Mungall + + Ron Rudnicki + 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. + Mark Ressler + Albert Goldfain + 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. + Alan Ruttenberg + Ludger Jansen + Bill Duncan + + + + For any queries contact chebi-help@ebi.ac.uk + 1.2 + Author: ChEBI curation team + developed by Michael Ashburner & Pankaj Jaiswal. + 26:05:2021 18:56 + ChEBI subsumes and replaces the Chemical Ontology first + ChEBI Release version 200 + + + 1.2 + + + + saved-by: kirill + 1.0 + autogenerated-by: DAG-Edit version 1.419 rev 3 + version: $Revision: 1.2 $ + date: Mon Apr 04 14:05:41 BST 2005 + 25:05:2005 12:37 + + + 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 + + + + + + +