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 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 has measurement unit label 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_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_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 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 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 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 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 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 SBO:SBO_0000002 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 SBO:SBO_0000009 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 SBO:SBO_0000331 Time interval over which a quantified entity is reduced to half its original value. half-life SBO:SBO_0000332 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> SBO:SBO_0000346 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 SBO:SBO_0000348 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> SBO:SBO_0000491 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 SBO:SBO_0000611 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 BFO:0000001 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 BFO:0000002 BFO:0000003 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 BFO:0000004 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 BFO:0000008 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 BFO:0000015 BFO:0000016 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 BFO:0000017 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 BFO:0000019 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 BFO:0000020 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 BFO:0000023 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 BFO:0000024 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 BFO:0000027 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 BFO:0000031 BFO:0000034 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 BFO:0000035 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 BFO:0000040 BFO:0000144 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 CHEBI:10545 Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite CHEBI:131604 A molecular entity that can undergo reduction by the gain of hydrogen atom(s). R * chebi_ontology A CHEBI:13193 hydrogen acceptor CHEBI:13193 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 CHEBI:134179 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 CHEBI:138103 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 CHEBI:138675 -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 CHEBI:13941 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 CHEBI:143130 A molecular entity that can transfer an electron to another molecular entity. electron donor chebi_ontology Elektronendonator donneur d'electron CHEBI:15022 electron donor CHEBI:15022 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 CHEBI:15339 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 CHEBI:15347 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 CHEBI:15734 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 CHEBI:15740 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 CHEBI:16134 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 CHEBI:16397 CHEBI:16670 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 CHEBI:166831 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 CHEBI:167095 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 CHEBI:16716 CHEBI:16991 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 CHEBI:17087 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 CHEBI:17499 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 CHEBI:17514 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 CHEBI:17578 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 CHEBI:17654 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 CHEBI:17741 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 CHEBI:17790 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 CHEBI:17824 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 CHEBI:17891 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 CHEBI:18044 '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 CHEBI:18059 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 CHEBI:18379 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 CHEBI:18407 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:22221 chebi_ontology CHEBI:22368 alpha-1-microglobulin-Ig alpha complex chromophores CHEBI:22368 A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion chebi_ontology Anionen aniones anions CHEBI:22563 anion CHEBI:22563 A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. chebi_ontology antioxidants antioxydant antoxidant CHEBI:22586 antioxidant CHEBI:22586 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 CHEBI:22695 Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. chebi_ontology CHEBI:22712 benzenes CHEBI:22712 Any ketone that is butane substituted by an oxo group at unspecified position. chebi_ontology butanones CHEBI:22951 butanone CHEBI:22951 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 CHEBI:23004 0 CO 28.01010 27.99491 O=C(*)* carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group CHEBI:23019 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 CHEBI:23240 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 CHEBI:23357 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 CHEBI:23367 Salts and C-organyl derivatives of hydrogen cyanide, HC#N. cyanides chebi_ontology CHEBI:23424 cyanides CHEBI:23424 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 CHEBI:23888 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 CHEBI:23924 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:24026 chebi_ontology CHEBI:24028 iron(3+) chelator CHEBI:24028 Amides with the general formula R(1)R(2)NCHO (R(1) and R(2) can be H). chebi_ontology CHEBI:24079 formamides CHEBI:24079 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 CHEBI:24431 A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role CHEBI:24432 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 CHEBI:24433 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 CHEBI:24532 A compound consisting of carbon and hydrogen only. hydrocarbon hydrocarbons chebi_ontology Kohlenwasserstoff Kohlenwasserstoffe hidrocarburo hidrocarburos hydrocarbure CHEBI:24632 hydrocarbon CHEBI:24632 Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides CHEBI:24651 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:24833 chebi_ontology inorganic anions CHEBI:24834 inorganic anion CHEBI:24834 A molecular entity that contains no carbon. chebi_ontology anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics CHEBI:24835 inorganic molecular entity CHEBI:24835 A compound which can carry specific ions through membranes of cells or organelles. Wikipedia:Ionophore ionophore chebi_ontology ionophores CHEBI:24869 ionophore CHEBI:24869 A molecular entity having a net electric charge. Ion ion chebi_ontology Ionen iones ions CHEBI:24870 ion CHEBI:24870 Any ionophore capable of transportation of iron ions across membranes. chebi_ontology iron ionophores CHEBI:24874 iron ionophore CHEBI:24874 A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. chebi_ontology CHEBI:25078 luciferin CHEBI:25078 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:25212 chebi_ontology mitochondrial electron transport chain inhibitors mitochondrial electron-transport chain inhibitor mitochondrial respiratory chain inhibitors CHEBI:25355 mitochondrial respiratory-chain inhibitor CHEBI:25355 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 CHEBI:25367 An oxoacid containing a single carboxy group. chebi_ontology monocarboxylic acids CHEBI:25384 monocarboxylic acid CHEBI:25384 0 N 14.007 14.00307 WebElements:N nitrogen chebi_ontology 7N N Stickstoff azote nitrogen nitrogeno CHEBI:25555 nitrogen atom CHEBI:25555 nonmetal chebi_ontology Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals CHEBI:25585 nonmetal atom CHEBI:25585 chebi_ontology organic heteromonocyclic compounds CHEBI:25693 organic heteromonocyclic compound CHEBI:25693 Any organic ion with a net negative charge. chebi_ontology organic anions CHEBI:25696 organic anion CHEBI:25696 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:25698 chebi_ontology organic ions CHEBI:25699 organic ion CHEBI:25699 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 CHEBI:2571 An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides CHEBI:25741 oxide CHEBI:25741 chebi_ontology CHEBI:25747 oxidized luciferins CHEBI:25747 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 CHEBI:25805 oxygen molecular entity chebi_ontology oxygen molecular entities CHEBI:25806 oxygen molecular entity CHEBI:25806 A ketone that is propane carrying at least one oxo substituent. chebi_ontology CHEBI:26292 propanones CHEBI:26292 chebi_ontology CHEBI:26671 sideramine CHEBI:26671 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 CHEBI:26672 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 CHEBI:26911 Any oxacycle having an oxolane (tetrahydrofuran) skeleton. chebi_ontology CHEBI:26912 oxolanes CHEBI:26912 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 CHEBI:27024 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 CHEBI:27207 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 CHEBI:27594 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 CHEBI:27780 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 CHEBI:28398 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 CHEBI:28616 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 CHEBI:28868 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 CHEBI:28938 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 CHEBI:29067 -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 CHEBI:29337 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-) CHEBI:29340 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 CHEBI:29347 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 CHEBI:30751 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 CHEBI:30879 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 CHEBI:32988 Intended use of the molecular entity or part thereof by humans. chebi_ontology CHEBI:33232 application CHEBI:33232 A particle not known to have substructure. elementary particle chebi_ontology elementary particles CHEBI:33233 fundamental particle CHEBI:33233 chebi_ontology oxoacid derivatives CHEBI:33241 oxoacid derivative CHEBI:33241 chebi_ontology inorganic hydrides CHEBI:33242 inorganic hydride CHEBI:33242 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 CHEBI:33245 Any substituent group which does not contain carbon. chebi_ontology inorganic groups CHEBI:33246 inorganic group CHEBI:33246 Any substituent group or skeleton containing carbon. chebi_ontology organic groups CHEBI:33247 organic group CHEBI:33247 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 CHEBI:33249 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 CHEBI:33250 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 CHEBI:33252 Heavy nuclear particle: proton or neutron. nucleon chebi_ontology Nukleon Nukleonen nucleons CHEBI:33253 nucleon CHEBI:33253 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 CHEBI:33256 An anion consisting of more than one atom. chebi_ontology polyatomic anions CHEBI:33273 polyatomic anion CHEBI:33273 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 CHEBI:33281 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 CHEBI:33282 A nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients CHEBI:33284 nutrient CHEBI:33284 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 CHEBI:33285 An energy-rich substance that can be transformed with release of usable energy. chebi_ontology CHEBI:33292 fuel CHEBI:33292 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 CHEBI:33300 A p-block molecular entity containing any pnictogen. pnictogen molecular entity chebi_ontology pnictogen molecular entities CHEBI:33302 pnictogen molecular entity CHEBI:33302 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 CHEBI:33303 Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities CHEBI:33304 chalcogen molecular entity CHEBI:33304 group 14 elements chebi_ontology carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements CHEBI:33306 carbon group element atom CHEBI:33306 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 CHEBI:33318 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:33405 chebi_ontology s-block element s-block elements CHEBI:33559 s-block element atom CHEBI:33559 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 CHEBI:33560 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 CHEBI:33575 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 CHEBI:33579 carbon group molecular entity chebi_ontology carbon group molecular entities CHEBI:33582 carbon group molecular entity CHEBI:33582 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 CHEBI:33595 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 CHEBI:33597 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:33598 chebi_ontology hydrogen compounds hydrogen molecular entities CHEBI:33608 hydrogen molecular entity CHEBI:33608 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 CHEBI:33655 Any monocyclic or polycyclic aromatic hydrocarbon. arene arenes chebi_ontology aromatic hydrocarbons CHEBI:33658 arene CHEBI:33658 chebi_ontology organic aromatic compounds CHEBI:33659 organic aromatic compound CHEBI:33659 chebi_ontology monocyclic compounds CHEBI:33661 monocyclic compound CHEBI:33661 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 CHEBI:33662 cyclic hydrocarbon chebi_ontology cyclic hydrocarbons CHEBI:33663 cyclic hydrocarbon CHEBI:33663 monocyclic hydrocarbon monocyclic hydrocarbons chebi_ontology monocyclic hydrocarbons CHEBI:33664 monocyclic hydrocarbon CHEBI:33664 heteromonocyclic compound heteromonocyclic compounds chebi_ontology CHEBI:33670 heteromonocyclic compound CHEBI:33670 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 CHEBI:33674 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 CHEBI:33675 Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology CHEBI:33692 hydrides CHEBI:33692 CHEBI:33696 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 CHEBI:33697 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 CHEBI:33709 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 CHEBI:33822 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:33832 chebi_ontology benzenoid aromatic compounds benzenoid compound CHEBI:33836 benzenoid aromatic compound CHEBI:33836 CHEBI:33839 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 CHEBI:33842 A monocyclic aromatic hydrocarbon. chebi_ontology monocyclic arenes CHEBI:33847 monocyclic arene CHEBI:33847 A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent chebi_ontology reactif reactivo reagents CHEBI:33893 reagent CHEBI:33893 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:33937 chebi_ontology nitrogen hydrides CHEBI:35106 nitrogen hydride CHEBI:35106 Saturated acyclic nitrogen hydrides having the general formula NnHn+2. chebi_ontology azanes CHEBI:35107 azane CHEBI:35107 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 CHEBI:35195 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 CHEBI:35197 A substance that diminishes the rate of a chemical reaction. inhibitor chebi_ontology inhibidor inhibiteur inhibitors CHEBI:35222 inhibitor CHEBI:35222 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 CHEBI:35223 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 CHEBI:35225 Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compounds chebi_ontology organonitrogens CHEBI:35352 organonitrogen compound CHEBI:35352 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 CHEBI:35366 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 CHEBI:35406 heterocyclic parent hydrides chebi_ontology heterocyclic fundamental parent heterocyclic organic fundamental parents organic heterocyclic fundamental parents CHEBI:35552 heterocyclic organic fundamental parent CHEBI:35552 chebi_ontology carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid CHEBI:35605 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 CHEBI:35681 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 CHEBI:35757 pnictogen hydride chebi_ontology pnictogen hydrides CHEBI:35881 pnictogen hydride CHEBI:35881 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 CHEBI:35942 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 CHEBI:36338 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 CHEBI:36339 Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion chebi_ontology fermions CHEBI:36340 fermion CHEBI:36340 A particle smaller than an atom. Wikipedia:Subatomic_particle chebi_ontology subatomic particles CHEBI:36342 subatomic particle CHEBI:36342 A subatomic particle known to have substructure (i.e. consisting of smaller particles). chebi_ontology composite particles CHEBI:36343 composite particle CHEBI:36343 Hadron is a subatomic particle which experiences the strong force. chebi_ontology hadrons CHEBI:36344 hadron CHEBI:36344 A nucleus or any of its constituents in any of their energy states. nuclear particle chebi_ontology CHEBI:36347 nuclear particle CHEBI:36347 Any molecular entity consisting of more than one atom. chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity CHEBI:36357 An ion consisting of more than one atom. chebi_ontology polyatomic ions CHEBI:36358 polyatomic ion CHEBI:36358 chebi_ontology saturated heterocyclic parent hydride saturated heterocyclic parent hydrides saturated organic heterocyclic parents CHEBI:36388 saturated organic heterocyclic parent CHEBI:36388 chebi_ontology saturated heteromonocyclic parent hydride saturated heteromonocyclic parent hydrides saturated organic heteromonocyclic parents CHEBI:36389 saturated organic heteromonocyclic parent CHEBI:36389 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 CHEBI:36586 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 CHEBI:36587 pseudohalide group chebi_ontology halogenoid group pseudohalido group pseudohalo groups pseudohalogen group CHEBI:36823 pseudohalo group CHEBI:36823 pseudohalide ions chebi_ontology pseudohalide anions pseudohalides pseudohalogen anion pseudohalogen ion CHEBI:36828 pseudohalide anion CHEBI:36828 chebi_ontology polyatomic monoanions CHEBI:36829 polyatomic monoanion CHEBI:36829 -1 chebi_ontology monoanions CHEBI:36830 monoanion CHEBI:36830 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:36856 chebi_ontology inorganic ions CHEBI:36914 inorganic ion CHEBI:36914 chebi_ontology inorganic cations CHEBI:36915 inorganic cation CHEBI:36915 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 CHEBI:36916 An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound chebi_ontology organochalcogen compounds CHEBI:36962 organochalcogen compound CHEBI:36962 An organochalcogen compound containing at least one carbon-oxygen bond. PMID:17586126 organooxygen compound chebi_ontology organooxygen compounds CHEBI:36963 organooxygen compound CHEBI:36963 amino-acid anion chebi_ontology amino acid anions amino-acid anions CHEBI:37022 amino-acid anion CHEBI:37022 chebi_ontology organic hydrides CHEBI:37175 organic hydride CHEBI:37175 mononuclear parent hydrides chebi_ontology mononuclear hydride mononuclear hydrides CHEBI:37176 mononuclear parent hydride CHEBI:37176 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 CHEBI:37407 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 CHEBI:37527 A molecular entity consisting of two or more chemical elements. chebi_ontology chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity CHEBI:37577 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 CHEBI:37622 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 CHEBI:37838 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 CHEBI:38104 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:38155 chebi_ontology iron chelating agents iron chelators CHEBI:38157 iron chelator CHEBI:38157 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:38161 chebi_ontology CHEBI:38162 iron(2+) chelator CHEBI:38162 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 CHEBI:38323 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:38472 chebi_ontology CHEBI:38496 electron-transport chain inhibitor CHEBI:38496 chebi_ontology CHEBI:38497 respiratory-chain inhibitor CHEBI:38497 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 CHEBI:38500 Any agent that affects the transport of molecular entities across a biological membrane. chebi_ontology membrane transport modulators CHEBI:38632 membrane transport modulator CHEBI:38632 A surfactant with an uncharged hydrophilic headgroup. chebi_ontology non-ionic surfactant nonionic surfactants CHEBI:38828 nonionic surfactant CHEBI:38828 Any alkylbenzene that is benzene substituted with one or more methyl groups. chebi_ontology methylbenzenes CHEBI:38975 methylbenzene CHEBI:38975 A monocyclic arene that is benzene substituted with one or more alkyl groups. alkylbenzene chebi_ontology Alkylbenzol alkylbenzenes CHEBI:38976 alkylbenzene CHEBI:38976 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 CHEBI:39011 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 CHEBI:39141 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 CHEBI:39142 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 CHEBI:39143 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 CHEBI:39144 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 CHEBI:43176 0 O 15.99940 15.99491 O=* CHEBI:29353 CHEBI:44607 PDBeChem:O OXO GROUP oxo chebi_ontology =O CHEBI:46629 oxo group CHEBI:46629 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 CHEBI:46787 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 CHEBI:46883 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:46923 chebi_ontology CHEBI:46926 dioxanes CHEBI:46926 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 CHEBI:47032 CHEBI:4705 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:48354 chebi_ontology CHEBI:48355 non-polar solvent CHEBI:48355 A polar solvent that is capable of acting as a hydron (proton) donor. protogenic solvent chebi_ontology CHEBI:48356 protic solvent CHEBI:48356 chebi_ontology CHEBI:48357 aprotic solvent CHEBI:48357 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 CHEBI:48358 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 CHEBI:48359 Self-ionizing solvent possessing both characteristics of Bronsted acids and bases. amphiprotic solvent chebi_ontology CHEBI:48360 amphiprotic solvent CHEBI:48360 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 CHEBI:48377 carboximidic acid carboximidic acids chebi_ontology carboximidic acids CHEBI:48378 carboximidic acid CHEBI:48378 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 CHEBI:48431 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 CHEBI:48578 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 CHEBI:48819 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 CHEBI:48873 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 CHEBI:49637 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 CHEBI:50047 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:50267 chebi_ontology CHEBI:50312 onium compound CHEBI:50312 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 CHEBI:50313 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 CHEBI:50566 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 CHEBI:50584 Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 chebi_ontology organic compounds organic entity organic molecular entities CHEBI:50860 organic molecular entity CHEBI:50860 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 CHEBI:50903 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 CHEBI:50907 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 CHEBI:50908 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 CHEBI:50910 A role played by the molecular entity or part thereof within a chemical context. chebi_ontology CHEBI:51086 chemical role CHEBI:51086 CHEBI:25556 CHEBI:7594 KEGG:C06061 chebi_ontology Nitrogenous compounds nitrogen compounds nitrogen molecular entities CHEBI:51143 nitrogen molecular entity CHEBI:51143 A role played by a compound that facilitates the rapid drying of gels without their cracking. chebi_ontology CHEBI:51268 drying control chemical additive CHEBI:51268 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:51422 chebi_ontology CHEBI:51446 organic divalent group CHEBI:51446 chebi_ontology CHEBI:51447 organic univalent group CHEBI:51447 A ketone of formula RC(=O)CH3 (R =/= H). chebi_ontology methyl ketones CHEBI:51867 methyl ketone CHEBI:51867 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 CHEBI:52090 A biological role played by the molecular entity or part thereof within a biochemical context. chebi_ontology CHEBI:52206 biochemical role CHEBI:52206 chebi_ontology CHEBI:52208 biophysical role CHEBI:52208 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 CHEBI:52209 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:52210 chebi_ontology CHEBI:52211 physiological role CHEBI:52211 Any molecule or ion capable of binding to a central metal atom to form coordination complexes. Wikipedia:Ligand chebi_ontology ligands CHEBI:52214 ligand CHEBI:52214 A chemical role played by the molecular entity or part thereof in a photochemical process. chebi_ontology photochemical roles CHEBI:52215 photochemical role CHEBI:52215 A role played by a molecular entity or part thereof in a photobiochemical process. chebi_ontology CHEBI:52216 photobiochemical role CHEBI:52216 Any substance introduced into a living organism with therapeutic or diagnostic purpose. CHEBI:33293 CHEBI:33294 chebi_ontology farmaco medicament pharmaceuticals CHEBI:52217 pharmaceutical CHEBI:52217 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 CHEBI:53431 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 CHEBI:5686 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 CHEBI:59739 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 CHEBI:59740 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 CHEBI:59752 A surfactant molecule possessing both hydrophilic and lipophilic properties. chebi_ontology amphiphiles CHEBI:59941 amphiphile CHEBI:59941 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 CHEBI:60242 Any organic molecular entity derived from a fatty acid. chebi_ontology FA derivative FA derivatives fatty acid derivatives CHEBI:61697 fatty acid derivative CHEBI:61697 Any donor that can transfer acyl groups between molecular entities. PMID:16100120 PMID:19052863 chebi_ontology CHEBI:62049 acyl donor CHEBI:62049 Any additive that enhances the efficiency of fuel. chebi_ontology fuel additives fuel enhancer CHEBI:62803 fuel additive CHEBI:62803 The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability. chebi_ontology emulgent emulgents emulsifiers CHEBI:63046 emulsifier CHEBI:63046 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 CHEBI:63047 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 CHEBI:63060 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 CHEBI:63064 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 CHEBI:63247 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 CHEBI:63248 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 CHEBI:63490 Any compound that can be used for the treatment of neurodegenerative disorders. chebi_ontology neuroprotectant neuroprotectants neuroprotective agents CHEBI:63726 neuroprotective agent CHEBI:63726 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 CHEBI:63908 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 CHEBI:64047 Any chemical substance produced during the conversion of a reactant to a product. Wikipedia:Reaction_intermediate chebi_ontology chemical intermediate CHEBI:64297 reaction intermediate CHEBI:64297 An organic molecular entity containing a single carbon atom (C1). chebi_ontology one-carbon compounds CHEBI:64708 one-carbon compound CHEBI:64708 Any organic molecular entity that is acidic and contains carbon in covalent linkage. chebi_ontology organic acids CHEBI:64709 organic acid CHEBI:64709 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 CHEBI:64909 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 CHEBI:65255 Any entity used to generate reactive oxygen species. chebi_ontology ROS generator ROS generators reactive oxygen species generators CHEBI:70982 reactive oxygen species generator CHEBI:70982 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 CHEBI:72695 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 CHEBI:73335 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 CHEBI:73693 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 CHEBI:74236 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 CHEBI:74783 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 CHEBI:75763 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 CHEBI:75767 Any animal metabolite produced during a metabolic reaction in mammals. CHEBI:77464 CHEBI:77744 chebi_ontology mammalian metabolites CHEBI:75768 mammalian metabolite CHEBI:75768 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 CHEBI:75771 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 CHEBI:75772 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 CHEBI:75787 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 CHEBI:76413 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 CHEBI:76648 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 CHEBI:76725 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 CHEBI:76736 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 CHEBI:76759 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 CHEBI:76764 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 CHEBI:76807 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 CHEBI:76870 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 CHEBI:76932 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 CHEBI:76946 Any prokaryotic metabolite produced during a metabolic reaction in bacteria. CHEBI:75760 CHEBI:76970 chebi_ontology CHEBI:76969 bacterial metabolite CHEBI:76969 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 CHEBI:76971 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 CHEBI:77521 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 CHEBI:77523 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 CHEBI:77746 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 CHEBI:77853 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 CHEBI:77941 An antioxidant that used as a food additives to help guard against food deterioration. chebi_ontology food antioxidants CHEBI:77962 food antioxidant CHEBI:77962 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 CHEBI:77963 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 CHEBI:78295 Any minor or unwanted substance introduced into the environment that can have undesired effects. chebi_ontology environmental contaminants CHEBI:78298 environmental contaminant CHEBI:78298 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 CHEBI:78299 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 CHEBI:78433 Any inorganic anion with a valency of two. chebi_ontology divalent inorganic anions CHEBI:79388 divalent inorganic anion CHEBI:79388 Any inorganic anion with a valency of one. chebi_ontology monovalent inorganic anions CHEBI:79389 monovalent inorganic anion CHEBI:79389 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 CHEBI:80291 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 CHEBI:82632 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 CHEBI:91015 An independent material continuant that is self-connected and retains its identity over time. CHMO:0000993 portion of material CHMO:0000993 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 CHMO:0000997 A method that results in the separation of two or more components according to some property. FIX:0000002 partition CHMO:0000999 separation method CHMO:0000999 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 CHMO:0001000 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 CHMO:0001001 Chromatography where the separation is caused by differing biological specificity of the analyte-ligand interactions. bioaffinity chromatography CHMO:0001006 affinity chromatography CHMO:0001006 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 CHMO:0001128 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 CHMO:0001129 A method used to synthesise a sample. CHMO:0001301 synthesis method CHMO:0001301 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 CHMO:0001310 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 CHMO:0001387 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 CHMO:0001458 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 CHMO:0001464 A heat treatment that alters the microstructure of a material causing changes in its properties such as strength and hardness CHMO:0001465 annealing CHMO:0001465 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 CHMO:0001477 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 CHMO:0001478 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 CHMO:0001479 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 CHMO:0001532 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 CHMO:0001533 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 CHMO:0001534 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 CHMO:0001535 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 CHMO:0001536 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 CHMO:0001537 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 CHMO:0001538 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 CHMO:0001539 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 CHMO:0001540 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 CHMO:0001541 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 CHMO:0001542 The process of removing a solvent from a substance. drying CHMO:0001549 sample drying CHMO:0001549 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 CHMO:0001550 The removal of solvent from a sample by the application of heated air. CHMO:0001551 direct drying CHMO:0001551 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 CHMO:0001552 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 CHMO:0001553 The removal of solvent from a sample by heating in an oven. CHMO:0001554 oven drying CHMO:0001554 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 CHMO:0001555 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 CHMO:0001556 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 CHMO:0001557 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 CHMO:0001574 The evaporation of solvent from a sample by placing it a centrifuge and spinning it rapidly. CHMO:0001575 centrifugal evaporation CHMO:0001575 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 CHMO:0001576 The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it. CHMO:0001577 extraction CHMO:0001577 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 CHMO:0001578 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 CHMO:0001583 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 CHMO:0001593 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 CHMO:0001594 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 CHMO:0001595 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 CHMO:0001596 An analytical process that sequentially chemically leaches metals from soils, sludges or sediments. sequential chemical extraction CHMO:0001597 sequentional extraction CHMO:0001597 The process of transferring a substance from any matrix to an appropriate liquid phase. CHMO:0001598 solvent extraction CHMO:0001598 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 CHMO:0001599 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 CHMO:0001600 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 CHMO:0001601 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 CHMO:0001604 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 CHMO:0001606 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 CHMO:0001607 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 CHMO:0001610 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 CHMO:0001612 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 CHMO:0001624 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 CHMO:0001625 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 CHMO:0001636 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 CHMO:0001637 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 CHMO:0001640 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 CHMO:0001641 A pressure-driven membrane-based separation process in which particles and dissolved macromolecules larger 200 Da are rejected. NF nanofiltration CHMO:0001642 nano-filtration CHMO:0001642 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 CHMO:0001643 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 CHMO:0001644 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 CHMO:0001645 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 CHMO:0001652 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 CHMO:0001653 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 CHMO:0001654 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 CHMO:0001655 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 CHMO:0001656 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 CHMO:0001657 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 CHMO:0001685 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 CHMO:0001686 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 CHMO:0001688 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 CHMO:0001689 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 CHMO:0001690 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 CHMO:0001696 The planned repetition of a precipitation to remove impurities from a precipitate or improve its stoichiometry. CHMO:0001697 reprecipitation CHMO:0001697 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 CHMO:0001904 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 CHMO:0001905 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 CHMO:0001945 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 CHMO:0001947 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 CHMO:0001987 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 CHMO:0001989 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 CHMO:0002011 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 CHMO:0002012 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 CHMO:0002014 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 CHMO:0002015 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 CHMO:0002020 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 CHMO:0002066 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 CHMO:0002106 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 CHMO:0002124 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 CHMO:0002157 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 CHMO:0002158 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 CHMO:0002159 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 CHMO:0002160 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 CHMO:0002198 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 CHMO:0002208 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 CHMO:0002217 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 CHMO:0002218 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 CHMO:0002219 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 CHMO:0002220 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 CHMO:0002221 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 CHMO:0002222 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 CHMO:0002223 Any synthesis method used to grow crystals. https://orcid.org/0000-0001-5985-7429 2009-07-28T04:05:29Z CHMO:0002224 crystal growth method CHMO:0002224 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 CHMO:0002225 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 CHMO:0002231 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 CHMO:0002465 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 CHMO:0002466 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 CHMO:0002523 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 CHMO:0002524 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 CHMO:0002634 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 CHMO:0002652 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 CHMO:0002653 A process wherein one material is extracted from another by interaction with a solvent. CHMO:0002742 elution CHMO:0002742 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 CHMO:0002770 A preparative step where the concentration of one component is increased. CHMO:0002771 concentrating CHMO:0002771 A preparative step involving the removal of dissolved gases from a sample. http://en.wikipedia.org/wiki/Degasification degasification CHMO:0002772 degassing CHMO:0002772 A mixing step where a soluble component is mixed with a liquid component. CHMO:0002773 dissolving CHMO:0002773 Mixing involving the agitation of a solution through circular motion. CHMO:0002774 stirring CHMO:0002774 Stirring achieved by rotating a magnetic stir bar in a solution. CHMO:0002775 magnetic stirring CHMO:0002775 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 CHMO:0002852 dispersive solid-phase extraction CHMO:0002863 dispersive solid phase extraction CHMO:0002863 Material processing in which a liquid or gas transitions into a solid. CHMO:0002916 sample solidification CHMO:0002916 Material processing in which a sample is cooled by immersion in a fluid. CHMO:0002917 sample quenching CHMO:0002917 fix.ontology FIX:0000277 reaction property FIX:0000277 fix.ontology Gibbs energy change FIX:0000279 Gibbs free energy change FIX:0000279 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:0000280 fix.ontology oxidation-reduction reaction property FIX:0000281 redox reaction property FIX:0000281 fix.ontology oxidation-reduction potential change FIX:0000285 redox potential change FIX:0000285 fix.ontology FIX:0000368 kinetic reaction property FIX:0000368 fix.ontology FIX:0000369 thermodynamic reaction property FIX:0000369 GO:0003674 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 GO:0003824 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 GO:0032991 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 GO:0034061 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 GO:0042575 DNA polymerase complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. DNA polymerase complex IAO:0000003 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 IAO:0000005 IAO:0000007 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 IAO:0000009 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 IAO:0000027 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 IAO:0000028 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 IAO:0000030 1 1 IAO:0000032 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 IAO:0000033 IAO:0000064 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 IAO:0000078 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 IAO:0000100 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 IAO:0000102 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 IAO:0000104 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 IAO:0000109 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 IAO:0000225 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 IAO:0000300 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 IAO:0000310 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 IAO:0000314 document part An abstract, introduction, method or results section. An information content entity that is part of a document. PERSON: Lawrence Hunter document part IAO:0000572 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 IAO:0000577 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 IAO:0000578 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 IAO:0000579 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 IAO:0000590 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 IAO:0020000 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 OBI:0000011 OBI:0000025 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 OBI:0000047 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 OBI:0000066 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 OBI:0000067 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 OBI:0000070 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 OBI:0000086 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 OBI:0000094 OBI:0000272 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 OBI:0000338 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 OBI:0000339 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 OBI:0000376 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 OBI:0000406 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 OBI:0000409 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 OBI:0000415 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 OBI:0000427 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 OBI:0000441 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 OBI:0000456 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 OBI:0000471 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 OBI:0000571 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 OBI:0000656 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 OBI:0000796 OBI:0000809 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 OBI:0000968 OBI:0001554 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 OBI:0001909 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 OBI:0001931 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification OBI:0001933 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 OBI:0002488 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 OBI:0200000 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 OBI:0200072 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 OBI:0200166 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 OBI:0200174 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 OBI:0302886 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 OBI:0302888 OBI:0500000 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 OBI:0600014 OBI:0600058 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 PATO:0000001 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 PATO:0000033 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 PATO:0000051 A 1-D extent quality which is equal to the distance between two points. quality PATO:0000122 length PATO:0000122 A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. quality PATO:0000125 mass PATO:0000125 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 PATO:0000965 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 PATO:0001536 A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. quality PATO:0001574 flow rate PATO:0001574 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 PATO:0002182 PROCO:0000001 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 PROCO:0000002 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 PROCO:0000003 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 PROCO:0000004 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 PROCO:0000005 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 PROCO:0000006 An information content entity that asserts the equality of two expressions. [Wikipedia] equation PROCO:0000008 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 PROCO:0000009 A process of systematically selecting possible synthetic routes to make a particular product or intermediate. Wes Schafer, Oliver He [PROCO] route scouting PROCO:0000010 A process boundary that represents a milestone decision on route selection. Wes, Oliver [PROCO] route selection milestone PROCO:0000011 A process profile that tracks some aspect of a reaction. [PROCO] reaction process profile PROCO:0000012 A temporal region that describes the length of time that a synthesis occurs. W Schafer [PROCO] synthesis reaction time PROCO:0000013 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 PROCO:0000014 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 PROCO:0000015 A directive information entity that specifies allowed ranges recorded for a process profile. [PROCO] process profile specification PROCO:0000016 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 PROCO:0000018 A directive information entity that species the acceptable range of values associated with a material quality W Schafer [PROCO] quality specification PROCO:0000019 A quality specification set against a critical quality attribute of a material [PROCO] CQA specification PROCO:0000025 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 PROCO:0000026 A chemical product that is used for commercial purpose. Oliver, Wes [PROCO] commercial chemical product PROCO:0000028 A process profile that is about temperature. Oliver, Wes [PROCO] temperature profile in synthesis process PROCO:0000029 A chemcial entity with the role starting material in a synthesis. [PROCO] starting material for synthesis PROCO:0000030 A chemical entity that is the product of a chemical reaction but not the last step in a synthesis. [PROCO] intermediate material for synthesis PROCO:0000031 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 PROCO:0000032 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 PROCO:0000033 A synthetic process governed by the cGMP regulations. Wes Schafer, Oliver He commercial synthetic process [PROCO] GMP synthetic process PROCO:0000034 A process measurement of the temperature in a process Wes, Oliver [PROCO] temperature measurement PROCO:0000036 A unit operation of adding a reagent or starting material to a chemical reaction Wes, Oliver inserting material [PROCO] charging material PROCO:0000041 A synthetic process governed by the GLP regulations. Wes Schafer, Oliver He [PROCO] GLP synthetic process PROCO:0000042 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 PROCO:0000043 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 PROCO:0000044 A process profile in synthesis process that is about material flow Oliver, Wes [PROCO] material flow profile in synthesis process PROCO:0000046 A planned process. Wes, Oliver [PROCO] process chemistry filing PROCO:0000047 A process profile that tracks the quality of some process participant. [PROCO] quality process profile PROCO:0000049 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 PROCO:0000050 A unit operation to remove portions of material from a synthesis stream by trapping it on a filter. Wes, Oliver [PROCO] filtering PROCO:0000051 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 PROCO:0000052 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 PROCO:0000053 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 PROCO:0000054 A substance or material consisting of very large molecules, or macromolecules, composed of many repeating subunits. https://en.wikipedia.org/wiki/Polymer polymer PROCO:0000055 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 PROCO:0000056 A sequenced plan of synthetic steps and defined intermediates to make a specific product from commercially available starting materials Wes, Oliver [PROCO] route specification PROCO:0000057 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 PROCO:0000058 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 PROCO:0000059 A process chemistry datum describing the ultimate final state and location of an impurity in a synthetic process. [PROCO] fate of impurity PROCO:0000060 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 PROCO:0000061 A fixed and well-defined number or other non-varying mathematical object. [Wikipedia] mathematical constant PROCO:0000062 A constant representing the concentration driving force Anna Dunn order kinetic order PROCO:0000064 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 PROCO:0000066 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 PROCO:0000067 The role of solids in a slurry Wes Schafer, Oliver He [PROCO] precipitate role PROCO:0000068 A suspension (AFM_0000442) that is a mix of solids in a liquid Wes Schafer, Oliver He [PROCO] slurry PROCO:0000069 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 PROCO:0000070 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 PROCO:0000071 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 PROCO:0000072 A debris role of the solution in a slurry resulting from a crystallization Wes Schafer, Oliver He [PROCO] mother liquor role PROCO:0000074 A solid with at least one crystalline phase [PROCO] crystalline solid PROCO:0000076 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 PROCO:0000077 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 PROCO:0000078 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 PROCO:0000079 A planned process with data output of commercial synthetic chemical route. Wes, Oliver [PROCO] chemical process development PROCO:0000080 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 PROCO:0000081 A planned process that is about optimizing a synthetic route. Wes, Oliver development optimization process optimization [PROCO] route development optimization PROCO:0000082 A planned process producing data to demonstrate that a commercial route meets regulatory requirements. Wes, Oliver [PROCO] route validation PROCO:0000083 A screening design to evaluate possible chemical reactions Wes, Oliver [PROCO] reaction screening design PROCO:0000084 A process that ends with a milestone where a selection will be made on route process. Wes, Oliver [PROCO] route selection PROCO:0000085 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 PROCO:0000086 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 PROCO:0000089 A screening design to discover polymorphs and solvates of a compound Wes, Oliver [PROCO] polymorph and solvate screening design PROCO:0000091 A process chemistry workflow plan that specifies how a multi-parallel screening study should be conducted. Wes, Oliver [PROCO] screening design PROCO:0000092 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 PROCO:0000093 A plan specification that specifies a process chemistry workflow consisting of a series of unit operations. Wes, Oliver [PROCO] process chemistry workflow plan PROCO:0000094 An investigation of published material to find prior art related to a synthetic route Wes, Oliver [PROCO] review of prior art PROCO:0000095 A document to secure permission or continuing permission to market a product from a regulatory body. [PROCO] product filing documentation PROCO:0000099 A planned process about a synthetic route Wes, Oliver [PROCO] route related process PROCO:0000100 A planned process of measuring a quality of a material associated with a process. Wes, Oliver [PROCO] process monitoring PROCO:0000101 A process measurement of the pressure in a process Wes, Oliver [PROCO] pressure measurement PROCO:0000102 A process monitoring to determine when a chemical reaction has ended. Wes, Oliver [PROCO] end reaction monitoring PROCO:0000103 A process boundary that represents a milestone of obtaining regulatory approval to sell a new product. Wes, Oliver [PROCO] product approval milestone PROCO:0000104 A process boundary that represents a milestone of obtaining regulatory approval to sell a new drug product. Wes, Oliver [PROCO] drug product approval milestone PROCO:0000105 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 PROCO:0000106 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. PROCO:0000107 The assessed reactivity of the mutagenic impurity in the processing conditions [PROCO] assessed reactivity purge factor PROCO:0000108 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 PROCO:0000109 A molecular quality that describes the unit cell of the crystal lattice W Schafer [PROCO] unit cell quality PROCO:0000110 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 PROCO:0000111 a geometric symmetry that keeps at least one point fixed Wes Schafer, Oliver He [PROCO] point symmetry PROCO:0000112 a point symmetry that contains a polar axis. Wes Schafer, Oliver He [PROCO] polar point symmetry PROCO:0000113 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 PROCO:0000114 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 PROCO:0000115 a non-centrosymmetric point symmetry that cannot be rotated to align with the original structure (chiral). Wes Schafer, Oliver He [PROCO] enantiomorphic point symmetry PROCO:0000116 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 PROCO:0000117 the length of the a-axis of a unit cell Wes Schafer, Oliver He [PROCO] unit cell a-axis length PROCO:0000118 the length of the b-axis of a unit cell Wes Schafer, Oliver He [PROCO] unit cell b-axis length PROCO:0000119 the length of the c-axis of a unit cell Wes Schafer, Oliver He [PROCO] unit cell c-axis length PROCO:0000120 The smallest, regularly repeating material portion of a crystalline lattice Wes Schafer, Oliver He [PROCO] unit cell PROCO:0000121 A unit cell that has three perpendicular axes of equal lengths. equivalent to ENM:9000035 isometric unit cell [PROCO] cubic unit cell PROCO:0000123 A unit cell that has three perpendicular axes, two of equal length [PROCO] tetragonal unit cell PROCO:0000124 A unit cell that has three perpendicular axes, all of different lengths [PROCO] orthorhombic unit cell PROCO:0000125 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 PROCO:0000126 A unit cell of three equal lateral axes intersecting at the same angle but not perpendicularly [PROCO] trigonal unit cell PROCO:0000127 A unit cell that has three axes of unequal length, two of which are perpendicular [PROCO] monoclinic unit cell PROCO:0000128 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 PROCO:0000129 A unit cell quality describing the angle between the b and c axes. [PROCO] unit cell alpha internal angle PROCO:0000130 A unit cell quality describing the angle between the a and c axes. [PROCO] unit cell beta internal angle PROCO:0000131 A unit cell quality describing the angle between the a and b axes. [PROCO] unit cell gamma internal angle PROCO:0000132 The volume of the unit cell [PROCO] unit cell volume PROCO:0000133 A unit cell quality indicating the number of formula units (molecules) in the unit cell [PROCO] unit cell Z value PROCO:0000134 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 PROCO:0000135 A unit cell quality indicating the density of the compound in the unit cell [PROCO] unit cell crystal density PROCO:0000136 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 PROCO:0000137 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 PROCO:0000138 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 PROCO:0000139 A crystalline phase is a single solid crystalline thermodynamic phase [PROCO] crystalline solid thermodynamic phase PROCO:0000141 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 PROCO:0000142 An object aggregate of two or more molecular entities that does not include covalent or ionic interactions [PROCO] molecular complex PROCO:0000143 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 PROCO:0000144 A solvate is a crystalline material that has solvent molecules incorporated into the crystal lattice in a stoichiometric amount. [Allotrope] [Allotrope] solvate PROCO:0000145 A hydrate is a solvate that has water as the solvent adduct. [PROCO] hydrate PROCO:0000146 A chemical substance composed of ions held together by electrostatic forces termed ionic bonding. [Wikipedia] ionic salt PROCO:0000147 A crystalline phase without solvent in the unit cell [PROCO] anhydrous phase PROCO:0000148 An anhydrous crystalline phase formed experimentally by removing the solvent from a solvate [PROCO] isomorphic desolvate PROCO:0000149 A heterogeneous ensemble of individual components whose crystal structures are like discontinuous solid solutions (phase separated). [PROCO] Chem. Commun., 2014, 50, 906 eutectic PROCO:0000150 A heterogeneous solid solution consisting of two or more polymorphs of the same chemical entity [PROCO] concomitant polymorphs PROCO:0000151 A heterogenous mixture in which one or more components is dispersed in a solid matrix [PROCO] solid dispersion PROCO:0000152 A group of geometric symmetries (isometries) that keep at least one point fixed. [wikipedia] point group symmetry PROCO:0000153 An open,one faced triclinic form with enantiomorphic and polar point symmetries [PROCO] pedial PROCO:0000154 2-faced triclinic form with centrosymmetric point symmetry [PROCO] pinacoidal PROCO:0000155 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 PROCO:0000156 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 PROCO:0000157 A cubic system crystal class with 24-faces and four fold rotoinversion axes and non-centrosymmetric point symmetry [PROCO] hextetrahedral PROCO:0000158 A cubic form with no mirror planes and enantiomorphic point symmetry [PROCO] gyroidal PROCO:0000159 An experiment performed on computer or via computer simulation [wikipedia] in-silico modeling PROCO:0000160 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 PROCO:0000161 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 PROCO:0000162 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 PROCO:0000166 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 PROCO:0000167 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 PROCO:0000168 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 PROCO:0000169 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 PROCO:0000170 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 PROCO:0000171 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 PROCO:0000172 A heating device (environmental control device) that utilizes an open flame for heating. [wikipedia] Bunsen burner PROCO:0000173 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 PROCO:0000174 A device to separate vaporized mixtures of liquid compounds with close volatility. [wikipedia] fractionating column PROCO:0000175 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 PROCO:0000176 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 PROCO:0000177 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 PROCO:0000178 A device used to condense vapors into liquid by cooling. [wikipedia] condensor PROCO:0000179 A condensor consisting of a simple tube surrounded by a jacket of cooling water [wikipedia] Liebig condenser PROCO:0000180 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 PROCO:0000181 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 PROCO:0000182 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 PROCO:0000183 A condensor consisting of a straight tube containing an internal spiral coil through which coolant flows. [Wikipedia] coil condenser PROCO:0000184 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 PROCO:0000185 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 PROCO:0000186 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 PROCO:0000187 A quality associated with a portion of material [PROCO] bulk substance quality PROCO:0000188 A device for controlling the environment of a particular space [PROCO] environmental control device PROCO:0000189 An environmental control device used to apply heat directly to containers. isomantel [wikipedia] heating mantle PROCO:0000190 A round-bottom flask is a flask with a spherical body and one or more necks with ground glass joints. [Wikipedia] round bottom flask PROCO:0000191 Flasks are narrow-necked glass containers, typically conical or spherical, used in a laboratory to hold reagents or samples. [Wikipedia] flask PROCO:0000192 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 PROCO:0000194 A syringe which has the function of pumping material into an experiment. [PROCO] [CHMO] term exists syringe pump PROCO:0000195 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 PROCO:0000196 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 PROCO:0000197 A device that evaporates [PROCO] evaporation device PROCO:0000198 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 PROCO:0000199 The structure of a chemical entity in terms of its molecular geometry and electronic structure. [PROCO] chemical structure PROCO:0000200 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 PROCO:0000201 The drug substance nomenclature section of the CTA [PROCO] CTA Section 3.2.S.1.1 Nomenclature PROCO:0000202 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 PROCO:0000203 The name assigned to a chemical substance by the Chemical Abstracts Service of the American Chemical Society [PROCO] chemical abstracts name PROCO:0000204 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 PROCO:0000205 The drug substance structure section of the CTA [PROCO] CTA Section 3.2.S.1.2 Structure PROCO:0000206 A two or three dimensional representation of a chemical structure. [PROCO] chemical drawing PROCO:0000208 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 PROCO:0000210 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 PROCO:0000211 A document certified by a vendor summarizing test results and specifications for a particular batch of its product. [PROCO] certificate of analysis PROCO:0000212 A data item that is about a material entity based on a visual inspection. [PROCO] appearance datum PROCO:0000213 The document part of the common technical document regarding manufacturers [PROCO] CTA Section 3.2.S.2.1 Manufacturers PROCO:0000214 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 PROCO:0000215 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 PROCO:0000216 A scalar measurement datum that quantifies the measured pH of a saturated solution of a material at a specified temperature. [PROCO] solution pH datum PROCO:0000217 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 PROCO:0000218 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 PROCO:0000219 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 PROCO:0000220 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 PROCO:0000221 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 PROCO:0000222 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 PROCO:0000223 An is-silico modeling based on DEREK that determines the risk of a chemical being a mutagenic impurity [PROCO] DEREK Mutagen Prediction PROCO:0000224 An is-silico modeling based on MCASE that determines the risk of a chemical being a mutagenic impurity [PROCO] MCASE Mutagen Prediction PROCO:0000225 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 PROCO:0000226 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 PROCO:0000227 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 PROCO:0000228 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 PROCO:0000229 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 PROCO:0000230 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 PROCO:0000231 A quality process profile that tracks the concentration changes of a species [PROCO] concentration profile PROCO:0000232 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 PROCO:0000233 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 PROCO:0000234 A kinetic determination method that measures reaction rate directly. (d[]/dt) [wikipedia] differential kinetic measurement PROCO:0000235 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 PROCO:0000236 A plot of the differential kinetic measurement as the y-axis vs. the integral measurement as the x-axis. [PROCO] graphical rate equation PROCO:0000237 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 PROCO:0000238 An impurity role of DNA reactive material that have significant carcinogenic risk [ICH] mutagenic impurity PROCO:0000239 A 2- faced open form monoclinic crystal with polar point symmetry. [PROCO] domatic PROCO:0000240 3, 4, 6, 8, or 12 faced monoclinic crystal with centrosymmetric point symmetry. [PROCO] prismatic PROCO:0000241 Four-faced closed orthorhombic form with enantiomorphic point symmetry [PROCO] rhombic-disphenoidal PROCO:0000242 3, 4, 6, 8, or 12 nonparallel faced orthorhombic system with polar point symmetry. [PROCO] rhombic-pyramidal PROCO:0000243 8-faced form orthorhombic crystal class with centrosymmetric point symmetry [PROCO] rhombic-dipyramidal PROCO:0000244 Isometric form with no 4 fold axes and centrosymmetric point symmetry [PROCO] diploidal PROCO:0000245 General cubic forms which only has 3-fold axes and 2-fold axes with no mirror plane with enantiomorphic point symmetry. [PROCO] tetartoidal PROCO:0000246 4-faced tetragonal form with polar point and enantiomorphic point symmetry. [PROCO] tetragonal-pyramidal PROCO:0000247 4-faced closed orthorhombic form with non-centrosymmetric point symmetry. [PROCO] tetragonal-disphenoidal PROCO:0000248 8-faced form with centrosymmetric point symmetry. [PROCO] tetragonal-dipyramidal PROCO:0000249 6-, 8-, 12-, or 24-trapezium faced closed tetragonal form with enantiomorphic point symmetry [PROCO] tetragonal-trapezohedral PROCO:0000250 8-faced tetragonal form with polar point and enantiomorphic point symmetry [PROCO] ditetragonal-pyramidal PROCO:0000251 8-faced (tetragonal) or 12-faced (hexagonal) closed tetragonal form with non-centrosymmetric point symmetry [PROCO] tetragonal-scalenohedral PROCO:0000252 16-faced form tetragonal crystal form with centrosymmetric point symmetry [PROCO] ditetragonal-dipyramidal PROCO:0000253 3-faced form where all faces are related by a 3-fold rotation axis with polar point and enantiomorphic point symmetry. [PROCO] trigonal-pyramidal PROCO:0000254 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 PROCO:0000255 6-, 8-, 12-, or 24-trapezohedral faced closed trigonal form with enantiomorphic point symmetry [PROCO] trigonal-trapezohedral PROCO:0000256 6-faced trigonal form where all faces are related by a 3-fold rotational axis with polar point symmetry. [PROCO] ditrigonal-pyramidal PROCO:0000257 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 PROCO:0000258 6-faced form where all faces are related by a 6 axis having polar point and enantiomorphic point symmetry. [PROCO] hexagonal-pyrimidal PROCO:0000259 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 PROCO:0000260 12-faced hexagonal form with faces related by a 6-fold axis with a perpendicular mirror with a centrosymmetric point symmetry [PROCO] hexagonal-dipyrimidal PROCO:0000261 6-faced closed hexagonal form with enantiomorphic point symmetry. [PROCO] hexagonal-trapezohedral PROCO:0000262 12-faced hexagonal crystal where all faces are related by a 6-fold axis. It has polar point symmetry [PROCO] dihexagonal-pyramidal PROCO:0000263 12-faced form tetragonal crystal class with non-centrosymmetric point symmetry [PROCO] ditrigonal-dipyramidal PROCO:0000264 24-faced form with faces related by a 6-fold axis with a perpendicular mirror plane and centrosymmetric point symmetry [PROCO] dihexagonal-dipyramidal PROCO:0000265 An ICH guideline about identifying, qualifying and specifying impurities in drug substance. [ICH] ICH Q3A Impurities in New Drug Substances PROCO:0000266 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 PROCO:0000267 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 PROCO:0000268 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 PROCO:0000269 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 PROCO:0000270 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 PROCO:0000271 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 PROCO:0000272 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 PROCO:0000273 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 PROCO:0000274 The maximum acceptable intake per day of residual solvent in pharmaceutical products [ICH] Permitted Daily Exposure PROCO:0000275 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 PROCO:0000276 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 PROCO:0000277 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 PROCO:0000278 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 PROCO:0000279 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 PROCO:0000280 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 PROCO:0000281 A centrally registered identifier assigned to a laboratory notebook experiment W Schafer [PROCO] laboratory notebook experiment identifier PROCO:0000282 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 PROCO:0000283 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 PROCO:0000284 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 PROCO:0000285 A screening design to determine to solubility of a compound [PROCO] solubility screening design PROCO:0000286 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 PROCO:0000287 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 PROCO:0000288 A portion of material with a debris role that is a material output of a process. Wes Schafer [PROCO] waste stream PROCO:0000289 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 PROCO:0000290 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 PROCO:0000291 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 PROCO:0000293 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 PROCO:0000294 A data item that is a recording of the output of a calculation. [PROCO] calculated datum PROCO:0000295 A data item about process chemistry [PROCO] process chemistry datum PROCO:0000296 A planned process of extracting information from chemical systems by data-driven means. [Wikipedia] chemometrics PROCO:0000297 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 PROCO:0000299 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 PROCO:0000301 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 PROCO:0000302 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 PROCO:0000303 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 PR:000000001 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 owl:Thing 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 PROCO release 20220414 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 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 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 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 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 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 has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification a relationship indicating that the process profile quantitates some aspect of the process (e.g. a quality of a material participant) [PROCO] profile 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 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 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 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. 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. 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 Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus Holger Stenzhorn James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Ron Rudnicki Selja Seppälä Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He 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. The BSD license on the BFO project site refers to code used to build BFO. 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. 26:05:2021 18:56 1.2 Author: ChEBI curation team ChEBI Release version 200 ChEBI subsumes and replaces the Chemical Ontology first For any queries contact chebi-help@ebi.ac.uk developed by Michael Ashburner & Pankaj Jaiswal. 1.2 25:05:2005 12:37 1.0 autogenerated-by: DAG-Edit version 1.419 rev 3 date: Mon Apr 04 14:05:41 BST 2005 saved-by: kirill version: $Revision: 1.2 $ 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 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 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