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
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
BFO CLIF specification label
editor preferred label
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
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.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
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.
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.
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.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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.
curator note
An administrative note of use for a curator but of no use for a user
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
The 'tracker item' can associate a tracker with a specific ontology term.
imported from
For external terms/classes, the ontology from which the term was imported
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:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
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
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
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
ISA tools project (http://isa-tools.org)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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
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.
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.
An entity primarily responsible for making the content of the resource.
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.
A date associated with an event in the life cycle of the resource.
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.
An account of the content of the resource.
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).
The physical or digital manifestation of the resource.
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.
A reference to a resource from which the present resource is derived.
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.
The topic of the content of the resource.
Subject and Keywords
The property that identifies the version IRI of an ontology.
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]
Inverse of quality influences. [Allotrope]
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.
Facet of relates two information content entities where one information content entity is an aspect of the other one. [Allotrope]
Relation between an information content entity and some part of it called a facet that is covers some general aspect of information context. [Allotrope]
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'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
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
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
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
has measurement unit label
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
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
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
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.
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
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
Alan Ruttenberg
is_specified_input_of
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.
is_specified_output_of
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
obsolete_has_role
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.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
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.
is thermodynically preferred at all temperatures
monotropically related to
a relationship indicating that the process profile quantitates some aspect of the process (e.g. a quality of a material participant)
profile of
a relationship between polymorphs that has a cross-over temperature at which one form becomes more thermodynamically favored than the other.
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.
is solvate of
an object property that represents a relation between polymorphs, i.e. different physical forms of the same chemical moiety.
is polymorph of
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
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
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
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
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
has measurement 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.
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.
A numerical value that defines certain characteristics of systems or system functions. It may be part of a calculation, but its value is not determined by the form of the equation itself, and may be arbitrarily assigned.
quantitative systems description parameter
Numerical parameter that quantifies the velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants.
Time interval over which a quantified entity is reduced to half its original value.
Time taken by a quantity decreasing according to a mono-exponential decay to be divided by two. Sometimes called t1/2.
<n0:math xmlns:n0="http://www.w3.org/1998/Math/MathML"> <n2:lambda xmlns:n2="http://biomodels.net/SBO/"> <n2:bvar><n2:ci definitionURL="http://biomodels.net/SBO/#SBO:0000356">l</n2:ci></n2:bvar> <n2:apply> <n2:divide /> <n2:apply> <n2:ln /> <n2:cn type="integer">2</n2:cn> </n2:apply> <n2:ci>l</n2:ci> </n2:apply> </n2:lambda> </n0:math>
Fundamental quantity of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions or the transformation of entities. The SI base unit for time is the SI second. The second is the duration of 9,192,631,770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
<n0:math xmlns:n0="http://www.w3.org/1998/Math/MathML"> <n2:lambda xmlns:n2="http://biomodels.net/SBO/"> <n2:bvar><n2:ci definitionURL="http://biomodels.net/SBO/#SBO:0000356">l</n2:ci></n2:bvar> <n2:apply> <n2:divide /> <n2:cn type="integer">1</n2:cn> <n2:ci>l</n2:ci> </n2:apply> </n2:lambda> </n0:math>
A proportionality constant between the molar flux due to molecular diffusion and the gradient in the concentration of the species (or the driving force for diffusion). Diffusivity is encountered in Fick's law and numerous other equations of physical chemistry.
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.
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]
A device that has the function to contain material. [Allotrope]
A device used for heating something. [Allotrope]
A transferring device is a device that is designed to transfer material. [Allotrope]
To alter or govern the size or amplitude of a flow (material, energy, signal). [NIST]
A function that gives thermal energy to a recipient. [Allotrope]
A DC electrical battery stores the energy in a flashlight. [NIST]
To cause a flow (material, energy, signal) to move from one location to another location. [NIST]
To adjust the flow of energy, signal, or material in a predetermined and fixed manner. [NIST]
To enlarge a flow in a predetermined and fixed manner. [NIST]
To accumulate or provide a material or energy flow. [NIST]
A vacuum bag contains debris vacuumed from a house. [NIST]
To shift, or convey, a flow (material, energy, signal) from one place to another. [NIST]
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]
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]
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]
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]
The state of keeping a flow within spatial limits. [Allotrope]
Transferring is channeling a flow (material, energy, signal) from one place to another. [NIST]
A processing that affects the spatial location or orientation of some participants. [Allotrope]
Controlling is changing or regulating a flow in its magnitude. [NIST, Allotrope]
A state is a homomeric, cumulative process in which all the temporal parts are described by the same expression used for the whole. [Allotrope]
Changing is a processing by which an entity gains or looses parts, qualities, roles, dispositions, functions etc in a predetermined and fixed manner but maintains its identity. [Allotrope]
Storing is containing or collecting flows to accumulate. [NIST]
Providing is the state of accumulating or supplying a material or energy flow. [NIST]
An activity is a process that is cumulative but not homomeric. [Allotrope, DOLCE]
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]
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]
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]
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]
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]
Green Book, 2nd ed.: IUPAC Quantities, Units and Symbols in Physical Chemistry. Second Edition, Blackwell Scientific Publications, Oxford, 1993.
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]
A chemical substance quality is a quality that inheres in some portion of chemical substance. [Allotrope]
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]
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]
A classification is a proposition that categorizes things into classes or collections of things differentiated by some criteria. [Allotrope]
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]
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
2019-10-02 Changed pref label. [Allotrope]
Material that is undergoing a cleaning process. [Allotrope]
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]
Hubka, Eder, Ernst, Design Science, Springer, 1996
The role of a participant that is being changed in the process (passive participant) from an input state to an output state. [Allotrope]
Additive is a role of material that is added to a mixture in order to achieve a supportive purpose. [Allotrope]
PAC, 1996, 68, 155 (Glossary of terms used in chemical kinetics, including reaction dynamics.)
A catalyst role is a reagent role of a substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction; the process is called catalysis. The catalyst is both a reactant and product of the reaction. [IUPAC]
Debris is a role of material to be waste. [Allotrope]
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
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]
Intermediate role is a role of material that is formed from reactants (or preceding intermediates) and reacts further to give the directly observed products of a chemical reaction. [Wikipedia]
Reactant role is a role of a chemical entity that is present at the start of a reaction. [Allotrope]
Cleaning agent role is a role of material used for cleaning something. [Allotrope]
Ingredient is a role of material that is used in a material combining process to produce a new material. [Allotrope]
The role of a participant of a cleaning process. [Allotrope]
A synthesis role is a role of a material that is participating in a synthesis (material conversion) process. [Allotrope]
A formulation role is a role of a material that is participating in a formulation process. [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]
A material role of an expected but not desired product of a synthesis. [Allotrope]
the leaving group in a de-protection step.
A role of a material that is intended and desired to be produced in a synthesis. [Allotrope]
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]
2019-08-27 Fixed OWL definition, bug #694. [Allotrope]
A filtration role is a role of a material in a filtration process. [Allotrope]
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]
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.
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]
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]
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]
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]
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]
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]
An extraneous contaminant role is an impurity role arising from any source extraneous to the manufacturing process. [ICH-Q3A]
An impurity for which a structural characterization has been achieved. [ICH-Q3A]
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]
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]
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]
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]
A degradation product role for which a structural characterization has been achieved. [ICH-Q3A]
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]
A sample role (preparation) is a role of a material that is prepared for a bearing the sample role in an experiment. [Allotrope]
A drying additive role is the role of a material in a drying process that supports the drying process. [Allotrope]
A drying role role is a role realized in some drying process. [Allotrope]
A drying medium role is a drying role of a material that takes or transports the solvent from the material being dried. [Allotrope]
Material dried role is the drying role of the material being dried. [Allotrope]
A reaction mixture role is a role of a chemical mixture undergoing some chemical reaction. [Allotrope]
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
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]
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
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
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
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]
process
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
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
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
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 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 > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
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]
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
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
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
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]
generically dependent continuant
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
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
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]
material entity
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.
Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium.
A molecular entity that can undergo reduction by the gain of hydrogen atom(s).
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.
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.
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
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.
A molecular entity that can transfer an electron to another molecular entity.
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
A methyl ketone that consists of propane bearing an oxo group at C2.
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.
A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
The simplest monocarboxylic acid amide, obtained by formal condensation of formic acid with ammonia. The parent of the class of formaldehydes.
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.
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.
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.
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.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
A molecular entity that can undergo oxidation by the loss of hydrogen atom(s).
A pseudohalide anion that is the conjugate base of hydrogen cyanide.
The simplest member of the class toluenes consisting of a benzene core which bears a single methyl substituent.
A substance to which an electron may be transferred.
A member of the class of formamides that is formamide in which the amino hydrogens are replaced by methyl groups.
The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
'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.
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.
A one-carbon compound consisting of a methine group triple bonded to a nitrogen atom
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.
alpha-1-microglobulin-Ig alpha complex chromophores
A monoatomic or polyatomic species having one or more elementary charges of the electron.
A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides.
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).
Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives.
Any ketone that is butane substituted by an oxo group at unspecified position.
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
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.
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).
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
Salts and C-organyl derivatives of hydrogen cyanide, HC#N.
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.
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.
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.
Amides with the general formula R(1)R(2)NCHO (R(1) and R(2) can be H).
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A role played by the molecular entity or part thereof within a biological context.
A defined linked collection of atoms or a single atom within a molecular entity.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
A compound consisting of carbon and hydrogen only.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
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).
A molecular entity that contains no carbon.
A compound which can carry specific ions through membranes of cells or organelles.
A molecular entity having a net electric charge.
Any ionophore capable of transportation of iron ions across membranes.
A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
mitochondrial electron transport chain inhibitors
mitochondrial electron-transport chain inhibitor
mitochondrial respiratory chain inhibitors
mitochondrial respiratory-chain inhibitor
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
An oxoacid containing a single carboxy group.
Any organic ion with a net negative charge.
An organooxygen compound with formula ROR, where R is not hydrogen.
An alcohol derived from an aliphatic compound.
An oxide is a chemical compound of oxygen with other chemical elements.
A ketone that is propane carrying at least one oxo substituent.
Any of low-molecular-mass iron(III)-chelating compounds produced by microorganisms for the purpose of the transport and sequestration of iron.
A cyclic ether that is butane in which one hydrogen from each methyl group is substituted by an oxygen.
Any oxacycle having an oxolane (tetrahydrofuran) skeleton.
Any member of the class of benzenes that is a substituted benzene in which the substituents include one (and only one) methyl group.
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
A surfactant (or a mixture containing one or more surfactants) having cleaning properties in dilute solutions.
A dialkyl ketone that is a four-carbon ketone carrying a single keto- group at position C-2.
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.
The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid.
An onium cation obtained by protonation of ammonia.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
A carboxamide derived from a monocarboxylic acid.
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.
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
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.
Intended use of the molecular entity or part thereof by humans.
A particle not known to have substructure.
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.
Any substituent group which does not contain carbon.
Any substituent group or skeleton containing carbon.
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Heavy nuclear particle: proton or neutron.
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.
An anion consisting of more than one atom.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A substance (or active part thereof) that kills or slows the growth of bacteria.
A nutrient is a food component that an organism uses to survive and grow.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
An energy-rich substance that can be transformed with release of usable energy.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block element belonging to the group 16 family of the periodic table.
Any p-block molecular entity containing a chalcogen.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
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).
Any main group element atom belonging to the p-block of the periodic table.
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.
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.
Any molecule that consists of a series of atoms joined together to form a ring.
A cyclic compound having as ring members atoms of the same element only.
A homocyclic compound in which all of the ring members are carbon atoms.
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.
Any monocyclic or polycyclic aromatic hydrocarbon.
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.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
Hydrides are chemical compounds of hydrogen with other chemical elements.
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.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A carboxylic acid containing one or more amino groups.
An organic compound having at least one hydroxy group attached to a carbon atom.
Any organic molecule that consists of atoms connected in the form of a ring.
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
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
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.
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
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.
A part of a molecular entity (atom or group of atoms) in which electronic excitation associated with a given emission band is approximately localized.
A substance that diminishes the rate of a chemical reaction.
A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction.
Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
heterocyclic organic fundamental parents
organic heterocyclic fundamental parents
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.
A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated.
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.
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A nucleus or any of its constituents in any of their energy states.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
saturated heteromonocyclic parent hydride
saturated heteromonocyclic parent hydrides
saturated organic heteromonocyclic parents
saturated organic heteromonocyclic parent
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
A monoatomic or polyatomic species having one or more elementary charges of the proton.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
Any ether in which the oxygen atom forms part of a ring.
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).
A molecular entity consisting of two or more chemical elements.
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.
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
Any organic heterocyclic compound containing at least one ring oxygen atom.
Any of low-molecular-mass iron(III)-chelating compounds produced by plants for the purpose of the transport and sequestration of iron.
A ligand with two or more separate binding sites that can bind to a single metallic central atom, forming a chelate.
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.
A nitrile that is hydrogen cyanide in which the hydrogen has been replaced by a methyl group.
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).
EC 1.9.3.1 (cytochrome c oxidase) inhibitors
complex IV (mitochondrial electron transport) inhibitor
complex IV (mitochondrial electron transport) inhibitors
cytochrome c oxidase (EC 1.9.3.1) inhibitor
cytochrome c oxidase (EC 1.9.3.1) inhibitors
ferrocytochrome-c:oxygen oxidoreductase inhibitor
ferrocytochrome-c:oxygen oxidoreductase inhibitors
mitochondrial cytochrome-c oxidase inhibitors
EC 1.9.3.1 (cytochrome c oxidase) inhibitor
Any agent that affects the transport of molecular entities across a biological membrane.
A surfactant with an uncharged hydrophilic headgroup.
Any alkylbenzene that is benzene substituted with one or more methyl groups.
A monocyclic arene that is benzene substituted with one or more alkyl groups.
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.
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
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.
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.
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
Any member of the class of dioxanes that is a cyclohexane in which two carbon atoms are replaced by oxygen atoms.
A dioxane with oxygen atoms at positions 1 and 4.
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
A polar solvent that is capable of acting as a hydron (proton) donor.
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.
Solvent that is capable of acting as a hydron (proton) acceptor.
Self-ionizing solvent possessing both characteristics of Bronsted acids and bases.
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).
A carboximidic acid that is formic acid in which the carbonyl oxygen is replaced by an imino group.
A role played by a substance that can react readily with, and thereby eliminate, radicals.
Any drug that binds to but does not activate cholinergic receptors, thereby blocking the actions of acetylcholine or cholinergic agonists.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
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.
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
An agent, with unique chemical structure and biochemical requirements, which generates nitric oxide.
An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position.
Any molecular entity that contains carbon.
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.
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).
A role played by a chemical compound exihibiting itself through the ability to induce damage to the liver in animals.
A poison that interferes with the functions of the nervous system.
A role played by the molecular entity or part thereof within a chemical context.
A role played by a compound that facilitates the rapid drying of gels without their cracking.
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
A ketone of formula RC(=O)CH3 (R =/= H).
An organic anion that is the conjugate base of methanol.
A biological role played by the molecular entity or part thereof within a biochemical context.
A role played by the molecular entity or part thereof which causes the development of a pathological process.
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
Any molecule or ion capable of binding to a central metal atom to form coordination complexes.
A chemical role played by the molecular entity or part thereof in a photochemical process.
A role played by a molecular entity or part thereof in a photobiochemical process.
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
The role played by a molecular entity, such as an atom or free radical, which is involved in chain-propagating reactions.
A cyclic compound having as ring members atoms of at least two different elements.
A reagent that forms a bond to its reaction partner (the nucleophile) by accepting both bonding electrons from that reaction partner.
A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
A surfactant molecule with hydrophilic groups at both ends of a hydrophobic hydrocarbon chain
A surfactant molecule possessing both hydrophilic and lipophilic properties.
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
Any organic molecular entity derived from a fatty acid.
Any donor that can transfer acyl groups between molecular entities.
Any additive that enhances the efficiency of fuel.
The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability.
A food additive used to form or maintain a uniform emulsion of two (or more) phases in a food.
A catalyst that facilitates the migration of a reactant from one phase into another phase where reaction occurs.
Chemical role played by a material when used to promote crystallisation.
The element or compound in a reduction-oxidation (redox) reaction that donates an electron to another species.
A substance that removes electrons from another reactant in a redox reaction.
A substance capable of undergoing rapid and highly exothermic decomposition.
Any compound that can be used for the treatment of neurodegenerative disorders.
Any compound that leaves a pliable, cohesive, and continuous covering over a surface when applied to it.
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
Any chemical substance produced during the conversion of a reactant to a product.
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
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.
Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes.
Any entity used to generate reactive oxygen species.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A photochemical role realized in the absorption of ultraviolet light, for example to protect skin cells from damage.
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.
Any compound used as a monomer for a polymerisation process. The term is generally used in relation to industrial polymerisation processes.
A compound that causes the contraction of body tissues, typically used to reduce bleeding from minor abrasions.
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
Any animal metabolite produced during a metabolic reaction in mammals.
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
Saccharomyces cerevisiae secondary metabolites
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.
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.
An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*).
An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on a heme group of donors (EC 1.9.*.*).
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
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitor
oxidoreductase acting on a heme group of donors (EC 1.9.*) inhibitors
EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
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.* (hydrolases acting on non-peptide C-N bonds) inhibitor
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) 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
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
An EC 1.9.* (oxidoreductase acting on donor heme group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.9.3.*).
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) 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
EC 1.9.3.* (oxidoreductase acting on donor heme group, oxygen as acceptor) inhibitor
An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
Any product obtained as a result of thermally induced non-enzymatic degradation.
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).
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
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.
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).
An antioxidant that used as a food additives to help guard against food deterioration.
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.
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.
Any minor or unwanted substance introduced into the environment that can have undesired effects.
Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage.
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.
Any inorganic anion with a valency of two.
Any inorganic anion with a valency of one.
Any nitrile derived from an aliphatic compound.
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.
A chemical compound that, when added to a liquid or gas, decreases the corrosion rate of a material, typically a metal or an alloy.
An independent material continuant that is self-connected and retains its identity over time.
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.
A method that results in the separation of two or more components according to some property.
A separation method where the components are distributed between two phases, one of which is stationary, while the other moves in a definite direction.
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).
Chromatography where the separation is caused by differing biological specificity of the analyte-ligand interactions.
Chromatography in which separation is based mainly on differences between the adsorption affinities of the sample components for the surface of an active solid.
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.
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.
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.
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.
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.
A heat treatment that alters the microstructure of a material causing changes in its properties such as strength and hardness
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.
The simultaneous crystallisation of two different substances or two different structural elements of the same substance.
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.
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.
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.
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.
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.
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.
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.
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°).
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.
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.
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.
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.
The process of removing a solvent from a substance.
The removal of solvent from a sample by the application of radio frequency (3 Hz to 300 GHz) or microwave (1–1000 mm) radiation.
The removal of solvent from a sample by the application of heated air.
The removal of solvent from a sample by applying it as a thin layer to the surface of a heated drum.
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.
The removal of solvent from a sample by heating in an oven.
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.
The removal of solvent from a sample without passing through the liquid–gas boundary, by immersion in a supercritical fluid and de-pressurisation.
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.
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.
The evaporation of solvent from a sample by placing it a centrifuge and spinning it rapidly.
The removal of solvent from a sample by applying heat and lowering the pressure above the sample whilst rotating it at 10–300 rpm.
The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it.
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.
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).
The transfer of a solute from one phase (the 'donor' or 'feed' phase) to another (the 'acceptor' or 'strip' phase) across a nonporous membrane.
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.
membrane extraction with sorbent interface
membrane extraction with trapping on a sorbent interface
membrane extraction with a sorbent interface
The transfer of a solute from one phase (the 'donor' or 'feed' phase) to another (the 'acceptor' or 'strip' phase) across a nonporous sillicon rubber membrane.
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.
supported liquid membrane (SLM) extraction
An analytical process that sequentially chemically leaches metals from soils, sludges or sediments.
The process of transferring a substance from any matrix to an appropriate liquid phase.
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.
The process of transferring a dissolved substance from one liquid phase to another (immiscible or partially miscible) liquid phase in contact with it.
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.
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).
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.
The process of transferring the soluble components of a solid to the liquid phase using a solvent.
The process of transferring a substance from any matrix to a liquid phase using a supercritical fluid.
The process of transferring a substance from any matrix to another where the amount of reagent used is lower than that dictated by stoichiometry.
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.
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.
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.
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.
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.
A pressure-driven membrane-based separation process in which particles and dissolved macromolecules larger than 0.1 micrometre are rejected.
A pressure-driven membrane-based separation process in which particles and dissolved macromolecules larger 200 Da are rejected.
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.)
The separation of a solid phase from a liquid phase by passing the sample through a porous medium under pressure.
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.
The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting.
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.
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.
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.
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).
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).
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.
The growth of larger crystals from those of smaller size, which have a higher solubility than the larger ones.
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.
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+).
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.
The subsequent precipitation of a chemically different species upon the surface of an initial precipitate usually, but not necessarily, including a common ion.
The planned repetition of a precipitation to remove impurities from a precipitate or improve its stoichiometry.
Any material processing method that uses a supercritical fluid.
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.
supercritical anti-solvent fractionation
supercritical anti-solvent precipitation
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.
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.
precipitation using compressed anti-solvent
precipitation using compressed antisolvent
precipitation with compressed anti-solvent
precipitation with compressed antisolvent
The removal of solvent from a sample without passing through the liquid–gas boundary, by immersion in supercritical CO2 and de-pressurisation.
The process of transferring a substance from any matrix into ethanol.
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.
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.
A method where a sample is purified by removing impurities on the basis of their density in a centrifuge.
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.
The intensive mixing of μtually insoluble phases (sometimes with addition of surfactants) to obtain a soluble suspension or emulsion.
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.
The process of making a polymer blend by mechanically mixing different polymers together in the melt.
The removal of solvent from a sample by the application of an inert gas or air.
The removal of ions from a solution using an ion-exchange method.
A method of producing large single crystals (of semiconductors or metals) by inserting a small seed crystal into a crucible filled with similar molten material, then slowly pulling the seed up from the melt while rotating it.
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).
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.
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.
The removal of solvent from a sample, usually by the application of heat.
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.
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).
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.
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.
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.
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').
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.
Any synthesis method used to grow crystals.
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.
Any technique used to physically separate an analyte from byproducts, reagents or contaminating substances.
The sedimentation of a solid material (a 'precipitate') from a liquid solution caused by the addition of an additional different solvent.
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'.
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.
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.
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.
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.
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.
surface assisted chemical vapor transport
surface assisted chemical vapour transport
surface-assisted chemical vapor transport
surface-assisted chemical-vapor-transport
surface-assisted chemical-vapour-transport
surface-assisted chemical vapour transport
A process wherein one material is extracted from another by interaction with a solvent.
A sample preparation step involving the increase in temperature of a sample.
ought to be in OBI. Will put here pro tem.
A preparative step where the concentration of one component is increased.
A preparative step involving the removal of dissolved gases from a sample.
A mixing step where a soluble component is mixed with a liquid component.
Mixing involving the agitation of a solution through circular motion.
Stirring achieved by rotating a magnetic stir bar in a solution.
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.
Material processing in which a liquid or gas transitions into a solid.
Material processing in which a sample is cooled by immersion in a fluid.
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.
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.
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.
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.
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.
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
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: Melanie Courtot
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: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
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.
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: Chris Stoeckert
PERSON: Jonathan Rees
data
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
based on Oxford English Dictionary
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.
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.
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
directive information entity
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
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)
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
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
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
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
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?
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.
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
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
document part
An abstract, introduction, method or results section.
An information content entity that is part of a document.
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
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.
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.
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
centrally registered identifier registry
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
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.
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.
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.
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)
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
OBI
reference substance role
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
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).
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
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")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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.
measuring
scientific observation
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
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
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]
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
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
drawing a conclusion based on data
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'.
planning
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
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.
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
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.
PCR
polymerase chain reaction
enzyme
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
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)
assay 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.
artifact creation objective
material transformation objective
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.
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.
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]
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.
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.
DNA that has been produced in an enzymatic amplification process
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.
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
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.
A value specification that consists of two parts: a numeral and a unit label
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.
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
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
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
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.
WEB: http://en.wikipedia.org/wiki/Curve_fitting
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
PERSON: James Malone
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.
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.
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.
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.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
A material processing in which components of an input material become segregated in space.
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
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
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.
A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid.
A physical quality inhering in a bearer by virtue of the bearer's motion characteristic.
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
Synthesis is a planned material process that combines, changes or converts material to produce a new material. [Allotrope]
synthetic chemical process
An experimental design to limit the number of experiments covering the space by assuming the Interactions between the factors are negligible
Plackett–Burman design
All information that has been made available to the public in any form before a given date that might be relevant to a patent's claims of originality.
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.
design space
A data item that is a member of a minimal set of independent variables that can be used to model the dependent reponses in a set of related experiments.
factor
An information content entity that asserts the equality of two expressions.
equation
An experimental design consisting of two or more factors, each with discrete possible values or "levels", and whose experimental units take on all or a subset of the possible combinations of these levels across all such factors.
factorial design
A process of systematically selecting possible synthetic routes to make a particular product or intermediate.
route scouting
A process boundary that represents a milestone decision on route selection.
route selection milestone
A process profile that tracks some aspect of a reaction.
A temporal region that describes the length of time that a synthesis occurs.
synthesis reaction time
A physical, chemical, biological, or microbiological property or characteristic that should be within an appropriate limit, range, or distribution to ensure the desired product quality.
critical quality attribute
An investigation carried out to support or refute a hypothesis. Experiments provide insight into cause-and-effect by demonstrating what outcome occurs when a particular factor is manipulated.
experiment
A directive information entity that specifies allowed ranges recorded for a process profile.
process profile specification
A process profile specification that is associated with a critical process parameter (CPP). Critical process parameters (CPPs) in pharmaceutical manufacturing are key variables affecting the production process.
CPP 'has facet' some specification (note: like has part, but it is for info).
critical process parameter specification
A directive information entity that species the acceptable range of values associated with a material quality
quality specification
A quality specification set against a critical quality attribute of a material
CQA specification
A chemical entity that is the end point product generated from a synthetic chemical process.
chemical product
A chemical product that is used for commercial purpose.
commercial chemical product
A process profile that is about temperature.
temperature profile in synthesis process
A chemcial entity with the role starting material in a synthesis.
starting material for synthesis
A chemical entity that is the product of a chemical reaction but not the last step in a synthesis.
intermediate material for synthesis
Chemical substance that is inside a confined amount of liquid, gas, or solid, and differs from the chemical composition of the material or compound. Impurities are either naturally occurring or added during synthesis of a chemical or commercial product. During production, impurities may be purposely, accidentally, inevitably, or incidentally added into the substance.
chemical impurity
A raw material, intermediate, or an AP chemical entity that is used in the production of an API and that is incorporated as a significant structural fragment into the structure of the API.
GMP starting material
A synthetic process governed by the cGMP regulations.
GMP synthetic process
A process measurement of the temperature in a process
temperature measurement
A unit operation of adding a reagent or starting material to a chemical reaction
charging material
A synthetic process governed by the GLP regulations.
GLP synthetic process
A plan specification that specifies the action and objective of a synthetic process, as defined in CFR - Code of Federal Regulations Title 21.
GMP specification of synthetic process
A process profile that represents the number of revolution of stirs given a specific time period
stirring profile in synthesis process
A process profile in synthesis process that is about material flow
material flow profile in synthesis process
process chemistry filing
A process profile that tracks the quality of some process participant.
quality process profile
Reaction rate is the rate of the changing concentration of a product during a reaction process.
reaction rate profile
A unit operation to remove portions of material from a synthesis stream by trapping it on a filter.
filtering
Unit operations involve a physical change or chemical transformation such as separation, crystallization, evaporation, filtration, polymerization, isomerization, and other reactions. For example, in milk processing, homogenization, pasteurization, and packaging are each unit operations which are connected to create the overall process. A process may require many unit operations to obtain the desired product from the starting materials, or feedstocks.
unit operation in chemical processing
A process that has as a material output a crystalline solid or a mixture that has as an ingredient a crystalline solid.
The formation of a crystalline solid from a solution, melt vapour, or a different solid phase, generally by lowering the temperature or by evaporation of a solvent. [CHMO]
Wes and Oliver: This term is currently defined as a planned process term although crystallization may occur in nature. Here we use to term to represent those synthetic chemical process processes that are man made and planned.
crystallization
The process mass intensity (PMI) calculates the ratio of the total mass of materials to the mass of the isolated product
process mass intensity
A substance or material consisting of very large molecules, or macromolecules, composed of many repeating subunits.
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.
impurity fate and purge determination
A sequenced plan of synthetic steps and defined intermediates to make a specific product from commercially available starting materials
route specification
A sequenced set of unit operations for a single synthetic reaction or simultaneous reactions that are executed in a single equipment train.
synthetic step specification
A process boundary that represents a milestone of filing the documentation required to obtain regulatory approval to sell a new product.
product filing milestone
A process chemistry datum describing the ultimate final state and location of an impurity in a synthetic process.
fate of impurity
A fixed and well-defined number or other non-varying mathematical object.
A constant representing the concentration driving force
The role of a solvent in a precipitation or crystallization in which the solute of a solution is sparingly soluble to induce its solidification.
antisolvent role
The role of a crystalline solid material input in a crystallization to promote nucleation or crystal growth.
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
precipitate role
A suspension (AFM_0000442) that is a mix of solids in a liquid
slurry
A physical quality indicating the structural order of a solid in which its atoms or molecules are arranged in a regular, periodic manner.[wikipedia]
crystalline state
A process chemistry datum that quantifies the ratio of the amount of an impurity in the waste stream of a process to that retained in the product stream.
purge factor
A process chemistry datum quantifying the ratio of the mass of desired compound recovered as crystalline material from a crystallization to mass of compound input into the crystallization.
crystallization yield
A debris role of the solution in a slurry resulting from a crystallization
mother liquor role
A solid with at least one crystalline phase
crystalline solid
A process chemistry datum quantifying the environmental impact of a synthetic reaction, and is computed by the ratio of the total mass of waste generated in the synthetic scheme to the mass of product isolated.
process environmental factor
The process excellence index (PEI) is a measure of process reproducibility where the robustness of the procedure is evaluated in terms of yield and cycle time of various operations.
process excellence index
The quality service level (QSL) is a measure of the reproducibility of the quality of the isolated intermediate or final API, and its calculation involves the ratio of satisfactory quality batches to the total number of batches. A reasonable QSL target is 98 to 100 percent.
quality service level
A planned process with data output of commercial synthetic chemical route.
chemical process development
A process boundary that represents a milestone of filing the documentation required to obtain regulatory approval to sell a new drug product.
drug product filing milestone
A planned process that is about optimizing a synthetic route.
route development optimization
A planned process producing data to demonstrate that a commercial route meets regulatory requirements.
route validation
A screening design to evaluate possible chemical reactions
reaction screening design
A process that ends with a milestone where a selection will be made on route process.
route selection
Chemical kinetics includes investigations of how experimental conditions influence the speed of a chemical reaction and yield information about the reaction's mechanism and transition states, as well as the construction of mathematical models that also can describe the characteristics of a chemical reaction.
mechanistic and kinetic determination
A planned process of demonstrating that a process produces product of adequate quality and yield through the definition of the design space or risk assessments.
process validation
A screening design to discover polymorphs and solvates of a compound
polymorph and solvate screening design
A process chemistry workflow plan that specifies how a multi-parallel screening study should be conducted.
screening design
A planned process of manufacturing one or more batches of a product in unbroken succession. It includes equipment turnover and cleaning can include dry-runs before committing the starting materials.
batch campaign
A plan specification that specifies a process chemistry workflow consisting of a series of unit operations.
process chemistry workflow plan
An investigation of published material to find prior art related to a synthetic route
review of prior art
A document to secure permission or continuing permission to market a product from a regulatory body.
product filing documentation
A planned process about a synthetic route
route related process
A planned process of measuring a quality of a material associated with a process.
process monitoring
A process measurement of the pressure in a process
pressure measurement
A process monitoring to determine when a chemical reaction has ended.
end reaction monitoring
A process boundary that represents a milestone of obtaining regulatory approval to sell a new product.
product approval milestone
A process boundary that represents a milestone of obtaining regulatory approval to sell a new drug product.
drug product approval milestone
A kinetic determination method to determine the partial order of a reactant by measuring the concentration of that reactant with all other reactants in large excess
A temporal region of initial kinetics of a chemical reaction after which the reaction accelerates.
In some catalytic reactions, a pre-catalyst needs to undergo a transformation to form the active catalyst, before the catalyst can take effect. Time is required for this transformation, hence the induction period. Similarly, for an autocatalytic reaction, where one of the reaction products catalyzes the reaction itself, the rate of reaction is low initially until sufficient products have formed to catalyze the reaction. Reactions generally accelerate when heat is applied. Where a reaction is exothermic, the rate of the reaction may initially be low. As the reaction proceeds, heat is generated, and the rate of reaction increases. This type of reaction often exhibits an induction period as well. The reactions to form Grignard reagents are notorious for having induction periods. This is usually due to two reasons: Firstly, the thin film of oxide on the magnesium reagent must be removed before the bulk magnesium can react. Secondly, Grignard reactions, while exothermic, are typically conducted at low temperature for better selectivity. For these two reasons, Grignard reactions often can have a long induction period, followed by a thermal runaway, even causing the reaction solvent to boil-off.
The assessed reactivity of the mutagenic impurity in the processing conditions
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.
A molecular quality that describes the unit cell of the crystal lattice
unit cell quality
a symmetry quality of a unit cell in three-dimensional space.
similar to http://purl.enanomapper.org/onto/ENM_9000037
Wes Schafer, Oliver He
space group
a geometric symmetry that keeps at least one point fixed
point symmetry
a point symmetry that contains a polar axis.
polar point symmetry
a point symmetry in which the original structure can be obtained by reflecting all lattice points through a single point.
centrosymmetric point symmetry
a point symmetry of a structure that is not identical to any inversion of that structure created by reflecting all of its points through a single point.
non-centrosymmetric point symmetry
a non-centrosymmetric point symmetry that cannot be rotated to align with the original structure (chiral).
enantiomorphic point symmetry
a non-centrosymmetric point symmetry that can be rotated to align with the original structure (achiral).
non-centrosymmetric achiral symmetry
the length of the a-axis of a unit cell
unit cell a-axis length
the length of the b-axis of a unit cell
unit cell b-axis length
the length of the c-axis of a unit cell
unit cell c-axis length
The smallest, regularly repeating material portion of a crystalline lattice
unit cell
A unit cell that has three perpendicular axes of equal lengths. equivalent to ENM:9000035
cubic unit cell
A unit cell that has three perpendicular axes, two of equal length
tetragonal unit cell
A unit cell that has three perpendicular axes, all of different lengths
orthorhombic unit cell
A unit cell of three equal lateral axes intersecting at angles of 60 degrees and a vertical axis of variable length at right angles
hexagonal unit cell
A unit cell of three equal lateral axes intersecting at the same angle but not perpendicularly
trigonal unit cell
A unit cell that has three axes of unequal length, two of which are perpendicular
monoclinic unit cell
A unit cell in which all axes are of different length and no angle is perpendicular nor equal to any other angles.
triclinic unit cell
A unit cell quality describing the angle between the b and c axes.
unit cell alpha internal angle
A unit cell quality describing the angle between the a and c axes.
unit cell beta internal angle
A unit cell quality describing the angle between the a and b axes.
unit cell gamma internal angle
unit cell volume
A unit cell quality indicating the number of formula units (molecules) in the unit cell
unit cell Z value
A unit cell quality indicating the number of asymmetric units in the unit cell. It is equal to the Z value divided by the lowest Wycoff position multiplicity
unit cell Z' value
A unit cell quality indicating the density of the compound in the unit cell
unit cell crystal density
A directive information entity issued by the International Conference on Harmonization of Technical Requirements for the Registration of Pharmaceuticals for Human Use with the objective of achieving greater harmonisation worldwide to ensure that safe, effective and high quality medicines are developed, and registered and maintained across the world in the most resource efficient manner whilst meeting high standards. [ICH]
ICH Guideline
A description of one of the characteristic external shapes (crystal class / point group) of an individual crystal family / system. Factors that impact growth rates on the various crystal faces produce different shapes but possess the same set of symmetry elements as parent crystal class.
habit
A portion of material within a a region of space in a system throughout which all physical properties of the material are essentially uniform.
thermodynamic phase
A crystalline phase is a single solid crystalline thermodynamic phase
crystalline solid thermodynamic phase
A solid in solid solution is a solution where the continuous phase is a solid and the dispersed phase is a solid. [Allotrope]
solid solution
An object aggregate of two or more molecular entities that does not include covalent or ionic interactions
molecular complex
A co-crystal is a solid solution and a molecular complex with two or more non-solvent molecules incorporated into the unit cell in a stoichiometric amount.
co-crystal
A solvate is a crystalline material that has solvent molecules incorporated into the crystal lattice in a stoichiometric amount. [Allotrope]
solvate
A hydrate is a solvate that has water as the solvent adduct.
hydrate
A chemical substance composed of ions held together by electrostatic forces termed ionic bonding.
ionic salt
A crystalline phase without solvent in the unit cell
anhydrous phase
An anhydrous crystalline phase formed experimentally by removing the solvent from a solvate
isomorphic desolvate
A heterogeneous ensemble of individual components whose crystal structures are like discontinuous solid solutions (phase separated).
eutectic
A heterogeneous solid solution consisting of two or more polymorphs of the same chemical entity
concomitant polymorphs
A heterogenous mixture in which one or more components is dispersed in a solid matrix
solid dispersion
A group of geometric symmetries (isometries) that keep at least one point fixed.
point group symmetry
An open,one faced triclinic form with enantiomorphic and polar point symmetries
pedial
2-faced triclinic form with centrosymmetric point symmetry
pinacoidal
A monoclinic crystal class with two nonparallel faces symmetrical to a 2- or 4-fold axis of symmetry that has enantiomorphic and polar point symmetry.
sphenoidal
A cubic system crystal class with 48 equal triangular faces and three identical crystallographic axes with four fold rotational axes and centrosymmetric point symmetry
hexoctahedral
A cubic system crystal class with 24-faces and four fold rotoinversion axes and non-centrosymmetric point symmetry
hextetrahedral
A cubic form with no mirror planes and enantiomorphic point symmetry
gyroidal
An experiment performed on computer or via computer simulation
in-silico modeling
An in-silico modeling to predict the unit cell of the crystal lattice based on the powder x-ray diffractogram
Powder Indexing
An in-silico modeling to calculate calculation of the crystal structures by simulated annealing, evolutionary algorithms, distributed multipole analysis, random sampling, basin-hopping, data mining, density functional theory and molecular mechanics.
crystal structure predictions
An ICH Guidance for developing and understanding the manufacturing process of the drug substance.
ICH Q11 Guidance for Development and Manufacture of Drug Substances
An assessed purge factor based on the relative boiling point of the impurity to the reaction solvent and therefore its propensity to be purged in the headspace of steps to which the impurity is subjected..
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.
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.
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.
common technical document
A chemical substance quality of a crystalline phase that manifests itself as a set of allowed and unallowed peaks corresponding to the diffraction of incident x-ray radiation as a function of the substance's unit cell and its space group.
X-Ray diffractivity
A beaker is a simple container for stirring, mixing and heating liquids commonly used in many laboratories. Beakers are generally cylindrical in shape, with a flat bottom. Most also have a small spout (or "beak") to aid pouring.
beaker
A heating device (environmental control device) that utilizes an open flame for heating.
Bunsen burner
A crucible is a ceramic or metal container in which metals or other substances may be melted or subjected to very high temperatures. [Wikipedia]
crucible
A device to separate vaporized mixtures of liquid compounds with close volatility.
fractionating column
A fractionating column made of a wide glass tube with multiple internal glass "fingers" that point downwards so that the vapor that enters from the lower opening condenses on the fingers and drips down from them.
Vigreux column
A fractionating column divided into sections (usually 3 to 6) by horizontal glass partitions or constrictions each of which seats a hollow glass bead with an inverted "teardrop" shape acting as check valves, closing and opening with vapor flow, and enhancing vapor-condensate mixing.
Snyder column
A fractionating column consisting of four concentric glass tubes and a central glass rod, with a thinner glass rod coiled around it to increase the surface area.
Widmer column
A device used to condense vapors into liquid by cooling.
condensor
A condensor consisting of a simple tube surrounded by a jacket of cooling water
Liebig condenser
A condensor consisting of a jacketed long glass tube with a series of bulbs on the tube to increase the surface area upon which the vapor constituents may condense.
Allihn condenser
A condensor with a coolant-jacketed spiral coil running the length of the condenser serving as the vapor–condensate path, providing more surface area for cooling.
Graham condensor
A condensor with three concentric glass tubes where coolant circulates in both the outer jacket and the central tube to increase the cooling surface,
Davies condenser
A condensor consisting of a straight tube containing an internal spiral coil through which coolant flows.
coil condenser
A condensor with an internal double spiral through which coolant flows such that the coolant inlet and outlet are both at the top
Dimroth condenser
A condensor consisting of a vertical rod that is flow-cooled from the inside that is to be immersed in the vapor to provide a condensing surface. This condensor is also used for sublimation.
cold finger
A condensor consisting of a large water-cooled finger tightly fitted inside a wide cylindrical housing. The finger has a helical ridge along its length, so as to leave a narrow helical path for the vapor.
Frederichs condensor
A quality associated with a portion of material
bulk substance quality
A device for controlling the environment of a particular space
environmental control device
An environmental control device used to apply heat directly to containers.
heating mantle
A round-bottom flask is a flask with a spherical body and one or more necks with ground glass joints.
round bottom flask
Flasks are narrow-necked glass containers, typically conical or spherical, used in a laboratory to hold reagents or samples.
flask
A flask for preparing liquids with volumes of high precision. It is a flask with an approximately pear-shaped body and a long neck with a circumferential fill line.
volumetric flask
A syringe which has the function of pumping material into an experiment.
syringe pump
An Erlenmeyer flask or conical flask is a type of laboratory flask which features a flat bottom, a conical body, and a cylindrical neck.
Erlenmeyer flask
A document that is a primary record of research used to document their hypotheses, experiments and initial analysis or interpretation of these experiments serving as an organizational tool, a memory aid, and can also have a role in protecting any intellectual property that comes from the research.
laboratory notebook
evaporation device
A centrally registered identifier given to a pharmaceutical drug or an active ingredient coordinated by the World Health Organization (WHO) that is unique generic and non-proprietary.
international nonproprietary name
The structure of a chemical entity in terms of its molecular geometry and electronic structure.
chemical structure
A synthesis role used to remove suspended solids from liquids by inducing flocculation (the solids begin to aggregate forming flakes, which either precipitate to the bottom or float to the surface of the liquid, and then they can be removed or collected). Flocculants, or flocculating agents (also known as flocking agents), are chemicals that promote flocculation by causing colloids and other suspended particles in liquids to aggregate, forming a floc.
flocculant
The drug substance nomenclature section of the CTA
CTA Section 3.2.S.1.1 Nomenclature
A unique name, assigned to a chemical substance and preferred among the possible names generated by IUPAC nomenclature. The "preferred IUPAC nomenclature" provides a set of rules for choosing between multiple possibilities in situations where it is important to decide on a unique name. It is intended for use in legal and regulatory situations.
preferred IUPAC name
The name assigned to a chemical substance by the Chemical Abstracts Service of the American Chemical Society
chemical abstracts name
A centrally registered identifier assigned by the Chemical Abstracts Service (CAS) to every chemical substance described in the open scientific literature.
chemical abstracts number
The drug substance structure section of the CTA
CTA Section 3.2.S.1.2 Structure
A two or three dimensional representation of a chemical structure.
chemical drawing
A molecular entity quality which identifies each constituent element by its chemical symbol and indicates the number of atoms of each element found in each discrete molecular entity of that compound.
molecular formula
The drug substance general properties section of the CTA that includes appearance, thermal behaviour, solubility, chirality /specific rotation, crystallinity / polymorphism, hygroscopicity, solution pH and acid/base diassociation constants.
CTA Section 3.2.S.1.3 General Properties
A document certified by a vendor summarizing test results and specifications for a particular batch of its product.
certificate of analysis
A data item that is about a material entity based on a visual inspection.
appearance datum
The document part of the common technical document regarding manufacturers
CTA Section 3.2.S.2.1 Manufacturers
A 2-D representation of a step-by-step progression through a synthesis or part of a synthesis showing reagents, intermediates and reaction conditions.
synthesis flow chart
The description of the drug substance manufacturing process represents the applicant’s commitment for the manufacture of the drug substance. Reference ICH guidances Q5A, Q5B, and Q6B.
CTA Section 3.2.S.2.2 Description of Manufacturing Process and Process Controls
A scalar measurement datum that quantifies the measured pH of a saturated solution of a material at a specified temperature.
solution pH datum
A scalar measurement datum that quantifies the measured change in orientation of monochromatic plane-polarized light, per unit distance–concentration product, as the light passes through a sample of a compound in solution.
specific rotation datum
Materials used in the manufacture of the drug substance (e.g., raw materials, starting materials, solvents, reagents, catalysts) should be listed, identifying where each material is used in the process. Information on the quality and control of these materials should be provided. Reference ICH guidances Q6A and Q6B.
CTA Section 3.2.S.2.3 Control of Materials
The document part of the common technical document that specifies tests and acceptance criteria (with justification including experimental data) performed at critical steps identified in 3.2.S.2.2 of the manufacturing process to ensure that the process is controlled. Information on the quality and control of intermediates isolated during the process is also provided. Reference ICH guidances Q6A and Q6B.
CTA Section 3.2.S.2.4 Controls of Critical Steps and Intermediates
The document part of the common technical document that provides confirmation of structure based on, for example, synthetic route and spectral analyses should be provided. Information such as the potential for isomerism, the identification of stereochemistry, or the potential for forming polymorphs. Reference ICH guidance Q6A.
CTA Section 3.2.S.3.1 Elucidation of Structure and other Characteristics
The document part of the common technical document that provides Information on impurities. Reference ICH guidances Q3A, Q3C, Q5C, Q6A, and Q6B.
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 M7 Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals To Limit Potential Carcinogenic Risk
An is-silico modeling based on DEREK that determines the risk of a chemical being a mutagenic impurity
An is-silico modeling based on MCASE that determines the risk of a chemical being a mutagenic impurity
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.
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.
A process chemistry workflow plan that utilizes online and at-line measurements to understand chemical processes by defining and monitoring ...
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
The exponent terms within the rate equation. For elementary (single step) reactions, the reactant order is equal to the stoichiometric coefficient of the reactant.
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.
A quality process profile that tracks the concentration changes of a species
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]
A kinetic determination method that measures the concentration of reaction species which is proportional to the integral of the reaction rate.
A kinetic determination method that measures reaction rate directly. (d[]/dt)
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.
A plot of the differential kinetic measurement as the y-axis vs. the integral measurement as the x-axis.
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.
An impurity role of DNA reactive material that have significant carcinogenic risk
A 2- faced open form monoclinic crystal with polar point symmetry.
3, 4, 6, 8, or 12 faced monoclinic crystal with centrosymmetric point symmetry.
Four-faced closed orthorhombic form with enantiomorphic point symmetry
3, 4, 6, 8, or 12 nonparallel faced orthorhombic system with polar point symmetry.
8-faced form orthorhombic crystal class with centrosymmetric point symmetry
Isometric form with no 4 fold axes and centrosymmetric point symmetry
General cubic forms which only has 3-fold axes and 2-fold axes with no mirror plane with enantiomorphic point symmetry.
4-faced tetragonal form with polar point and enantiomorphic point symmetry.
4-faced closed orthorhombic form with non-centrosymmetric point symmetry.
8-faced form with centrosymmetric point symmetry.
6-, 8-, 12-, or 24-trapezium faced closed tetragonal form with enantiomorphic point symmetry
8-faced tetragonal form with polar point and enantiomorphic point symmetry
8-faced (tetragonal) or 12-faced (hexagonal) closed tetragonal form with non-centrosymmetric point symmetry
16-faced form tetragonal crystal form with centrosymmetric point symmetry
3-faced form where all faces are related by a 3-fold rotation axis with polar point and enantiomorphic point symmetry.
6 faced closed rhombohedral form of six identical faces in which none of the intersection edges is perpendicular and having centrosymmetric point symmetry
6-, 8-, 12-, or 24-trapezohedral faced closed trigonal form with enantiomorphic point symmetry
6-faced trigonal form where all faces are related by a 3-fold rotational axis with polar point symmetry.
8-faced (tetragonal) or 12-faced (hexagonal) closed form in which the faces are grouped in symmetrical pairs with centrosymmetric point symmetry
6-faced form where all faces are related by a 6 axis having polar point and enantiomorphic point symmetry.
6-faced hexagonal form with faces related by a 3-fold axis with a perpendicular mirror plane having non-centrosymmetric point symmetry
12-faced hexagonal form with faces related by a 6-fold axis with a perpendicular mirror with a centrosymmetric point symmetry
6-faced closed hexagonal form with enantiomorphic point symmetry.
12-faced hexagonal crystal where all faces are related by a 6-fold axis. It has polar point symmetry
12-faced form tetragonal crystal class with non-centrosymmetric point symmetry
24-faced form with faces related by a 6-fold axis with a perpendicular mirror plane and centrosymmetric point symmetry
An ICH guideline about identifying, qualifying and specifying impurities in drug substance.
ICH Q3A Impurities in New Drug Substances
An ICH guideline for the use residual solvents (organic volatile impurities) in the manufacture of drug substances and dosage forms, and sets pharmaceutical limits for in drug products.
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 Q3D Guidance for Elemental Impurities
An ICH guidance on the setting and justification of acceptance criteria and the selection of test procedures for new drug substances of synthetic chemical origin, and new drug products produced from them, which have not been registered previously in the ICH regions.
ICH Q6A Specifications: Test Procedures and Acceptance Criteria for Chemical Substances
An ICH Guideline for the manufacture of APIs for use in human drug (medicinal) products.
Q7 Good Manufacturing Practice Guide for Active Pharmaceutical Ingredients
Residual solvents in pharmaceuticals are defined here as organic volatile chemicals that are used or produced in the manufacture of drug substances or excipients, or in the preparation of drug products. The solvents are not completely removed by practical manufacturing techniques.
Solvents to be avoided and with strict low limits as they are human carcinogens, strongly suspected human carcinogens, and environmental hazards.
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
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.
The maximum acceptable intake per day of residual solvent in pharmaceutical products
An experimental design involving the testing of factors, or causes, one at a time instead of multiple factors simultaneously.
one-factor-at-a-time experimental design
The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions.
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.
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.
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
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.
A centrally registered identifier assigned to a laboratory notebook experiment
laboratory notebook experiment identifier
A document that contemporaneously records when, how, by whom each step to produce a specific batch is executed as well as the specific equipment and the specific materials including exact weights and lot numbers.
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. .
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.
A screening design to determine to solubility of a compound
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.
A process chemistry datum quantifying the sum of the costs of all raw materials, intermediates, reagents, solvents and catalysts procured from external vendor.
A portion of material with a debris role that is a material output of a process.
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.
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.
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).
A planned process that converts input data into output data based on some equation or set of equations
A data item that is a recording of the output of a calculation.
A planned process of extracting information from chemical systems by data-driven means.
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.
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.
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.
An equation for the temperature dependence of reaction rates used in determining rate of chemical reactions and for calculation of energy of activation.
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.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
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
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.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
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."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
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.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
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 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.
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
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.
## 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
Adam Goldstein
Albert Goldfain
Barry Smith
Carlo Torniai
Chris Mungall
Chris Stoeckert
Christian A. Boelling
Darren Natale
David Osumi-Sutherland
Gwen Frishkoff
Holger Stenzhorn
James A. Overton
Jennifer Fostel
Jie Zheng
Jonathan Rees
Larisa Soldatova
Lawrence Hunter
Mathias Brochhausen
Matt Brush
Michel Dumontier
Paolo Ciccarese
Pat Hayes
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.
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
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Allyson Lister
Bill Bug
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Jay Greenbaum
Jeffrey Grethe
Jessica Turner
Joe White
John Westbrook
Kevin Clancy
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philip Lord
Pierre Grenon
Richard Bruskiewich
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Trish Whetzel
Yongqun He
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.
An ontology for the annotation of biomedical and functional genomics experiments.
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.
A relation between an information content entity and a value specification that specifies its value.
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.
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.
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: 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: 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.
For any queries contact chebi-help@ebi.ac.uk
developed by Michael Ashburner & Pankaj Jaiswal.
ChEBI subsumes and replaces the Chemical Ontology first
autogenerated-by: DAG-Edit version 1.419 rev 3
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