prefer.obo

format-version: 1.2
data-version: releases/2026-03-10
idspace: dc http://purl.org/dc/elements/1.1/ 
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# 
idspace: swrl http://www.w3.org/2003/11/swrl# 
idspace: swrlb http://www.w3.org/2003/11/swrlb# 
idspace: terms http://purl.org/dc/terms/ 
idspace: uom https://w3id.org/uom/ 
ontology: prefer
property_value: dc:description "An ontology for PREcision FERmentation." xsd:string
property_value: dc:title "PREFER Ontology" xsd:string
property_value: IAO:0000700 BFO:0000019
property_value: IAO:0000700 BFO:0000023
property_value: IAO:0000700 BFO:0000040
property_value: IAO:0000700 IAO:0000003
property_value: IAO:0000700 PREFER:0000008
property_value: IAO:0000700 PREFER:0000015
property_value: IAO:0000700 PREFER:9000000
property_value: IAO:0000700 PREFER:9000001
property_value: IAO:0000700 PREFER:9000002
property_value: IAO:0000700 PREFER:9000003
property_value: owl:versionInfo "2026-03-10" xsd:string
property_value: terms:contributor https://orcid.org/0000-0001-7258-9596
property_value: terms:contributor https://orcid.org/0000-0002-9163-7730
property_value: terms:contributor https://orcid.org/0009-0009-0018-4253
property_value: terms:license http://creativecommons.org/licenses/by/4.0/

[Term]
id: APOLLO_SV:00000008
name: software development
def: "A planned process that has specified output a software product and that involves the creation of source code." []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process

[Term]
id: APOLLO_SV:00000796
name: dataset creating
def: "A planned process that has a data set as its specified output." []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
intersection_of: OBI:0000011 ! obsolete planned process
intersection_of: OBI:0000299 IAO:0000100 ! has specified output data set
relationship: OBI:0000299 IAO:0000100 ! has specified output data set

[Term]
id: BAO_0000362
name: mammalian
def: "This includes animal models typically used in drug discovery for toxicity or pharmacology studies, such as mouse, rat (mammals)." []
is_a: BAO_0000510 ! vertebrate

[Term]
id: BAO_0000509
name: eukaryote
def: "This includes fungi, vertebrates and invertebrates. Eukaryotic cells have a well-defined nucleus and membrane enveloped organelles namely, mitochondria, endoplasmic reticulum, golgi apparatus, and lysosomes." []
is_a: BAO_0000658 ! cellular organisms

[Term]
id: BAO_0000510
name: vertebrate
def: "This includes animals having a vertebral column, and model organisms from this group include the zebrafish, mouse, rat, etc" []
is_a: BAO_0000659 ! metazoa

[Term]
id: BAO_0000551
name: organism
def: "The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote." []
is_a: BAO_0003114 ! assay biology component

[Term]
id: BAO_0000658
name: cellular organisms
def: "This includes all organisms which are made up of cells, e.g. bacteria, plants and animals." []
is_a: BAO_0000551 ! organism

[Term]
id: BAO_0000659
name: metazoa
def: "Metazoa comprises of animals, which are multicellular eukaryotic organisms. This includes those having a vertebral column (e.g. fish, frog, snake, bird, human) and those that do not (e.g. worm, fly, star fish, etc)." []
is_a: BAO_0000509 ! eukaryote

[Term]
id: BAO_0003114
name: assay biology component

[Term]
id: BFO:0000001
name: entity

[Term]
id: BFO:0000002
name: continuant
def: "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." []
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant

[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
is_a: BFO:0000001 ! entity
relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent

[Term]
id: BFO:0000004
name: independent continuant
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant

[Term]
id: BFO:0000015
name: process
is_a: BFO:0000003 ! occurrent

[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role

[Term]
id: BFO:0000017
name: realizable entity
def: "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." []
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity

[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality

[Term]
id: BFO:0000020
name: specifically dependent continuant
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant

[Term]
id: BFO:0000023
name: role
def: "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." []
is_a: BFO:0000017 ! realizable entity

[Term]
id: BFO:0000031
name: generically dependent continuant
is_a: BFO:0000002 ! continuant
relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant

[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition

[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant

[Term]
id: CHEBI:24431
name: chemical entity
namespace: chebi_ontology
def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." []
is_a: BFO:0000040 ! material entity

[Term]
id: CL:0000000
name: cell
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
xref: CALOHA:TS-2035
xref: FMA:68646
xref: GO:0005623
xref: KUPO:0000002
xref: MESH:D002477
xref: VHOG:0001533
xref: WBbt:0004017
xref: XAO:0003012
is_a: UBERON:0000061 ! anatomical structure
relationship: RO:0002162 NCBITaxon:131567 ! in taxon

[Term]
id: COB:0000035
disjoint_from: GO:0008150 ! biological_process

[Term]
id: GO:0003674
name: molecular_function
namespace: molecular_function
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
synonym: "molecular function" EXACT []
is_a: BFO:0000015 ! process
disjoint_from: GO:0008150 ! biological_process

[Term]
id: GO:0006091
name: generation of precursor metabolites and energy
namespace: biological_process
synonym: "energy pathways" BROAD []
synonym: "metabolic energy generation" RELATED []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006113
name: fermentation
namespace: biological_process
comment: PMID:38821505 mentions exceptions regarding organic compounds and electron transport chain. Fermentation sub-processes exclude glycolysis to prevent redundancy with the glycolytic pathway.
xref: MetaCyc:Fermentation
xref: Wikipedia:Fermentation_(biochemistry)
is_a: GO:0015980 ! energy derivation by oxidation of organic compounds

[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
is_a: BFO:0000015 ! process
relationship: BFO:0000051 GO:0003674 ! has part molecular_function

[Term]
id: GO:0008152
name: metabolic process
namespace: biological_process
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
synonym: "metabolism" EXACT []
xref: Wikipedia:Metabolism
is_a: GO:0009987 ! cellular process

[Term]
id: GO:0009987
name: cellular process
namespace: biological_process
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
synonym: "cell growth and/or maintenance" NARROW []
synonym: "cell physiology" EXACT []
synonym: "cellular physiological process" EXACT []
synonym: "single-organism cellular process" RELATED []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0015980
name: energy derivation by oxidation of organic compounds
namespace: biological_process
synonym: "chemoorganotrophy" EXACT []
is_a: GO:0006091 ! generation of precursor metabolites and energy

[Term]
id: IAO:0000003
name: measurement unit label
def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." []
is_a: IAO:0000009 ! datum label

[Term]
id: IAO:0000005
name: objective specification
def: "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." []
is_a: IAO:0000033 ! directive information entity

[Term]
id: IAO:0000007
name: action specification
def: "A directive information entity that describes an action the bearer will take." []
is_a: IAO:0000033 ! directive information entity

[Term]
id: IAO:0000009
name: datum label
def: "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" []
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000010
name: software
def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." []
is_a: IAO:0000104 ! plan specification

[Term]
id: IAO:0000015
name: information carrier
def: "A quality of an information bearer that imparts the information content" []
is_a: BFO:0000019 ! quality
intersection_of: BFO:0000019 ! quality
intersection_of: RO:0000059 IAO:0000030 ! concretizes information content entity
relationship: RO:0000059 IAO:0000030 ! concretizes information content entity

[Term]
id: IAO:0000027
name: data item
def: "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." []
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000030
name: information content entity
def: "A generically dependent continuant that is about some thing." []
is_a: BFO:0000031 ! generically dependent continuant
relationship: IAO:0000136 BFO:0000001 ! is about entity

[Term]
id: IAO:0000033
name: directive information entity
def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." []
is_a: IAO:0000030 ! information content entity
relationship: IAO:0000136 BFO:0000017 ! is about realizable entity

[Term]
id: IAO:0000037
name: dot plot
def: "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions." []
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000038
name: graph
def: "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way." []
is_a: IAO:0000309 ! diagram

[Term]
id: IAO:0000064
name: algorithm
def: "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." []
is_a: IAO:0000104 ! plan specification

[Term]
id: IAO:0000078
name: curation status specification
def: "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." []
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: IAO:0000096
name: source code module
def: "A source code module is a directive information entity that specifies, using a programming language, some algorithm." []
is_a: IAO:0000033 ! directive information entity

[Term]
id: IAO:0000098
name: data format specification
def: "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" []
is_a: IAO:0000033 ! directive information entity

[Term]
id: IAO:0000100
name: data set
def: "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." []
is_a: IAO:0000027 ! data item

[Term]
id: IAO:0000101
name: image
def: "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." []
is_a: IAO:0000308 ! figure

[Term]
id: IAO:0000102
name: data about an ontology part
def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
is_a: IAO:0000027 ! data item

[Term]
id: IAO:0000104
name: plan specification
def: "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." []
comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them
is_a: IAO:0000033 ! directive information entity
relationship: BFO:0000051 IAO:0000005 ! has part objective specification
relationship: BFO:0000051 IAO:0000007 ! has part action specification

[Term]
id: IAO:0000178
name: material information bearer
def: "A material entity in which a concretization of an information content entity inheres." []
is_a: BFO:0000040 ! material entity

[Term]
id: IAO:0000179
name: histogram
def: "A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." []
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000180
name: heatmap
def: "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." []
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000183
name: dendrogram
def: "A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." []
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000184
name: scatter plot
def: "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis." []
is_a: IAO:0000038 ! graph

[Term]
id: IAO:0000225
name: obsolescence reason specification
def: "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." []
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: IAO:0000308
name: figure
def: "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." []
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000309
name: diagram
def: "A figure that expresses one or more propositions" []
is_a: IAO:0000308 ! figure

[Term]
id: IAO:0000310
name: document
def: "A collection of information content entities intended to be understood together as a whole" []
is_a: IAO:0000030 ! information content entity

[Term]
id: IAO:0000311
name: publication
def: "A document that is the output of a publishing process." []
comment: Revisit the term in Octorber 2020. Improve the defintion.
is_a: IAO:0000310 ! document
intersection_of: IAO:0000310 ! document
intersection_of: OBI:0000312 IAO:0000444 {all_only="true"} ! is specified output of publishing process

[Term]
id: IAO:0000409
name: denotator type
def: "A denotator type indicates how a term should be interpreted from an ontological perspective." []
is_a: IAO:0000102 ! data about an ontology part

[Term]
id: IAO:0000444
name: publishing process
def: "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free." []
is_a: OBI:0000011 ! obsolete planned process

[Term]
id: IAO:0000572
name: documenting
def: "A planned process in which a document is created or added to by including the specified input in it." []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
relationship: OBI:0000293 IAO:0000030 ! has specified input information content entity
relationship: OBI:0000299 IAO:0000310 ! has specified output document

[Term]
id: NCBITaxon:1
is_a: COB:0000022

[Term]
id: NCBITaxon:10239
is_a: NCBITaxon_Union:0000030 ! cellular organisms or viruses

[Term]
id: NCBITaxon:131567
is_a: NCBITaxon_Union:0000030 ! cellular organisms or viruses

[Term]
id: NCBITaxon:9606
name: Homo sapiens
is_a: BAO_0000362 ! mammalian

[Term]
id: NCBITaxon_Union:0000030
name: cellular organisms or viruses
is_a: NCBITaxon:1
union_of: NCBITaxon:10239
union_of: NCBITaxon:131567

[Term]
id: OBI:0000011
name: obsolete planned process
def: "A process that realizes a plan which is the concretization of a plan specification." []
is_a: BFO:0000015 ! process
is_a: oboInOwl:ObsoleteClass ! Obsolete Class

[Term]
id: OBI:0000014
name: regulator role
def: "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders" []
is_a: OBI:0000017 ! regulatory role

[Term]
id: OBI:0000017
name: regulatory role
def: "a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body." []
is_a: BFO:0000023 ! role

[Term]
id: OBI:0000018
name: material supplier role
def: "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation." []
is_a: OBI:0000947 ! service provider role

[Term]
id: OBI:0000023
name: classified data set
def: "A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels." []
is_a: IAO:0000100 ! data set
relationship: OBI:0000312 OBI:0000663 ! is specified output of class prediction data transformation

[Term]
id: OBI:0000066
name: investigation
def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." []
is_a: COB:0000082
is_a: OBI:0000011 ! obsolete planned process
relationship: BFO:0000051 IAO:0000572 ! has part documenting
relationship: BFO:0000051 OBI:0000338 ! has part drawing a conclusion based on data
relationship: BFO:0000051 OBI:0000471 ! has part study design execution

[Term]
id: OBI:0000067
name: evaluant role
def: "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" []
is_a: BFO:0000023 ! role
relationship: BFO:0000054 OBI:0000070 {all_only="true"} ! realized in
relationship: RO:0000052 BFO:0000040 ! characteristic of material entity

[Term]
id: OBI:0000070
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
disjoint_from: OBI:0000339 ! planning
disjoint_from: OBI:0200000 ! data transformation
relationship: BFO:0000055 OBI:0000067 ! realizes evaluant role
relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective

[Term]
id: OBI:0000112
name: specimen role
def: "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." []
is_a: BFO:0000023 ! role

[Term]
id: OBI:0000202
name: investigation agent role
def: "A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing." []
comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
is_a: BFO:0000023 ! role
relationship: BFO:0000054 OBI:0000066 {all_only="true"} ! realized in investigation

[Term]
id: OBI:0000245
name: organization
def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." []
is_a: BFO:0000040 ! material entity

[Term]
id: OBI:0000272
name: protocol
def: "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." []
is_a: IAO:0000104 ! plan specification

[Term]
id: OBI:0000338
name: drawing a conclusion based on data
def: "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" []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
relationship: OBI:0000293 IAO:0000027 ! has specified input data item
relationship: OBI:0000299 OBI:0001909 ! has specified output conclusion based on data

[Term]
id: OBI:0000339
name: planning
def: "a process of creating or modifying a plan specification" []

[Term]
id: OBI:0000441
name: assay objective
def: "an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)" []
is_a: IAO:0000005 ! objective specification

[Term]
id: OBI:0000450
name: regulatory agency
def: "A regulatory agency is a organization that has responsibility over or for  the legislation (acts and regulations) for a given sector of the government." []
is_a: OBI:0000245 ! organization
intersection_of: OBI:0000245 ! organization
intersection_of: RO:0000087 OBI:0000014 ! has role regulator role
relationship: RO:0000087 OBI:0000014 ! has role regulator role

[Term]
id: OBI:0000456
name: material transformation objective
def: "an objective specifiction that creates an specific output object from input materials." []
is_a: IAO:0000005 ! objective specification

[Term]
id: OBI:0000457
name: manufacturing
def: "A planned process with the objective to produce a processed material which will have a function for future use." []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
relationship: OBI:0000293 BFO:0000040 ! has specified input material entity
relationship: OBI:0000299 COB:0000026 ! has specified output
relationship: OBI:0000417 OBI:0000458 ! achieves_planned_objective manufacturing objective

[Term]
id: OBI:0000458
name: manufacturing objective
def: "is the objective to manufacture a material of a certain function (device)" []
is_a: OBI:0000456 ! material transformation objective

[Term]
id: OBI:0000471
name: study design execution
def: "a planned process that carries out a study design" []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process

[Term]
id: OBI:0000571
name: manufacturer role
def: "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process." []
is_a: BFO:0000023 ! role
relationship: BFO:0000054 OBI:0000457 {all_only="true"} ! realized in manufacturing

[Term]
id: OBI:0000648
name: clustered data set
def: "A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels." []
is_a: IAO:0000100 ! data set
relationship: OBI:0000312 OBI:0200175 ! is specified output of class discovery data transformation

[Term]
id: OBI:0000659
name: specimen collection process
def: "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
intersection_of: COB:0000035
intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective
relationship: OBI:0000293 BFO:0000040 ! has specified input material entity
relationship: OBI:0000299 OBI:0100051 ! has specified output specimen
relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective

[Term]
id: OBI:0000663
name: class prediction data transformation
def: "A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction." []
is_a: OBI:0200000 ! data transformation

[Term]
id: OBI:0000684
name: specimen collection objective
def: "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." []
is_a: IAO:0000005 ! objective specification

[Term]
id: OBI:0000700
name: support vector machine
def: "A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space." []
is_a: OBI:0000663 ! class prediction data transformation
relationship: OBI:0000417 OBI:0200179 ! achieves_planned_objective class prediction objective

[Term]
id: OBI:0000704
name: decision tree induction objective
def: "A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made." []
is_a: OBI:0200166 ! data transformation objective

[Term]
id: OBI:0000707
name: decision tree building data transformation
def: "A decision tree building data transformation is a data transformation that has objective decision tree induction." []
is_a: OBI:0200000 ! data transformation
relationship: OBI:0000417 OBI:0000704 ! achieves_planned_objective decision tree induction objective

[Term]
id: OBI:0000713
name: GenePattern software
def: "a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks." []
is_a: IAO:0000010 ! software

[Term]
id: OBI:0000726
name: peak matching
def: "Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold" []
is_a: OBI:0200000 ! data transformation

[Term]
id: OBI:0000727
name: k-nearest neighbors
def: "A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned." []
is_a: APOLLO_SV:00000796 ! dataset creating
is_a: OBI:0200171 ! partitioning data transformation
is_a: OBI:0200175 ! class discovery data transformation
relationship: OBI:0000299 OBI:0000648 ! has specified output clustered data set
relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective

[Term]
id: OBI:0000749
name: CART
def: "A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure." []
is_a: OBI:0000707 ! decision tree building data transformation

[Term]
id: OBI:0000792
name: statistical model validation
def: "A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set." []
is_a: OBI:0200171 ! partitioning data transformation
relationship: OBI:0000417 OBI:0200188 ! achieves_planned_objective cross validation objective

[Term]
id: OBI:0000835
name: manufacturer
def: "A person or organization that has a manufacturer role." []
is_a: BFO:0000040 ! material entity
relationship: RO:0000087 OBI:0000571 ! has role manufacturer role

[Term]
id: OBI:0000947
name: service provider role
def: "is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person" []
is_a: BFO:0000023 ! role
relationship: BFO:0000054 COB:0000035 {all_only="true"} ! realized in

[Term]
id: OBI:0000953
name: processed specimen
def: "A specimen that has been intentionally physically modified." []
is_a: COB:0000026
is_a: OBI:0100051 ! specimen

[Term]
id: OBI:0000963
name: categorical label
def: "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale." []
is_a: IAO:0000009 ! datum label

[Term]
id: OBI:0001000
name: questionnaire
def: "A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study." []
is_a: IAO:0000310 ! document

[Term]
id: OBI:0001468
name: cell specimen
def: "A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture." []
is_a: OBI:0001479 ! specimen from organism
intersection_of: OBI:0001479 ! specimen from organism
intersection_of: BFO:0000051 CL:0000000 ! has part cell
relationship: BFO:0000051 CL:0000000 ! has part cell

[Term]
id: OBI:0001479
name: specimen from organism
def: "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)." []
is_a: OBI:0100051 ! specimen

[Term]
id: OBI:0001909
name: conclusion based on data
def: "An information content entity that is inferred from data." []
is_a: IAO:0000030 ! information content entity
relationship: OBI:0000124 IAO:0000027 ! is_supported_by_data data item
relationship: OBI:0000312 OBI:0000338 ! is specified output of drawing a conclusion based on data

[Term]
id: OBI:0001930
name: categorical value specification
def: "A value specification that is specifies one category out of a fixed number of nominal categories" []
is_a: OBI:0001933 ! value specification

[Term]
id: OBI:0001933
name: value specification
def: "An information content entity that specifies a value within a classification scheme or on a quantitative scale." []
is_a: IAO:0000030 ! information content entity

[Term]
id: OBI:0001977
name: cytometry assay
def: "An assay that counts and/or measures characteristics of cells." []
is_a: OBI:0000070

[Term]
id: OBI:0002076
name: collection of specimens
def: "A material entity that has two or more specimens as its parts." []
is_a: BFO:0000040 ! material entity
intersection_of: BFO:0000040 ! material entity
intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen

[Term]
id: OBI:0002205
name: histologic grade according to AJCC 7th edition
def: "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002210
name: histologic grade according to the Fuhrman Nuclear Grading System
def: "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002215
name: histologic grade for ovarian tumor
def: "A categorical value specification that is a histologic grade assigned to a ovarian tumor." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002216
name: histologic grade for ovarian tumor according to a two-tier grading system
def: "A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors." []
is_a: OBI:0002215 ! histologic grade for ovarian tumor

[Term]
id: OBI:0002219
name: histologic grade for ovarian tumor according to the World Health Organization
def: "A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO)." []
is_a: OBI:0002215 ! histologic grade for ovarian tumor

[Term]
id: OBI:0002224
name: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002232
name: pathologic primary tumor stage for lung according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002243
name: pathologic primary tumor stage for kidney according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002256
name: pathologic primary tumor stage for ovary according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002270
name: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002279
name: pathologic lymph node stage for lung according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002284
name: pathologic lymph node stage for kidney according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002287
name: pathologic lymph node stage for ovary according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002290
name: pathologic distant metastases stage for colon according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002298
name: pathologic distant metastases stage for lung according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002306
name: pathologic distant metastases stage for kidney according to AJCC 7th edition
def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002310
name: pathologic distant metastases stage for ovary according to AJCC 7th edition
def: "A categorical value specification that is a  pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002314
name: clinical tumor stage group according to AJCC 7th edition
def: "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002326
name: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
def: "A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002341
name: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002356
name: performance status value specification
def: "A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life)." []
is_a: OBI:0001930 ! categorical value specification

[Term]
id: OBI:0002357
name: Eastern Cooperative Oncology Group score value specification
def: "A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient." []
is_a: OBI:0002356 ! performance status value specification

[Term]
id: OBI:0002363
name: Karnofsky score vaue specification
def: "A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment." []
is_a: OBI:0002356 ! performance status value specification

[Term]
id: OBI:0002989
name: material supplier
def: "A person or organization that provides material supplies to other people or organizations." []
is_a: BFO:0000040 ! material entity
relationship: RO:0000087 OBI:0000018 ! has role material supplier role

[Term]
id: OBI:0100051
name: specimen
def: "A material entity that is collected for potential use as an input upon which measurements or observations are performed." []
is_a: BFO:0000040 ! material entity
intersection_of: BFO:0000040 ! material entity
intersection_of: RO:0000087 OBI:0000112 ! has role specimen role
relationship: RO:0000087 OBI:0000112 ! has role specimen role

[Term]
id: OBI:0200000
name: data transformation
def: "A completely executed planned process that produces output data from input data." []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
relationship: OBI:0000293 IAO:0000027 {all_only="true"} ! has specified input data item
relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective

[Term]
id: OBI:0200033
name: leave one out cross validation method
def: "is a data transformation :  leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data" []
is_a: OBI:0000792 ! statistical model validation

[Term]
id: OBI:0200041
name: k-means clustering
def: "A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed)." []
is_a: APOLLO_SV:00000796 ! dataset creating
is_a: OBI:0200171 ! partitioning data transformation
is_a: OBI:0200175 ! class discovery data transformation
relationship: OBI:0000299 OBI:0000648 ! has specified output clustered data set
relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective

[Term]
id: OBI:0200042
name: hierarchical clustering
def: "A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root)." []
is_a: APOLLO_SV:00000796 ! dataset creating
is_a: OBI:0200175 ! class discovery data transformation
relationship: OBI:0000299 OBI:0000648 ! has specified output clustered data set
relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective

[Term]
id: OBI:0200050
name: dimensionality reduction
def: "A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m." []
is_a: APOLLO_SV:00000796 ! dataset creating
is_a: OBI:0200175 ! class discovery data transformation
relationship: OBI:0000299 OBI:0000648 ! has specified output clustered data set
relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective

[Term]
id: OBI:0200051
name: principal components analysis dimensionality reduction
def: "A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones." []
is_a: OBI:0200050 ! dimensionality reduction

[Term]
id: OBI:0200111
name: data visualization
def: "A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations." []
is_a: COB:0000035
is_a: OBI:0000011 ! obsolete planned process
relationship: OBI:0000293 IAO:0000027 ! has specified input data item
relationship: OBI:0000293 IAO:0000027 {all_only="true"} ! has specified input data item

[Term]
id: OBI:0200166
name: data transformation objective
def: "An objective specification to transformation input data into output data" []
is_a: IAO:0000005 ! objective specification

[Term]
id: OBI:0200171
name: partitioning data transformation
def: "A partitioning data transformation is a data transformation that has objective partitioning." []
is_a: OBI:0200000 ! data transformation
relationship: OBI:0000417 OBI:0200172 ! achieves_planned_objective partitioning objective

[Term]
id: OBI:0200172
name: partitioning objective
def: "A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set." []
is_a: OBI:0200166 ! data transformation objective

[Term]
id: OBI:0200175
name: class discovery data transformation
def: "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery." []
is_a: OBI:0200000 ! data transformation

[Term]
id: OBI:0200178
name: class discovery objective
def: "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data  (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic." []
is_a: OBI:0200166 ! data transformation objective

[Term]
id: OBI:0200179
name: class prediction objective
def: "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and\nclass labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data." []
is_a: OBI:0200166 ! data transformation objective

[Term]
id: OBI:0200188
name: cross validation objective
def: "A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis." []
is_a: OBI:0200172 ! partitioning objective

[Term]
id: OBI:0200190
name: clustered data visualization
def: "A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type." []
is_a: OBI:0200111 ! data visualization
relationship: OBI:0000293 OBI:0000648 {all_only="true"} ! has specified input clustered data set

[Term]
id: OBI:0500000
name: study design
def: "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." []
is_a: IAO:0000104 ! plan specification
relationship: BFO:0000051 OBI:0000272 ! has part protocol

[Term]
id: PATO:0000001
name: quality
namespace: quality
is_a: BFO:0000020 ! specifically dependent continuant

[Term]
id: PATO:0000033
name: concentration of
namespace: quality
synonym: "concentration" EXACT []
is_a: PATO:0000070 ! amount

[Term]
id: PATO:0000070
name: amount
namespace: quality
comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.
synonym: "count in organism" RELATED []
synonym: "number" RELATED []
synonym: "presence" RELATED []
synonym: "presence or absence in organism" EXACT []
synonym: "quantitative" EXACT []
is_a: PATO:0103000 ! quantitative
relationship: RO:0015012 PATO:0001555 ! reciprocal of has number of

[Term]
id: PATO:0001555
name: has number of
namespace: quality
synonym: "cardinality" RELATED []
synonym: "extra or missing physical or functional parts" EXACT []
synonym: "has or lacks parts of type" EXACT []
synonym: "mereological quality" EXACT []
synonym: "number" RELATED []
synonym: "number of" EXACT []
xref: OBO_REL:has_part
is_a: PATO:0000070 ! amount

[Term]
id: PATO:0001842
name: acidity
namespace: quality
synonym: "pH" EXACT []
is_a: PATO:0000033 ! concentration of

[Term]
id: PATO:0103000
name: quantitative
namespace: quality
is_a: PATO:0000001 ! quality

[Term]
id: PREFER:0000000
name: process rate metric
def: "A key process metric that represents a quantitative metric, describing rates or fluxes associated, for instance, wiht growth, product formation, substrate consumption, or respiration, during a fermentation process." []
synonym: "key precision fermentation process rate metric" EXACT []
is_a: PREFER:0000078 ! key process metric

[Term]
id: PREFER:0000002
name: fermentation project
namespace: precision_fermentation
def: "A precision fermentation process that consist of a single fermentation experiment or multiple related experiments." []
synonym: "project" EXACT []
is_a: OBI:0000066 ! investigation
is_a: PREFER:9000003 ! precision fermentation process

[Term]
id: PREFER:0000003
name: fermentation experiment
namespace: precision_fermentation
def: "A precision fermentation process that consists of sets of fermentation runs conducted within the same project, all following a shared experimental approach or protocol." []
synonym: "experiment" EXACT []
is_a: OBI:0000070
is_a: PREFER:9000003 ! precision fermentation process
relationship: BFO:0000050 PREFER:0000002 ! part of fermentation project

[Term]
id: PREFER:0000004
name: fermentation run
namespace: precision_fermentation
def: "A precision fermentation process that is carried out under defined experimental conditions (e.g., temperature, pH, agitation) using a single bioreactor system." []
synonym: "cell culture process" BROAD []
xref: CHMO:0001624
is_a: PREFER:9000003 ! precision fermentation process
relationship: BAO_0002922 PREFER:0000011 ! fermentation medium
relationship: BFO:0000050 PREFER:0000003 ! part of fermentation experiment
relationship: PREFER:8000006 PREFER:0000014 ! uses bioreactor bioreactor
relationship: PREFER:8000011 PREFER:0000008 ! has cultivation condition cultivation condition
relationship: PREFER:8000015 PREFER:0000012 ! cultures cell cell biocatalyst
relationship: PREFER:8000016 PREFER:0000018 ! has collected offline sample
relationship: PREFER:8000017 CHEBI:24431 ! has measured compound chemical entity

[Term]
id: PREFER:0000005
name: alkaline cultivation condition
def: "A cultivation condition that represents the alkalinity related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the pH and buffering state of the cultivation environment." []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000006
name: gravimetric feed rate control variable
def: "A process control variable that represents the target rate at which the feed (based on its weight) is added to a bioreactor or fermentation system during a fermentation process." []
is_a: PREFER:0000009 ! feed control variable
relationship: BAO_0002874 uom:g.h-1 ! gram per hour
relationship: PREFER:8000020 PREFER:0000075 ! setpoint of gravimetric feed rate measurement variable

[Term]
id: PREFER:0000007
name: temperature cultivation condition
def: "A cultivation condition that represents the temperature related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the thermal state of the cultivation environment." []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000008
name: cultivation condition
namespace: precision_fermentation
def: "An information content entity that represents a set of process conditions, grouping relevant process control variables and process measurement variables, describing the environmental and physicochemical conditions under which cells are cultivated." []
synonym: "fermentation culture condition" EXACT []
xref: EDAM:3724
is_a: IAO:0000030 ! information content entity
relationship: BFO:0000051 PREFER:0000015 ! has part operational parameter

[Term]
id: PREFER:0000009
name: feed control variable
def: "A precision fermentation process control variable that defines the feed control of a bioreactor or fermentation system during the fermentation process." []
synonym: "precision fermentation process feed control variable" EXACT []
is_a: PREFER:0000037 ! feed medium cultivation condition
is_a: PREFER:9000000 ! precision fermentation process control variable

[Term]
id: PREFER:0000010
name: fermentation culture
namespace: precision_fermentation
def: "A material entity consisting of a cell population that is cultivated under controlled environmental conditions supporting a fermentation process." []
comment: Fermentation cultures are used in bioprocesses for various applications including precision fermentation, bioremediation, and production of biofuels and pharmaceuticals.
synonym: "cultured cell population" NARROW [OBI:0100060]
is_a: BFO:0000040 ! material entity
relationship: PREFER:8000010 PREFER:0000200 ! has fermentation culture type fermentation culture role

[Term]
id: PREFER:0000011
name: fermentation medium
namespace: precision_fermentation
def: "A material entity consisting of an aqueous mixture of macronutrients, micronturients, and buffering agents that is used to support cell growth, metabolic activity and product formation during a fermentation process." []
synonym: "cultivation medium" EXACT []
is_a: BFO:0000040 ! material entity
relationship: PREFER:8000004 CHEBI:24431 ! has medium ingredient chemical entity

[Term]
id: PREFER:0000012
name: cell biocatalyst
namespace: precision_fermentation
def: "A material entity consisting of a whole living cell that is used as a catalyst for bioproduction, catalyzing a biochemical reaction or transformation through their intrinsec or genetically modified metabolic activity." []
comment: In a biotransformation process or bioprocess, a cell biocatalyst converts substrates (organic or inorganic compounds) into outputs such as products, by-products, and cell biomass. Energy derived from substrate conversion is used for product formation, growth and cellular maintenance.
synonym: "biocatalyst" BROAD []
synonym: "biological catalyst" BROAD []
synonym: "catalyst" BROAD []
synonym: "cell catalyst" EXACT []
synonym: "cell factory" EXACT []
synonym: "microbial cell factory" NARROW []
synonym: "WCB" EXACT OMO:0003012 [DOI: 10.1201/9781003413134]
synonym: "whole-cell biocatalyst" EXACT [DOI: 10.1186/s12934-017-0724-7]
is_a: BFO:0000040 ! material entity
is_a: CL:0000000 ! cell

[Term]
id: PREFER:0000013
name: taxon quality
namespace: precision_fermentation
def: "A quality of one or more biological organisms, as well as of parts of organism pertaining to a biological taxon." [PMID:18586729]
synonym: "taxon" BROAD [NCBITaxon:1]
xref: http://purl.org/biotop/btl2.owl#TaxonQuality
is_a: BFO:0000019 ! quality

[Term]
id: PREFER:0000014
name: bioreactor
namespace: precision_fermentation
def: "A device or system that is a material entity designed to support the run of a biological and biochemical process by controlling regulated environmental and cultivation conditions, such as temperature, agitation or nutrient injection at different scales, including lab-scale, pilot plant, and industrial-scale systems." [OBI:0001046]
comment: While this term is equivalent to OBI:0001046, PREFER has specific modelling that makes it more difficult to maintain if used directly. A decision was hence made to create this new term in PREFER and map it to OBI:0001046 instead.
synonym: "bioreactor system" EXACT []
synonym: "fermenter" NARROW [MSIO:0000167]
xref: OBI:0001046
is_a: BFO:0000040 ! material entity
relationship: PREFER:8000008 PREFER:0000185 ! has bioreactor scale bioreactor scale
relationship: PREFER:8000018 PREFER:0000180 ! has operational mode operation mode control variable

[Term]
id: PREFER:0000015
name: operational parameter
namespace: precision_fermentation
def: "An information content entity that represents a set of configurable settings used to operate and control a fermentation process, grouping process control variables and mode dependent parameters that define how cultivation conditions are regulated in a bioreactor or fermentation system during the process." []
comment: Operational parameters may vary depending on the selected fermentation operational mode (e.g. batch, fed-batch, continuous) and are realized through instrument or system configuration.
synonym: "operational setting" BROAD []
synonym: "parameter" BROAD [NCIT:C44175]
xref: REPR:InstrumentSetting
is_a: IAO:0000030 ! information content entity

[Term]
id: PREFER:0000016
name: fermentation phase
namespace: precision_fermentation
def: "A time interval of a fermentation process." []
is_a: PREFER:9000003 ! precision fermentation process
relationship: BFO:0000050 PREFER:0000004 ! part of fermentation run

[Term]
id: PREFER:0000017
name: phase event
namespace: precision_fermentation
def: "An operational intervention set by user that triggers the start or end of the fermentation phase." []
is_a: PREFER:9000003 ! precision fermentation process

[Term]
id: PREFER:0000018
name: offline sample
namespace: precision_fermentation
def: "A material entity consisting of a sample that has been withdrawn from a bioprocess system or bioreactor at a specific time point during the ongoing fermentation run for subsequent offline analysis of various compounds, such as substrates, products, and by-products, and biomass." []
synonym: "collected sample" EXACT []
synonym: "material sample" BROAD [OBI:0000747]
is_a: BFO:0000040 ! material entity

[Term]
id: PREFER:0000019
name: temperature setpoint control variable
namespace: precision_fermentation
def: "A precision fermentation process control variable that represents the target temperature value to be regulated and maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process temperature setpoint control variable" EXACT []
synonym: "target temperature" EXACT []
synonym: "target temperature value" EXACT []
synonym: "target Tº" EXACT []
synonym: "temperature control setpoint" EXACT []
synonym: "temperature reference point" EXACT []
synonym: "temperature reference value" EXACT []
synonym: "temperature setting" EXACT [AFO_/result#AFR:0001255]
synonym: "Tº setpoint" EXACT []
is_a: PREFER:0000007 ! temperature cultivation condition
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:9000000 ! precision fermentation process control variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000020 PREFER:0000041 ! setpoint of temperature measurement variable

[Term]
id: PREFER:0000020
name: pH setpoint control variable
namespace: precision_fermentation
def: "A precision fermentation process control variable that represents the target pH value to be regulated and maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "pH control setpoint" EXACT []
synonym: "ph control setpoint" EXACT []
synonym: "ph setpoint" EXACT []
synonym: "precision fermentation process pH setpoint control variable" EXACT []
synonym: "target pH" EXACT []
synonym: "target ph" EXACT []
is_a: PREFER:0000005 ! alkaline cultivation condition
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:9000000 ! precision fermentation process control variable
relationship: BAO_0002874 uom:%5BpH%5D ! pH based unit
relationship: PREFER:8000020 PREFER:0000040 ! setpoint of pH measurement variable

[Term]
id: PREFER:0000021
name: pH base solution
namespace: precision_fermentation
def: "A liquid material entity with basic (alkaline) properties that is used to increase the pH of a solution or system.\n\nIn a fermentation process, it is added manually or automatically to the fermentation run to control and maintain the pH at the defined setpoint or desired value." []
synonym: "pH control base solution" EXACT []
is_a: BFO:0000040 ! material entity

[Term]
id: PREFER:0000022
name: pH acid solution
namespace: precision_fermentation
def: "A liquid material entity with acidic properties that is used to decrease the pH of a solution or system.\n\nIn a fermentation process, it is added manually or automatically to the fermentation run to control and maintain the pH at the defined setpoint or desired value." []
synonym: "pH control acid solution" EXACT []
is_a: BFO:0000040 ! material entity

[Term]
id: PREFER:0000023
name: core balance metric
def: "A precision fermentation process calculated variable that represents a quantitative metric derived from balance calculations over a process, used to characterize the balance of inputs and outputs within a bioreactor or fermenter system during the fermentation process." []
synonym: "elemental balance metric" EXACT []
is_a: PREFER:9000002 ! precision fermentation process calculated variable

[Term]
id: PREFER:0000024
name: fermentation medium cultivation condition
def: "A cultivation condition that represents the fermentation medium related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the state of the fermentation medium within the cultivation environment." []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000025
name: dissolved oxygen setpoint control variable
namespace: precision_fermentation
def: "A precision fermentation process dissolved oxygen control variable that represents the target dissolved oxygen value to be regulated and maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "dissolved oxygen setpoint" EXACT []
synonym: "DO setpoint" EXACT OMO:0003012 []
synonym: "precision fermentation process dissolved oxygen setpoint control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000119 ! dissolved oxygen control variable
relationship: BAO_0002874 uom:%25 ! percent
relationship: PREFER:8000020 PREFER:0000039 ! setpoint of dissolved oxygen measurement variable

[Term]
id: PREFER:0000026
name: dissolved oxygen cascade level control variable
namespace: precision_fermentation
def: "A precision fermentation process dissolved oxygen control variable that represents the cascade control system linked to a parameter to achieve the desired dissolved oxygen level within a bioreactor or fermentation system during a fermentation process." []
comment: For instance, in fed-batch operation mode there could be three different cascade levels. Level 1 involves adjusting the stirrer speed parameter. Level 2 involves adjusting the air flow parameter. Level 3 involves adjusting the oxygen flow parameter.
synonym: "dissolved oxygen control strategy variable" EXACT []
synonym: "DO cascade level control variable" EXACT []
synonym: "precision fermentation process dissolved oxygen cascade level control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000119 ! dissolved oxygen control variable

[Term]
id: PREFER:0000027
name: maximum stirring setpoint control variable
namespace: precision_fermentation
def: "A precision fermentation process dissolved oxygen control variable that represents the target maximum revolutions per minute (rpm) of the bioreactor stirrer to be regulated and or maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "maximum shaking speed setpoint" EXACT []
synonym: "maximum shaking speed setpoint control variable" EXACT []
synonym: "maximum stirring speed setpoint" EXACT []
synonym: "precision fermentation process maximum stirring setpoint control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000119 ! dissolved oxygen control variable
relationship: BAO_0002874 PREFER:7000008 ! revolution per minute
relationship: PREFER:8000020 PREFER:0000054 ! setpoint of stirrer speed measurement variable

[Term]
id: PREFER:0000028
name: minimum stirring setpoint control variable
namespace: precision_fermentation
def: "A precision fermentation process dissolved oxygen control variable that represents the target minimum revolutions per minute (rpm) of the bioreactor stirrer to be regulated and or maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "minimum shaking speed setpoin" EXACT []
synonym: "minimum shaking speed setpoint control variable" EXACT []
synonym: "minimum stirring speed setpoin" EXACT []
synonym: "minimum stirring speed setpoint control variable" EXACT []
synonym: "precision fermentation process minimum aeration setpoint control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000119 ! dissolved oxygen control variable
relationship: BAO_0002874 PREFER:7000008 ! revolution per minute
relationship: PREFER:8000020 PREFER:0000054 ! setpoint of stirrer speed measurement variable

[Term]
id: PREFER:0000029
name: pressure cultivation condition
def: "A cultivation condition that represents the pressure related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the pressure state within the cultivation environment." []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000030
name: aeration gas type control variable
namespace: precision_fermentation
def: "A precision fermentation process dissolved oxygen control variable that represents the type of gas used for aeration in a bioreactor or fermentation system during a fermentation process, which may include aire or specific gases such as pure oxygen, nitrogen or carbon dioxide." []
synonym: "precision fermentation process aeration gas type control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000119 ! dissolved oxygen control variable

[Term]
id: PREFER:0000031
name: maximum aeration setpoint control variable
namespace: precision_fermentation
def: "A precision fermentation process dissolved oxygen control variable that represents the target maximum rate of at which gas can be supplied to be regulated and or maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "maximum aeration setpoint" EXACT []
synonym: "precision fermentation process maximum aeration setpoint control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000119 ! dissolved oxygen control variable
relationship: BAO_0002874 uom:L.min-1 ! liter per minute
relationship: PREFER:8000020 PREFER:0000055 ! setpoint of air flow rate measurement variable

[Term]
id: PREFER:0000032
name: minimum aeration setpoint control variable
namespace: precision_fermentation
def: "A precision fermentation process dissolved oxygen control variable that represents the target minimum rate of at which gas can be supplied to be regulated and or maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "minimum aeration setpoint" EXACT []
synonym: "precision fermentation process minimum aeration setpoint control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000119 ! dissolved oxygen control variable
relationship: BAO_0002874 uom:L.min-1 ! liter per minute
relationship: PREFER:8000020 PREFER:0000055 ! setpoint of air flow rate measurement variable

[Term]
id: PREFER:0000033
name: dissolved oxygen cultivation condition
namespace: precision_fermentation
def: "A cultivation condition that represents the dissolved oxygen related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the concentration of oxygen dissolved in the cultivation environment." []
synonym: "DO cultivation condition" EXACT []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000034
name: starting optical density measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the initial optical density (OD) of the fermentation culture from a bioreactor or fermentation system during a fermentation process." []
comment: The starting OD measurement is either measured (by taking a sample after inoculation and measuring the cell density spectophotometrically at 600nm or 900nm wavelength) or  calculated (by knowing the final OD of the seed culture, volume inoculated and final cultivation volume).
synonym: "precision fermentation process starting optical density measurement variable" EXACT []
synonym: "starting OD measurement variable" EXACT OMO:0003012 []
is_a: PREFER:0000045 ! optical density cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:7000006 ! unit of optical density

[Term]
id: PREFER:0000035
name: final seed optical density measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the cell density of the seed culture for the process at the time it is inoculated  to the bioreactor or fermentation system." []
synonym: "final seed OD measurement variable" EXACT []
synonym: "precision fermentation project final seed optical density measurement variable" EXACT []
is_a: PREFER:0000073 ! seed cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:7000006 ! unit of optical density

[Term]
id: PREFER:0000036
name: initial culture volume measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the total volume of the culture of a bioreactor or fermentation system, at the beginning of the process, representing the sum of fermentation medium and seed culture." []
synonym: "initial production culture volume measurement variable" EXACT []
synonym: "precision fermentation process initial culture volume measurement variable" EXACT []
synonym: "starting culture volume measurement variable" EXACT []
synonym: "starting production culture volume measurement variable" EXACT []
is_a: PREFER:0000046 ! volume cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000037
name: feed medium cultivation condition
namespace: precision_fermentation
def: "A fermentation medium cultivation condition that represents the feed related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the addition and state of fresh feed media within the cultivation environment." []
is_a: PREFER:0000024 ! fermentation medium cultivation condition
relationship: PREFER:8000013 PREFER:0000189 ! has feed profile type feed profile type control variable

[Term]
id: PREFER:0000038
name: batch medium pH measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the negative decadic logarithm of the hydrogen ion concentration in the batch fermentation medium of a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation project batch medium pH measurement variable" EXACT []
is_a: PREFER:0000024 ! fermentation medium cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:%5BpH%5D ! pH based unit

[Term]
id: PREFER:0000039
name: dissolved oxygen measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the concentration of oxygen molecules (O₂) dissolved in the fermentation medium of a bioreactor or fermentation system during a fermentation process." []
synonym: "DO measurement variable" EXACT OMO:0003012 []
synonym: "precision fermentation process dissolved oxygen measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:7000007 ! dimensionless unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000040
name: pH measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the potential of hydrogen of the production culture from a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process pH measurement variable" EXACT []
xref: NCIT:C205029
is_a: PREFER:0000005 ! alkaline cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:%5BpH%5D ! pH based unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000041
name: temperature measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the temerature of the production culture from a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process temperature measurement variable" EXACT []
is_a: PREFER:0000007 ! temperature cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000042
name: pressure measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the pressure in a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process pressure measurement variable" EXACT []
is_a: PREFER:0000029 ! pressure cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000043
name: volume measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the total volume of aqueous solution in the bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process volume measurement variable" EXACT []
is_a: PREFER:0000046 ! volume cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000044
name: offline sample mass compound measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the mass of a compound present in a withdrawn process sample from a bioreactor or fermentation system during a fermentation process, used to quantify the amount of biomass, product, and other compounds." []
synonym: "precision fermentation process offline sample mass compound measurement variable" EXACT []
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000154 ! has data acquisition quality offline data acquisition

[Term]
id: PREFER:0000045
name: optical density cultivation condition
def: "A cultivation condition that represents the optical density related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the optical density state of the fermentation culture." []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000046
name: volume cultivation condition
def: "A cultivation condition that represents the volume related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the working or total fermentation volume of the cultivation system." []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000047
name: acid volume measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the volume of the acidic solution added to a bioreactor or fermenetation system to maintain the pH of cultivation at a setpoint or desired value during a fermentation process." []
synonym: "acid added volume measurement variable" EXACT []
synonym: "acid consumption volume measurement variable" EXACT []
synonym: "acid solution volume measurement variable" EXACT []
synonym: "acid used volume measurement variable" EXACT []
synonym: "precision fermentation process acid volume measurement variable" EXACT []
is_a: PREFER:0000005 ! alkaline cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000048
name: base volume measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the volume of the basic solution added to a bioreactor or fermentation system to maintain the pH of cultivation at a setpoint or desired value during a fermentation process." []
synonym: "base added volume measurement variable" EXACT []
synonym: "base consumption volume measurement variable" EXACT []
synonym: "base solution volume measurement variable" EXACT []
synonym: "base used volume measurement variable" EXACT []
synonym: "precision fermentation process base volume measurement variable" EXACT []
is_a: PREFER:0000005 ! alkaline cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000049
name: acid rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the flow rate at which an acid solution is added to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process acid rate measurement variable" EXACT []
is_a: PREFER:0000005 ! alkaline cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:L.h-1 ! liters per hour
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000050
name: base rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the flow rate at which the base solution is added to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process base rate measurement variable" EXACT []
is_a: PREFER:0000005 ! alkaline cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:L.h-1 ! liters per hour
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000051
name: feed amount measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the quantity of feed added to a bioreactor or fermentation system, during a fermentation process." []
synonym: "precision fermentation process feed amount measurement variable" EXACT []
is_a: PREFER:0000037 ! feed medium cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000052
name: feed volume measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the volume of the feed solution added to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process feed volume measurement variable" EXACT []
is_a: PREFER:0000037 ! feed medium cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000053
name: volumetric feed rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the rate at which the feed (based on its volume) is added to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process volumetric feed rate measurement variable" EXACT []
is_a: PREFER:0000037 ! feed medium cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:L.h-1 ! liters per hour
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000054
name: stirrer speed measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the speed at which the impeller shaft of a bioreactor or fermentation system shaft rotates during a fermentation process." []
synonym: "precision fermentation process stirrer speed measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:7000008 ! revolution per minute
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000055
name: air flow rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the rate at which air is supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process air flow rate measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:L.min-1 ! liter per minute
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000056
name: nitrogen flow rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the rate at which nitrogen, in form of a ammonium solution, is supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process nitrogen flow rate measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:L.min-1 ! liter per minute
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000057
name: oxygen flow rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the rate at which oxygen is supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process oxygen flow rate measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:L.min-1 ! liter per minute
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000058
name: inlet air oxygen measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the percentage of oxygen in the gas mixture that is being supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "inlet air o2 measurement variable" EXACT []
synonym: "precision fermentation project inlet air oxygen measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:%25 ! percent
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000059
name: inlet air carbon dioxide measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the percentage of carbon dioxide in the gas mixture that is being supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "inlet air co2 measurement variable" EXACT []
synonym: "precision fermentation process inlet air carbon dioxide measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:%25 ! percent
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000060
name: optical density measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the absorbance of the culture's turbidity at a specified wavelength of a bioreactor or fermentation system during a fermentation process." []
synonym: "OD measurement variable" EXACT OMO:0003012 []
synonym: "precision fermentation process optical density measurement variable" EXACT []
xref: NCIT:C85776
is_a: PREFER:0000045 ! optical density cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:7000006 ! unit of optical density

[Term]
id: PREFER:0000061
name: oxygen uptake rate variable
namespace: precision_fermentation
def: "A respiratory rate metric that represents the rate at which oxygen is consumed by the cell culture from a bioreactor or fermentation system during a fermentation process." []
comment: Biorespiration. Dynamic respiratory metric
synonym: "o2 uptake rate variable" EXACT []
synonym: "OUR variable" EXACT OMO:0003012 []
is_a: PREFER:0000158 ! respiratory rate metric
relationship: BAO_0002874 uom:mmol.h-1 ! millimole per hour

[Term]
id: PREFER:0000062
name: carbon dioxide evolution rate variable
namespace: precision_fermentation
def: "A respiratory rate metric that represents the rate at which carbon dioxide is released by the cell culture in a bioreactor or fermentation system during a fermentation process." []
comment: Physical gas transfer. Dynamic respiratory metric
synonym: "CER variable" EXACT OMO:0003012 []
synonym: "co2 evolution rate variable" EXACT []
is_a: PREFER:0000158 ! respiratory rate metric
relationship: BAO_0002874 uom:mmol.h-1 ! millimole per hour

[Term]
id: PREFER:0000063
name: oxygen transfer rate variable
namespace: precision_fermentation
def: "A respiratory rate metric variable that represents the rate at which oxygen is transferred from the gas phase or fermenter air into the liquid phase within a bioreactor or fermentation system during a fermentation process." []
comment: Physical gas transfer. Dynamic respiratory metric
synonym: "OTR variable" EXACT OMO:0003012 []
is_a: PREFER:0000158 ! respiratory rate metric
relationship: BAO_0002874 uom:mol.h-1 ! mole per hour

[Term]
id: PREFER:0000064
name: carbon dioxide transfer rate variable
namespace: precision_fermentation
def: "A respiratory rate metric that represents the rate at which carbon dioxide is transferred out of the bioreactor or fermentation system during a fermentation process." []
comment: Physical gas transfer. Dynamic respiratory metric. Important as carbon dioxide is considered a by-product in aerobic processes, and so is a parameter used for predicting biomass concentration, evaluating energetic efficiencies of growth, monitoring growth yields and controlling fed batch processes like airflow rates or stir speeds.
synonym: "CTR variable" EXACT OMO:0003012 []
is_a: PREFER:0000158 ! respiratory rate metric
relationship: BAO_0002874 uom:mol.h-1 ! mole per hour

[Term]
id: PREFER:0000065
name: respiratory quotient variable
namespace: precision_fermentation
def: "A respiratory rate metric that represent the ratio of carbon dioxide produced/formed to oxygen consumed during cellular metabolism in a bioreactor or fermentation system during a fermentation process, commmonly used to assess the metabolic state of cells." []
comment: Derived metabolic indicator.
synonym: "RQ variable" EXACT OMO:0003012 []
is_a: PREFER:0000158 ! respiratory rate metric
relationship: BAO_0002874 PREFER:7000007 ! dimensionless unit

[Term]
id: PREFER:0000068
name: offgas carbon dioxide measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the percentage of carbon dioxide present in the exhaust stream leaving the bioreactor or fermentation system during a fermentation process." []
synonym: "offgas co2 measurement variable" EXACT []
synonym: "pecision fermentation process offgas carbon dioxide measurement variable" EXACT []
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:%25 ! percent
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000069
name: offgas oxygen measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the percentage of oxygen present in the exhaust stream leaving the bioreactor or fermentation system during a fermentation process." []
synonym: "offgas o2 measurement variable" EXACT []
synonym: "precision fermentation process offgas oxygen measurement variable" EXACT []
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:%25 ! percent
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000071
name: biomass concentration variable
namespace: precision_fermentation
def: "A process titer metric that represents the concentration of biomass present in a withdrawn process sample from a bioreactor or fermentation system during a fermentation process." []
synonym: "biomass concentracion calculated variable" EXACT []
is_a: PREFER:0000091 ! process titer metric
relationship: BAO_0002874 uom:g.L-1 ! gram per litre

[Term]
id: PREFER:0000072
name: carbon dioxide flow rate measurement variable
def: "A precision fermentation process measurement variable that indicates the rate at which carbon dioxide is supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process carbon dioxide flow rate measurement variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:L.min-1 ! liter per minute
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000073
name: seed cultivation condition
def: "A cultivation condition that represents the seed related aspects of a fermentation cultivation process, grouping process control varibales and process measurement variables that describe or regulate the inoculum or seed state within the cultivation environment." []
is_a: PREFER:0000008 ! cultivation condition

[Term]
id: PREFER:0000074
name: compound concentration variable
def: "A process titer metric that represents the concentration of a specific compound present in a withdrawn process sample from a bioreactor or fermentation system during a fermentation process." []
synonym: "compound concentration calculated variable" EXACT []
is_a: PREFER:0000091 ! process titer metric
relationship: BAO_0002874 uom:g.L-1 ! gram per litre

[Term]
id: PREFER:0000075
name: gravimetric feed rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the amount of feed fed per unit time or the mass flow rate of the feed solution added to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process gravimetric feed rate measurement variable" EXACT []
is_a: PREFER:0000037 ! feed medium cultivation condition
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 uom:g.h-1 ! gram per hour
relationship: PREFER:8000012 PREFER:0000150 ! has data acquisition quality data acquisition quality

[Term]
id: PREFER:0000077
name: dilution feed rate control variable
namespace: precision_fermentation
def: "A feed process control variable that represents the target rate at which fresh feed medium is fed into a production culture relative to the total volume of the fermentation culture, representing the rate at which the production culture is diluted." []
synonym: "D" EXACT OMO:0003012 []
synonym: "dilution feed rate" EXACT []
is_a: PREFER:0000009 ! feed control variable
is_a: PREFER:0000015 ! operational parameter
relationship: BAO_0002874 uom:h-1 ! per hour (h⁻¹ or 1/h)

[Term]
id: PREFER:0000078
name: key process metric
def: "A precision fermentation process calculated variable that represents a set of quantitative metrics used to asses the efficiency or performance of the fermentation process impacting technoeconomic analysis." []
synonym: "key performance metric" EXACT []
synonym: "key precision fermentation process metric" EXACT []
is_a: PREFER:9000002 ! precision fermentation process calculated variable

[Term]
id: PREFER:0000079
name: carbon balance variable
namespace: precision_fermentation
def: "A carbon balance metric that represents the general carbon balance, which compares the total amount of carbon entering a bioreactor or fermenter system (through the substrate) to the total carbon leaving the system (through products, biomass or by-products)." []
synonym: "C balance variable" EXACT OMO:0003012 []
synonym: "carbon balance calculated variable" EXACT []
is_a: PREFER:0000157 ! carbon balance metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000081
name: degree of reduction balance variable
namespace: precision_fermentation
def: "A carbon balance metric that quantifies the redox state in a bioreactor or fermentar system during a fermentation process, by ensuring that the total electrons entering the system are equal to those leaving it, reflecting electron conservation." []
synonym: "degree of reduction balance calculated variable" EXACT []
synonym: "DoR balance variable" EXACT OMO:0003012 []
is_a: PREFER:0000157 ! carbon balance metric
relationship: BAO_0002874 uom:%25 ! percent

[Term]
id: PREFER:0000083
name: compound consumed variable
namespace: precision_fermentation
def: "A compound balance metric that represents the total amount of compound consumed, substrate taken up by the cells, in a bioreactor or fermentation system, during the fermentation process." []
synonym: "compound consumed calculated variable" EXACT []
is_a: PREFER:0000162 ! compound balance metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000085
name: microbioreactor scale
def: "A laboratory bioreactor scale that refers to very small volume bioreactor systems designed for high-throughput screening, typically operated at working volumes in the range of approximately a few microliters." []
comment: For instance, microtiter plates (MTPs) fall within this category.
is_a: PREFER:0000186 ! laboratory bioreactor scale

[Term]
id: PREFER:0000086
name: minibioreactor scale
def: "A laboratory bioreactor scale that refers to small volume bioreactor systems designed for parallelized process development and experimentation, typically operated at working volumes in the range of approximately 10 milliliters to a few liters." []
comment: For instance, Ambr250 or Pioreactors fall within this category.
is_a: PREFER:0000186 ! laboratory bioreactor scale

[Term]
id: PREFER:0000087
name: substrate uptake rate variable
namespace: precision_fermentation
def: "A bioproduction rate metric that represents the rate at which substrate is taken up by the cells, in a bioreactor or fermentation system during a fermentation process." []
synonym: "QS variable" EXACT OMO:0003012 []
is_a: PREFER:0000159 ! bioproduction rate metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000088
name: batch phase
def: "A fermentation phase that is a time interval of a batch fermentation process." []
is_a: PREFER:0000016 ! fermentation phase

[Term]
id: PREFER:0000089
name: specific substrate uptake rate variable
namespace: precision_fermentation
def: "A bioproduction rate metric that represents the rate of substrate uptake per unit of biomass, in a bioreactor or fermentation system during a fermentation process." []
is_a: PREFER:0000159 ! bioproduction rate metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000090
name: feed phase
def: "A fermentation phase that is a time interval within a fermentation process, where feed medium injection is observed." []
is_a: PREFER:0000016 ! fermentation phase

[Term]
id: PREFER:0000091
name: process titer metric
def: "A key process metric that represents a quantitative metric of the final concentration of the product or biomass in a fermentation process." []
synonym: "key precision fermentation process titer metric" EXACT []
is_a: PREFER:0000078 ! key process metric

[Term]
id: PREFER:0000094
name: substrate yield (biomass) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of a compound consumed (substrate) per biomass (X), quantifying how efficiently substrate compound is consumed relative to biomass produced in a bioreactor or fermentation system, during a fermentation process." []
synonym: "substrate yield (X) variable" EXACT []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000095
name: growth phase
def: "A fermentation phase that is a time interval within a fermentation process, where culture growth is observed." []
is_a: PREFER:0000016 ! fermentation phase

[Term]
id: PREFER:0000096
name: production phase
def: "A fermentation phase that is a time interval within a fermentation process, where product formation is observed." []
is_a: PREFER:0000016 ! fermentation phase

[Term]
id: PREFER:0000101
name: oxygen production rate variable
namespace: precision_fermentation
def: "A bioproduction rate metric that represents the rate of oxygen consumed over time, in a bioreactor or fermentation system during a fermentation process." []
synonym: "o2 Q variable" EXACT OMO:0003012 []
synonym: "oxygen bioproduction rate variable" EXACT []
synonym: "oxygen volumetric rate variable" EXACT []
is_a: PREFER:0000159 ! bioproduction rate metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000103
name: specific oxygen uptake rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the specific rate at which oxygen is consumed in a bioreactor or fermentation system during a fermentation process, normalized per unit of biomass (X), reflecting how efficiently oxygen is consumed in relation to biomass production." []
synonym: "precision fermentation process specific oxygen uptake rate measurement variable" EXACT []
synonym: "specific OUR measurement variable" EXACT OMO:0003012 []
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:7000001 ! mole per carbon mole per hour

[Term]
id: PREFER:0000104
name: oxygen yield (substrate) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of oxygen consumed per substrate (S) consumed, describing how much oxygen is consumed relative to the substrate used in a bioreactor or fermentation system, during a fermentation process." []
synonym: "o2 yield (S) variable" EXACT []
synonym: "oxygen yield (S) variable" EXACT []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000105
name: seed culture
def: "A fermentation culture role that serves as the inoculum for initiating or scaling up another fermentation culture." []
synonym: "fermentation starter" NARROW [ENVO:03600040]
synonym: "inoculum culture" EXACT []
synonym: "pre-culture" EXACT []
synonym: "starter culture" EXACT []
is_a: PREFER:0000200 ! fermentation culture role

[Term]
id: PREFER:0000106
name: oxygen yield (biomass) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of oxygen consumed per biomass (X), describing how much oxygen is consumed relative to the amount of biomass generated in a bioreactor or fermentation system, during a fermentation process." []
synonym: "o2 yield (X) variable" EXACT []
synonym: "oxygen yield (X) variable" EXACT []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:7000000 ! mole per carbon mole

[Term]
id: PREFER:0000107
name: compound formed variable
namespace: precision_fermentation
def: "A compound balance metric that represents the total amount of compound produced or formed in a bioreactor or fermentation system, representing the cumulative production of the compound during the fermentation process." []
synonym: "compound formed calculated variable" EXACT []
synonym: "compound produced calculated variable" EXACT []
synonym: "compound produced variable" EXACT []
is_a: PREFER:0000162 ! compound balance metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000108
name: fermentation medium role
def: "A role that inheres in a fermentation medium and that involves the medium supporting the growth of a fermentation culture by providing nutrients, physicochemical conditions, or specific additives." []
synonym: "cultivation medium role" EXACT []
is_a: BFO:0000023 ! role

[Term]
id: PREFER:0000109
name: batch medium
def: "A fermentation medium role that, when realized, involves supporting a batch fermentation process in which all nutrients are provided at the start of the process." []
synonym: "BM" EXACT OMO:0003012 []
is_a: PREFER:0000108 ! fermentation medium role

[Term]
id: PREFER:0000110
name: feed medium
def: "A fermentation medium role that, when realized, involves supporting a fed-batch fermentation process by providing nutrients or substrates in a rate based on the feed profile type (e.g. constant, exponential,etc)." []
synonym: "FM" EXACT OMO:0003012 []
is_a: PREFER:0000108 ! fermentation medium role

[Term]
id: PREFER:0000111
name: residual compound amount variable
namespace: precision_fermentation
def: "A compound balance metric that represents the remaining amount of compound left in a bioreactor or fermentation system during a fermentation process." []
comment: It is calculated substracting the compound concentration measured offline, multiplied by the liquid volume downscaled to get the residual amount.
synonym: "residual compound amount calculated variable" EXACT []
is_a: PREFER:0000162 ! compound balance metric
relationship: BAO_0002874 uom:g ! gram

[Term]
id: PREFER:0000112
name: seed medium
def: "A fermentation medium role that, when realized, involves supporting the growth and propagation of a seed culture used to inoculate to the production culture(main experimental culture)." []
synonym: "SM" EXACT OMO:0003012 []
synonym: "starter medium" EXACT []
is_a: PREFER:0000108 ! fermentation medium role

[Term]
id: PREFER:0000113
name: compound production rate variable
namespace: precision_fermentation
def: "A bioproduction rate metric that represents the rate of compound produced over time, in a bioreactor or fermentation system during a fermentation process." []
synonym: "compound formation rate variable" RELATED []
synonym: "Qcompound" EXACT OMO:0003012 []
is_a: PREFER:0000159 ! bioproduction rate metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000114
name: inlet air oxygen setpoint control variable
def: "A precision fermentation process dissolved oxygen control variable indicates the target percentage of oxygen value to be regulated and maintained in the gas mixture that is being supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process inlet air oxygen setpoint control variable" EXACT []
is_a: PREFER:0000119 ! dissolved oxygen control variable

[Term]
id: PREFER:0000115
name: specific compound production rate variable
namespace: precision_fermentation
def: "A bioproduction rate metric that represents the rate of compound produced per unit of biomass, in a bioreactor or fermentation system during a fermentation process, providing the efficiency of compound production relative to biomass." []
synonym: "specific compound bioproduction rate variable" EXACT []
synonym: "specific compound formation rate variable" EXACT []
is_a: PREFER:0000159 ! bioproduction rate metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000116
name: inlet air carbon dioxide setpoint control variable
def: "A precision fermentation process dissolved oxygen control variable that indicates the target percentage of carbon dioxide value to be regulated and maintained in the gas mixture that is being supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process inlet air carbon dioxide setpoint control variable" EXACT []
is_a: PREFER:0000119 ! dissolved oxygen control variable

[Term]
id: PREFER:0000117
name: compound produced yield (substrate) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of a compound produced per substrate (S) consumed, quantifying how efficiently compound is produced relative to substrate consumption in a bioreactor or fermentation system, during a fermentation process." []
synonym: "compound yield (S) variable" EXACT []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000118
name: optical density control variable
def: "A precision fermentation process control variable that represents the target optical density value to be regulated and or maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "OD control setpoint" EXACT []
synonym: "OD setpoint" EXACT []
synonym: "optical density control setpoint" EXACT []
synonym: "optical density setpoint" EXACT []
synonym: "precision fermentation process optical density control variable" EXACT []
synonym: "target OD" EXACT []
synonym: "target optical density" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000045 ! optical density cultivation condition
is_a: PREFER:9000000 ! precision fermentation process control variable
relationship: BAO_0002874 PREFER:7000006 ! unit of optical density
relationship: PREFER:8000020 PREFER:0000060 ! setpoint of optical density measurement variable

[Term]
id: PREFER:0000119
name: dissolved oxygen control variable
def: "A precision fermentation process control variable that represents the dissolved oxygen control variables of a bioreactor or fermentation system during a fermentation process." []
synonym: "DO process control variable" EXACT []
synonym: "precision fermentation process dissolved oxygen control variable" EXACT []
is_a: PREFER:0000033 ! dissolved oxygen cultivation condition
is_a: PREFER:9000000 ! precision fermentation process control variable

[Term]
id: PREFER:0000120
name: compound produced yield (biomass) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of a compound produced per biomass (X), quantifying how efficiently compound is produced relative to biomass generation in a bioreactor or fermentation system, during a fermentation process." []
synonym: "compound produced yield (X) variable" EXACT []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000121
name: pressure setpoint control variable
def: "A precision fermentation process control variable that represents the target pressure value to be regulated and maintained within a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process pressure setpoint control variable" EXACT []
synonym: "pressure control setpoint" EXACT []
synonym: "pressure reference point" EXACT []
synonym: "pressure reference value" EXACT []
synonym: "pressure setpoint" EXACT []
synonym: "target pressure" EXACT []
synonym: "target pressure value" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:0000029 ! pressure cultivation condition
is_a: PREFER:9000000 ! precision fermentation process control variable
relationship: BAO_0002874 PREFER:9000004 ! unit
relationship: PREFER:8000020 PREFER:0000042 ! setpoint of pressure measurement variable

[Term]
id: PREFER:0000122
name: volumetric feed rate control variable
def: "A process control variable that represents the target rate at which the feed (based on its volume) is added to a bioreactor or fermentation system during a fermentation process." []
is_a: PREFER:0000009 ! feed control variable
is_a: PREFER:0000015 ! operational parameter
relationship: BAO_0002874 uom:L.h-1 ! liters per hour
relationship: PREFER:8000020 PREFER:0000053 ! setpoint of volumetric feed rate measurement variable

[Term]
id: PREFER:0000128
name: carbon dioxide production rate variable
namespace: precision_fermentation
def: "A bioproduction rate metric that represents the rate of carbon dioxide produced over time, in a bioreactor or fermentation system during a fermentation process." []
synonym: "carbon dioxide bioproduction rate variable" EXACT []
synonym: "co2 Q variable" EXACT OMO:0003012 []
is_a: PREFER:0000159 ! bioproduction rate metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000129
name: inlet air nitrogen setpoint control variable
def: "A precision fermentation process dissolved oxygen control variable that indicates the target percentage of nitrogen value to be regulated and maintained in the gas mixture that is being supplied to a bioreactor or fermentation system during a fermentation process." []
synonym: "precision fermentation process inlet air nitrogen setpoint control variable" EXACT []
is_a: PREFER:0000119 ! dissolved oxygen control variable

[Term]
id: PREFER:0000130
name: specific carbon dioxide evolution rate measurement variable
namespace: precision_fermentation
def: "A precision fermentation process measurement variable that indicates the specific rate at which carbon dioxide is produced in a bioreactor or fermentation system during a fermentation process, normalized per unit of biomass (X) allowing metabolic efficiency comparisions between production strains." []
synonym: "precision fermentation process specific carbon dioxide evolution rate measurement variable" EXACT []
synonym: "specific CER measurement variable" EXACT OMO:0003012 []
synonym: "specific co2 evolution rate measurement variable" EXACT []
is_a: PREFER:9000001 ! precision fermentation process measurement variable
relationship: BAO_0002874 PREFER:7000001 ! mole per carbon mole per hour

[Term]
id: PREFER:0000131
name: carbon dioxide yield (substrate) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of carbon dioxide produced per substrate consumed (S), describing how much carbon dioxide is produced relative to the amount of substrate consumed in a bioreactor or fermentation system, during a fermentation process." []
synonym: "carbon dioxide yield (S) variable" EXACT []
synonym: "co2 yield (S) variable" EXACT OMO:0003012 []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000133
name: carbon dioxide yield (biomass) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of carbon dioxide produced per biomass (X), describing how much carbon dioxide is produced relative to the amount of biomass generated in a bioreactor or fermentation system, during a fermentation process." []
synonym: "carbo dioxide yield (X) variable" EXACT []
synonym: "co2 yield (X) variable" EXACT OMO:0003012 []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:7000000 ! mole per carbon mole

[Term]
id: PREFER:0000134
name: biomass amount variable
namespace: precision_fermentation
def: "A biomass balance metric that represents the absolute quantity of cellular biomass present in a bioreactor or fermentation system, at a certain time point, during a fermentation process." []
synonym: "biomass amount calculated variable" EXACT []
is_a: PREFER:0000161 ! biomass balance metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000135
name: genomics sample calculated variable
def: "An omics sample calculated variable that represents genomic values derived from computational analysis using DNA sequence data from an offline sample associated with a fermentation process." []
is_a: PREFER:0000209 ! omics sample calculated variable

[Term]
id: PREFER:0000136
name: biomass lost in sampling variable
namespace: precision_fermentation
def: "A biomass balance metric that represents the amount of biomass removed from a bioreactor or fermentation system, at a certain sampling time point, during a fermentation process." []
synonym: "biomass lost in sampling calculated variable" EXACT []
is_a: PREFER:0000161 ! biomass balance metric
relationship: BAO_0002874 uom:g ! gram

[Term]
id: PREFER:0000137
name: biomass formed variable
namespace: precision_fermentation
def: "A biomass balance metric that represents the cumulative quantity of cellular biomass generated in a bioreactor or fermentation system, during a fermentation process." []
synonym: "biomass formed calculated variable" EXACT []
synonym: "biomass production calculated variable" EXACT []
synonym: "biomass production variable" EXACT []
is_a: PREFER:0000161 ! biomass balance metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000138
name: transcriptomics sample calculated variable
def: "An omics sample calculated variable that represents transcript features derived from computational analysis using transcriptomics data from an offline sample associated with a process." []
is_a: PREFER:0000209 ! omics sample calculated variable

[Term]
id: PREFER:0000139
name: proteomics sample calculated variable
def: "An omics sample calculated variable that represents protein features derived from computational analysis using proteomic data from an offline sample associated with a fermentation process." []
is_a: PREFER:0000209 ! omics sample calculated variable

[Term]
id: PREFER:0000140
name: biomass formation rate variable
namespace: precision_fermentation
def: "A growth rate metric that represents the rate at which the biomass is formed over time in a bioreactor or fermentation system during a fermentation process." []
synonym: "biomass production rate variable" EXACT []
synonym: "Rx variable" EXACT OMO:0003012 []
is_a: PREFER:0000160 ! growth rate metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000141
name: fluxomics sample calculated variable
def: "An omics sample calculated variable that represents metabolic flux values derived from computational analysis using experimental data from an offline sample associated with a fermentation process." []
is_a: PREFER:0000209 ! omics sample calculated variable

[Term]
id: PREFER:0000142
name: specific biomass formation rate variable
namespace: precision_fermentation
def: "A growth rate metric that represents the rate of increase of biomass per unit of exisitng biomass, typically expressed as the fractional increase in biomass concentration per unit time, in a bioreactor or fermentation system during a fermentation process." []
synonym: "growth rate variable" EXACT []
synonym: "specific biomass production rate variable" EXACT []
synonym: "μ variable" EXACT OMO:0003012 []
is_a: PREFER:0000160 ! growth rate metric
relationship: BAO_0002874 uom:h-1 ! per hour (h⁻¹ or 1/h)

[Term]
id: PREFER:0000147
name: biomass yield (substrate) variable
namespace: precision_fermentation
def: "A process yield metric that represents the yield of biomass produced per substrate consumed, describing the efficiency of substrate conversion into biomass in a bioreactor or fermentation system, during a fermentation process." []
synonym: "biomass yield (S) variable" EXACT []
synonym: "Ysx variable" EXACT OMO:0003012 []
is_a: PREFER:0000155 ! process yield metric
relationship: BAO_0002874 PREFER:9000004 ! unit

[Term]
id: PREFER:0000148
name: metabolomics sample calculated variable
def: "An omics sample calculated variable that represents metabolite features derived from computational analysis using metabolomic data from an offline sample associated with a fermentation process." []
is_a: PREFER:0000209 ! omics sample calculated variable

[Term]
id: PREFER:0000149
name: metagenomics sample calculated variable
def: "A genomics sample calculated variable that represents metagenomic features derived from computational analysis using DNA sequence data from an offline sample associated with a fermentation process." []
is_a: PREFER:0000135 ! genomics sample calculated variable

[Term]
id: PREFER:0000150
name: data acquisition quality
namespace: precision_fermentation
def: "A quality that inheres in data or samples and specifies how, where, and when measurements are obtained in a bioreactor or fermentation system during the process." []
is_a: BFO:0000019 ! quality

[Term]
id: PREFER:0000151
name: inline data acquisition
namespace: precision_fermentation
def: "A data acquisition quality in which the analyzer or sensor is physically integrated into the bioreactor or process stream, allowing continuous measurement without removal of samples, typically providing high-frequency or real-time data for process monitoring and control." []
is_a: PREFER:0000150 ! data acquisition quality

[Term]
id: PREFER:0000152
name: online data acquisition
namespace: precision_fermentation
def: "A data acquisition quality in which samples are automatically withdrawn from the bioreactor or process stream and introduced into a measurement zone, with measurement results made available in near real time for monitoring and control. The analyzed sample may be discarded or returned to the process." []
is_a: PREFER:0000150 ! data acquisition quality

[Term]
id: PREFER:0000153
name: atline data acquisition
namespace: precision_fermentation
def: "A data acquisition quality in which samples are withdrawn from the process stream and transported a short distance to a nearby analytical device for measurement, involving a short delay between sampling and data availability. The analyzed sample is discarded and not returned to the process." []
synonym: "at-line data acquisition" EXACT []
is_a: PREFER:0000150 ! data acquisition quality

[Term]
id: PREFER:0000154
name: offline data acquisition
namespace: precision_fermentation
def: "A data acquisition quality in which samples are collected from the process and transported to an external laboratory or analysis location for measurement, with the sample not returned to the process line and with a significant delay between sampling and data availability." []
is_a: PREFER:0000150 ! data acquisition quality

[Term]
id: PREFER:0000155
name: process yield metric
namespace: precision_fermentation
def: "A key process metric that represents a quantitative metric, tipically expressed as yield coefficients, that quantify the efficiency of converting inputs(e.g. substrates) into desired outputs(e.g. products), expressed as the ratio of output formed per unit of substrate or biomass consumed." []
synonym: "key precision fermentation process yield metric" EXACT []
is_a: PREFER:0000078 ! key process metric

[Term]
id: PREFER:0000157
name: carbon balance metric
def: "A core balance metric that represents a quantitative metric derived from carbon balance calculations over a process, used to characterize the carbon flow within a bioreactor or fermenter system during the fermentation process." []
is_a: PREFER:0000023 ! core balance metric

[Term]
id: PREFER:0000158
name: respiratory rate metric
namespace: precision_fermentation
def: "A process rate metric variable that represents a rate describing respiratory activity of a production culture in a bioreactor or fermentation system during a fermentation process." []
synonym: "gas exchange metric" EXACT []
synonym: "metabolic metric" EXACT []
is_a: PREFER:0000000 ! process rate metric

[Term]
id: PREFER:0000159
name: bioproduction rate metric
namespace: precision_fermentation
def: "A process rate metric that represents a rate describing substrate consumptions, compound production (e.g. product formation) and biomass production in a bioreactor or fermentation system during a fermentation process." []
is_a: PREFER:0000000 ! process rate metric

[Term]
id: PREFER:0000160
name: growth rate metric
namespace: precision_fermentation
def: "A process rate metric that represents a rate describing biomass formation or growth in a bioreactor or fermentation system during a fermentation process." []
is_a: PREFER:0000000 ! process rate metric

[Term]
id: PREFER:0000161
name: biomass balance metric
def: "A core balance metric that represents a quantitative metric derived from biomass balance calculations over a process, used to characterize the balance of biomass output within a bioreactor or fermenter system during the fermentation fermentation process." []
is_a: PREFER:0000023 ! core balance metric

[Term]
id: PREFER:0000162
name: compound balance metric
def: "A core balance metric that represents a quantitative metric derived from compound balance calculations over a process, used to characterize the compound balabce within a bioreactor or fermenter system during the fermentation process." []
is_a: PREFER:0000023 ! core balance metric

[Term]
id: PREFER:0000180
name: operation mode control variable
namespace: precision_fermentation
def: "A precision fermentation process control variable that defines the operating stategy of a bioreactor or fermentation system, specifying how substrate, products and biomass are introduced, maintained, and removed during a fermentation process." []
synonym: "fermentation cultivation mode control variable" EXACT []
synonym: "operational mode control variable" BROAD []
synonym: "precision fermenation process feed control variable" EXACT []
is_a: PREFER:0000015 ! operational parameter
is_a: PREFER:9000000 ! precision fermentation process control variable

[Term]
id: PREFER:0000181
name: batch operation mode
namespace: precision_fermentation
def: "An operation mode control variable in which all required medium components and the inoculum are supplied at the start of the fermentation process, with no subsequent addition of medium components during operation, and in which products are harvested only at the end of the fermentation process." []
synonym: "batch bioprocess mode" EXACT []
synonym: "batch cell culture" RELATED [MSIO:0000181]
synonym: "batch cultivation" BROAD [PMID: 38806369]
synonym: "batch mode" BROAD []
is_a: PREFER:0000180 ! operation mode control variable

[Term]
id: PREFER:0000182
name: fed-batch operation mode
namespace: precision_fermentation
def: "An operation mode control variable in which additional nutrients, through feed medium, are intermittently or continuously supplied to the bioreactor or fermentar system during a fermentation process, without removal of production culture fluid, until termination of the fermentation process." []
synonym: "fed-batch cultivation" BROAD []
synonym: "fed-batch fermentation mode" EXACT []
synonym: "fed-batch mode" BROAD []
is_a: PREFER:0000180 ! operation mode control variable

[Term]
id: PREFER:0000183
name: continuous operation mode-chemostat
namespace: precision_fermentation
def: "An operation mode control variable in which fresh fermentation medium is supplied and fermentation culture fluid removed at a constant rate, such that the specific growth rate of the biomass is controlled by the limiting nutrient concentration and equals the dilution rate." []
synonym: "continuous fermentation mode, chemostat" EXACT []
synonym: "continuous mode, chemostat" BROAD []
is_a: PREFER:0000180 ! operation mode control variable

[Term]
id: PREFER:0000184
name: continuous operation mode-turbidostat
namespace: precision_fermentation
def: "An operation mode control variable in which fresh fermentation medium is supplied and fermentation culture fluid removed in response to feedback control, such that the biomass concentration is maintained constant at a predefined turbidity or optical density." []
synonym: "continuous fermentation mode, turbidostat" EXACT []
synonym: "continuous mode, turbidostat" BROAD []
is_a: PREFER:0000180 ! operation mode control variable

[Term]
id: PREFER:0000185
name: bioreactor scale
namespace: precision_fermentation
def: "A quality that inheres in a bioreactor and that characterizes its working volume, and used to classify bioreactors based on their intended application, ranging from laboratory research to industrial production." []
is_a: BFO:0000019 ! quality

[Term]
id: PREFER:0000186
name: laboratory bioreactor scale
namespace: precision_fermentation
def: "A bioreactor scale that refers to small volume bioreactor systems used for laboratory scale experimentation, research, development, and process optimization, typically ranging from a few milliliters to several liters in working volume." []
synonym: "bench bioreactor scale" EXACT []
synonym: "bench scale" EXACT []
synonym: "benchtop bioreactor scale" EXACT []
synonym: "benchtop scale" EXACT []
synonym: "lab bioreactor scale" EXACT []
synonym: "lab-scale" EXACT []
synonym: "laboratory scale" EXACT []
is_a: PREFER:0000185 ! bioreactor scale

[Term]
id: PREFER:0000187
name: pilot bioreactor scale
namespace: precision_fermentation
def: "A bioreactor scale that serves as an intermediate step between laboratory scale and industrial scale, typically ranging from several liters to a few hundred liters in working volume." []
synonym: "pilont plant bioreactor scale" EXACT []
synonym: "pilot-scale" EXACT []
synonym: "pre pilot plant-scale" EXACT []
synonym: "pre pilot-scale" EXACT []
synonym: "pre-pilot plant bioreactor scale" NARROW []
is_a: PREFER:0000185 ! bioreactor scale

[Term]
id: PREFER:0000188
name: industrial bioreactor scale
namespace: precision_fermentation
def: "A bioreactor scale used for large-scale production, typically ranging from several hundred liters to thousands of liters or more in working volume." []
synonym: "industrial scale" EXACT []
synonym: "industrial-scale" EXACT []
is_a: PREFER:0000185 ! bioreactor scale

[Term]
id: PREFER:0000189
name: feed profile type control variable
namespace: precision_fermentation
def: "The feeding strategies typically found in a fed-batch or continuous fermentation types." []
comment: The type of feeding profiles applied is process specific.
synonym: "feed profile type" EXACT []
synonym: "feeding profile" EXACT []
synonym: "feeding strategy" EXACT []
is_a: PREFER:0000009 ! feed control variable
is_a: PREFER:0000015 ! operational parameter

[Term]
id: PREFER:0000190
name: constant feeding rate
namespace: precision_fermentation
def: "A feed profile type control variable in which the feed rate is maintained at a constant value throughout the feeding phase." []
is_a: PREFER:0000189 ! feed profile type control variable

[Term]
id: PREFER:0000191
name: linear feeding rate
namespace: precision_fermentation
def: "A feed profile type control variable in which the feed rate changes linearly with time throughout the feeding phase." []
is_a: PREFER:0000189 ! feed profile type control variable

[Term]
id: PREFER:0000192
name: exponential feeding rate
namespace: precision_fermentation
def: "A feed profile type control variable in which the feed rate increases exponentially with time throughout the feeding phase." []
is_a: PREFER:0000189 ! feed profile type control variable

[Term]
id: PREFER:0000193
name: constant-linear feeding rate
namespace: precision_fermentation
def: "A feed profile type control variable in which the feed rate begins at a constant rate and subsequently transitions to a linearly changing feed rate with time throughout the feeding phase." []
is_a: PREFER:0000189 ! feed profile type control variable

[Term]
id: PREFER:0000194
name: constant-exponential feeding rate
namespace: precision_fermentation
def: "A feed profile type control variable in which the feed rate begins at a constant rate and subsequently transitions to a exponentially increasing feed rate with time throughout the feeding phase." []
is_a: PREFER:0000189 ! feed profile type control variable

[Term]
id: PREFER:0000195
name: exponential-linear feeding rate
namespace: precision_fermentation
def: "A feed profile type control variable in which the feed rate begins with an exponentially increasing rate and subsequently transitions to a linearly changing feed rate with time throughout the feeding phase." []
is_a: PREFER:0000189 ! feed profile type control variable

[Term]
id: PREFER:0000200
name: fermentation culture role
namespace: precision_fermentation
def: "A role that inheres in a fermentation culture and that involves the culture participating in, enabling or initiating a fermentation process." []
is_a: BFO:0000023 ! role

[Term]
id: PREFER:0000203
name: production culture
namespace: precision_fermentation
def: "A fermentation culture role that is involved in carrying out the main fermentation process to generate the desired product or cell biomass." []
synonym: "main culture" EXACT []
is_a: PREFER:0000200 ! fermentation culture role

[Term]
id: PREFER:0000204
name: unpublished strain
namespace: precision_fermentation
def: "An isolate or group of isolates that have not been published (it is not available in deposits or collections nor do you know the strain history) and hence do not yet have a universal identifier." []
comment: Unpublished strain is a quality used to tag strains that do not yet have a universal identifier. If or when they get published, this tag should be removed. All strains should still be under taxon. Strain and subtype are often used interchangeably, although the term strain is often used to describe a set of isolates with common biochemical and/or physiological characteristics, while the term subtype is often used to describe a set of isolates with common genetic or molecular characteristics. {xref="doi:10.1093/jaoac/85.2.524"}
is_a: BFO:0000019 ! quality

[Term]
id: PREFER:0000205
name: cell culture
namespace: precision_fermentation
def: "A material entity consisting of prokaryotic or eukaryotic living cells, whether unicellular or multicellular, that are maintaned, cultivated, or propagated under controlled environmental conditions." []
xref: ENVO:02000008
xref: OBI:0001876
is_a: BFO:0000040 ! material entity
relationship: BFO:0000051 CL:0000000 ! has part cell

[Term]
id: PREFER:0000206
name: microbial culture
namespace: precision_fermentation
def: "A material entity consisting of microorganisms-unicellular microbial cell cultures- either prokaryotic (such as bacteria, archaea, or cyanobactreia) or eukaryotic (such as yeast, microalgae and protozoa), that are maintaned, cultivated, or propagated under controlled environmental conditions." []
synonym: "microbiological culture" EXACT []
is_a: BFO:0000040 ! material entity
relationship: BFO:0000051 CL:0000000 ! has part cell
property_value: oboInOwl:synoymn "microbial cell culture" xsd:string

[Term]
id: PREFER:0000207
name: tissue culture
namespace: precision_fermentation
def: "A material entity consisting of multicellular tissue, such as plant tissue cultures, animal cell-derived tissue cultures (including mammalian), or cultures of filamentous fungi, that is maintaned, cultivated, or propagated under controlled environmental conditions." []
is_a: BFO:0000040 ! material entity
relationship: BFO:0000051 CL:0000000 ! has part cell

[Term]
id: PREFER:0000209
name: omics sample calculated variable
def: "A precision fermentation process calculated variable that represents a set of values derived from computational analysis or omics data procesing from an offline sample associated with a fermentation process." []
synonym: "calculated omics offline sample variable" EXACT []
synonym: "computed omics offline sample variable" EXACT []
synonym: "computed omics sample variable" EXACT []
is_a: PREFER:9000002 ! precision fermentation process calculated variable

[Term]
id: PREFER:7000000
name: mole per carbon mole
namespace: precision_fermentation
def: "A unit representing a mol-based ratio, typically used to express product, output substance or input - such as compound and substrate -  in moles per carbon mole of biomass(X) generated or substrate(S) consumed (mol/cmol)." []
synonym: "mol/c-mol" EXACT []
synonym: "mol/cmol" EXACT []
synonym: "mole per carbon mole" RELATED []
is_a: PREFER:9000004 ! unit
relationship: PREFER:8000021 PREFER:7000002 ! has denominator unit carbon mole
relationship: PREFER:8000022 uom:mol ! has numerator unit mole

[Term]
id: PREFER:7000001
name: mole per carbon mole per hour
namespace: precision_fermentation
def: "A unit representing a compound rate, expressed as moles per carbon mole(X) per hour ((mol/cmol)/h)." []
synonym: "(mol/c-mol)/h" EXACT []
synonym: "(mol/cmol)/h" EXACT []
synonym: "mole per carbon mole per hour" RELATED []
is_a: PREFER:9000004 ! unit
relationship: PREFER:8000021 uom:h ! has denominator unit hour
relationship: PREFER:8000022 PREFER:7000000 ! has numerator unit mole per carbon mole

[Term]
id: PREFER:7000002
name: carbon mole
namespace: precision_fermentation
def: "Semantically equivalent in magnitude to the SI mole (1 C-mol = 1 mol) but used to indicate mole of carbon atoms (cmol)." []
synonym: "C-mol" EXACT []
synonym: "carbon mole" RELATED []
synonym: "cmol" EXACT []
synonym: "mole of carbon atoms" EXACT []
is_a: PREFER:9000004 ! unit

[Term]
id: PREFER:7000003
name: carbon mole per gram
namespace: precision_fermentation
def: "A unit representing a carbon-based ratio, typically used to express product or output substance - such as biomass or compound - in carbon moles per gram of initial material or input substrate consumed (cmol/g)." []
synonym: "c-mol/g" EXACT []
synonym: "carbon mole per gram" RELATED []
synonym: "cmol/g" EXACT []
is_a: PREFER:9000004 ! unit
relationship: PREFER:8000021 uom:g ! has denominator unit gram
relationship: PREFER:8000022 PREFER:7000002 ! has numerator unit carbon mole

[Term]
id: PREFER:7000004
name: carbon mole per carbon mole
namespace: precision_fermentation
def: "A unit representing a carbon-based ratio, typically used to express product, output substance or input - such as biomass, compound and substrate -  in carbon moles per carbon mole of biomass generated, initial material consumed or input substrate consumed (cmol/cmol)." []
synonym: "c-mol/c-mol" EXACT []
synonym: "carbon mole per carbon mole" RELATED []
synonym: "cmol/cmol" EXACT []
is_a: PREFER:9000004 ! unit
relationship: PREFER:8000021 PREFER:7000002 ! has denominator unit carbon mole
relationship: PREFER:8000022 PREFER:7000002 ! has numerator unit carbon mole

[Term]
id: PREFER:7000005
name: carbon mole per hour
namespace: precision_fermentation
def: "A unit of mass flow rate representing a carbon mole of substance passing through a given surface or system in one hour (cmol/h)." []
synonym: "c-mol/h" EXACT []
synonym: "carbon mole per hour" RELATED []
synonym: "cmol/h" EXACT []
is_a: PREFER:9000004 ! unit
relationship: PREFER:8000021 uom:h ! has denominator unit hour
relationship: PREFER:8000022 PREFER:7000002 ! has numerator unit carbon mole

[Term]
id: PREFER:7000006
name: unit of optical density
is_a: PREFER:9000004 ! unit

[Term]
id: PREFER:7000007
name: dimensionless unit
is_a: PREFER:9000004 ! unit

[Term]
id: PREFER:7000008
name: revolution per minute
is_a: PREFER:9000004 ! unit

[Term]
id: PREFER:9000000
name: precision fermentation process control variable
def: "An information content entity that represents a parameter or setting about a system, which is realized as input or configuration in controlling or regulating a fermentation process, thereby affecting the behavior, operation, or outcome of that process." []
comment: A decision was made to classify this as a information content entity rather than realizable entity (a realizable entity that inheres in a system and is realized in processes of controlling or regulating a process, serving as a parameter or setting that affects or determines the behavior, operation, or outcome of that process) as the intention was to emphasize the informational role rather than physical realisation of the control.
is_a: IAO:0000030 ! information content entity
property_value: dc:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string

[Term]
id: PREFER:9000001
name: precision fermentation process measurement variable
def: "An information content entity about a precision fermentation process that specifically represents measurable attributes or values that are the outcomes of a measurement process aimed at determining characteristics of said process." []
synonym: "PREcision FERmentation process measurement variable" EXACT []
synonym: "process measurement variable" BROAD []
xref: VO:0010241
is_a: IAO:0000030 ! information content entity
property_value: dc:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string

[Term]
id: PREFER:9000002
name: precision fermentation process calculated variable
def: "An information content entity about a process that is the output of a calculation or computation based on one or more measured or other input variables, representing derived or computed attributes related to the fermentation process." []
synonym: "process calculated variable" EXACT []
synonym: "process computed variable" EXACT []
is_a: IAO:0000030 ! information content entity
property_value: dc:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string

[Term]
id: PREFER:9000003
name: precision fermentation process
def: "A process that involves precision fermentation." []
comment: Precision fermentation is a biotechnological method used in industrial or research settings that employs genetically engineered or adaptatively laboratory-evolved (ALE) microorganisms (such as bacteria, yeast, fungi or microalgae) to produce specific, high-value compounds with precise molecular structures. This process involves controlled environments—such as operating bioreactor parameters(e.g., temperature, pH, dissolved oxygen, agitation, nutrient feed) and upstream preparation conditions(e.g., pre-culture growth, strain storage, and defined media composition)—where microbial metabolism is optimized to synthesize target products, such as proteins, enzymes, or bioactive molecules, often with greater efficiency, yield, and specificity than traditional fermentation methods.
is_a: BFO:0000015 ! process
relationship: BAO_0002009 GO:0006113 ! fermentation

[Term]
id: PREFER:9000004
name: unit
def: "An information content entity that represents a standard quantity or measurement used to express the magnitude of a quantity." []
comment: The decision to utilise https://units-of-measurement.org/ meant that we did not want to commit to any unit ontologies. We hence created our own parent class to parent units. Interoperability of units can be achieved by the matches in units-of-measurement, and this term should only be used to constraining in modelling.
is_a: IAO:0000030 ! information content entity

[Term]
id: UBERON:0000061
name: anatomical structure
namespace: uberon
def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." []
synonym: "biological structure" EXACT []
synonym: "connected biological structure" EXACT []
xref: AAO:0010825
xref: AEO:0000003
xref: BILA:0000003
xref: CARO:0000003
xref: EHDAA2:0003003
xref: EMAPA:0
xref: FBbt:00007001
xref: FMA:305751
xref: FMA:67135
xref: GAID:781
xref: HAO:0000003
xref: http://dbpedia.org/ontology/AnatomicalStructure
xref: MA:0003000
xref: MESH:D000825
xref: SCTID:362889002
xref: TAO:0000037
xref: TGMA:0001823
xref: VHOG:0001759
xref: XAO:0003000
xref: ZFA:0000037
is_a: UBERON:0001062 ! anatomical entity

[Term]
id: UBERON:0001062
name: anatomical entity
namespace: uberon
def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." []
xref: AAO:0010841
xref: AEO:0000000
xref: BFO:0000004
xref: BILA:0000000
xref: BIRNLEX:6
xref: CARO:0000000
xref: EHDAA2:0002229
xref: FBbt:10000000
xref: FMA:62955
xref: HAO:0000000
xref: MA:0000001
xref: NCIT:C12219
xref: TAO:0100000
xref: TGMA:0001822
xref: UMLS:C1515976
xref: WBbt:0000100
xref: XAO:0000000
xref: ZFA:0100000
is_a: BAO_0003114 ! assay biology component

[Term]
id: oboInOwl:ObsoleteClass
name: Obsolete Class

[Term]
id: uom:%25
name: percent
is_a: PREFER:9000004 ! unit

[Term]
id: uom:%5BdegF%5D
name: degree Fahrenheit based unit
is_a: PREFER:9000004 ! unit

[Term]
id: uom:%5BpH%5D
name: pH based unit
is_a: PREFER:9000004 ! unit

[Term]
id: uom:Cel
name: degree Celsius
is_a: PREFER:9000004 ! unit

[Term]
id: uom:L
name: liter
is_a: PREFER:9000004 ! unit

[Term]
id: uom:L.h-1
name: liters per hour
def: "A volumetric flow rate unit which is equal to one liter volume through a given surface in one hour (L/h)." []
synonym: "L/h" EXACT []
synonym: "l/h" EXACT []
synonym: "Liters per Hour" EXACT []
synonym: "Litres per Hour" EXACT []
synonym: "litres per hour" EXACT []
is_a: PREFER:9000004 ! unit

[Term]
id: uom:L.min-1
name: liter per minute
def: "A volumetric flow rate unit which is equal to one liter volume through a given surface in a minute (L/min)." []
synonym: "L/min" EXACT [NCIT]
synonym: "l/min" EXACT [NCIT]
synonym: "Liter per Minute" EXACT [NCIT]
synonym: "Liter per minute" EXACT []
synonym: "Liter/Minute" EXACT [NCIT]
synonym: "liter/minute" EXACT [NCIT]
synonym: "Liters per Minute" EXACT []
synonym: "Liters per minute" EXACT []
synonym: "Litres per Minute" EXACT [NCIT]
synonym: "Litres per minute" EXACT []
synonym: "litres per minute" EXACT []
is_a: PREFER:9000004 ! unit

[Term]
id: uom:Pa
name: pascal
is_a: PREFER:9000004 ! unit

[Term]
id: uom:bar
name: bar
is_a: PREFER:9000004 ! unit

[Term]
id: uom:g
name: gram
is_a: PREFER:9000004 ! unit

[Term]
id: uom:g.L-1
name: gram per litre
is_a: PREFER:9000004 ! unit

[Term]
id: uom:g.g-1
name: gram per gram
def: "A unit representing a mass ratio, typically used to express product or output substance - such as biomass or compound -  in grams per gram of initial material, input substrate consumed(S), or biomass(X) generated(cell dry weight(CDW))(g/g)." []
synonym: "g/g" EXACT []
synonym: "Gram per Gram" EXACT []
is_a: PREFER:9000004 ! unit

[Term]
id: uom:g.g-1.h-1
name: gram per gram per hour
is_a: PREFER:9000004 ! unit

[Term]
id: uom:g.h-1
name: gram per hour
def: "A unit of mass flow rate representing one gram of substance passing through a given surface or system in one hour (g/h)." []
synonym: "g/h" EXACT []
is_a: PREFER:9000004 ! unit

[Term]
id: uom:h
name: hour
is_a: PREFER:9000004 ! unit

[Term]
id: uom:h-1
name: per hour (h⁻¹ or 1/h)
is_a: PREFER:9000004 ! unit

[Term]
id: uom:kg
name: kilogram
is_a: PREFER:9000004 ! unit

[Term]
id: uom:mL
name: milliliter
is_a: PREFER:9000004 ! unit

[Term]
id: uom:mg
name: milligram
is_a: PREFER:9000004 ! unit

[Term]
id: uom:mmol
name: millimole
is_a: PREFER:9000004 ! unit

[Term]
id: uom:mmol.h-1
name: millimole per hour
def: "A unit of mass flow rate represenitn one millimole of substance passing through a given surface or system in one hour (mmol/h)." []
synonym: "mmol/h" EXACT [NCIT]
is_a: PREFER:9000004 ! unit

[Term]
id: uom:mol
name: mole
is_a: PREFER:9000004 ! unit

[Term]
id: uom:mol.h-1
name: mole per hour
def: "A unit of mass flow rate represenitn one mole of substance passing through a given surface or system in one hour (mol/h)." []
synonym: "mol/h" EXACT [NCIT]
is_a: PREFER:9000004 ! unit

[Term]
id: uom:mol.mol-1
name: mole per mole
def: "A unit representing a mol-based ratio, typically used to express product, output substance or input - such as compound and substrate -  in moles per mole of substrate(S) consumed (mol/mol)." []
synonym: "mol/mol" EXACT [NCIT]
synonym: "Mole per Mole" EXACT [NCIT]
synonym: "Mole/Mole" EXACT [NCIT]
is_a: PREFER:9000004 ! unit

[Typedef]
id: BAO_0002009
name: involves biological process

[Typedef]
id: BAO_0002872
name: is unit of
inverse_of: BAO_0002874 ! has unit

[Typedef]
id: BAO_0002874
name: has unit

[Typedef]
id: BAO_0002922
name: has assay medium

[Typedef]
id: BFO:0000050
name: part of
def: "a core relation that holds between a part and its whole" []
is_transitive: true
is_a: RO:0002131 ! overlaps
inverse_of: BFO:0000051 ! has part

[Typedef]
id: BFO:0000051
name: has part
namespace: chebi_ontology
def: "a core relation that holds between a whole and its part" []
xref: BFO:0000051
is_transitive: true
is_a: RO:0002131 ! overlaps

[Typedef]
id: BFO:0000054
name: realized in
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
domain: BFO:0000017 ! realizable entity
range: BFO:0000015 ! process
inverse_of: BFO:0000055 ! realizes

[Typedef]
id: BFO:0000055
name: realizes
def: "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" []
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
domain: BFO:0000015 ! process
range: BFO:0000017 ! realizable entity

[Typedef]
id: IAO:0000136
name: is about
def: "A (currently) primitive relation that relates an information artifact to an entity." []
domain: IAO:0000030 ! information content entity

[Typedef]
id: OBI:0000124
name: is_supported_by_data
def: "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" []
domain: OBI:0001909 ! conclusion based on data
range: IAO:0000027 ! data item

[Typedef]
id: OBI:0000293
name: has specified input
def: "The inverse property of is specified input of" []
domain: COB:0000035
domain: OBI:0000011 ! obsolete planned process
is_a: RO:0000057 ! has participant
inverse_of: OBI:0000295 ! is specified input of

[Typedef]
id: OBI:0000295
name: is specified input of
def: "A relation between a completely executed 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." []
range: COB:0000035
is_a: RO:0000056 ! participates in

[Typedef]
id: OBI:0000299
name: has specified output
def: "The inverse property of is specified output of" []
domain: COB:0000035
domain: OBI:0000011 ! obsolete planned process
is_a: RO:0000057 ! has participant
inverse_of: OBI:0000312 ! is specified output of

[Typedef]
id: OBI:0000312
name: is specified output of
def: "A relation between a completely executed 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." []
range: COB:0000035
range: OBI:0000011 ! obsolete planned process
is_a: RO:0000056 ! participates in

[Typedef]
id: OBI:0000417
name: achieves_planned_objective
def: "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." []
domain: COB:0000035
range: IAO:0000005 ! objective specification
inverse_of: OBI:0000833 ! objective_achieved_by

[Typedef]
id: OBI:0000833
name: objective_achieved_by
def: "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." []
domain: IAO:0000005 ! objective specification
range: COB:0000035

[Typedef]
id: PREFER:8000000
name: has fermentation experiment
def: "inverse of is fermentation experiment of." []
is_transitive: true
is_a: BFO:0000051 ! has part
inverse_of: PREFER:8000001 ! is fermentation experiment of

[Typedef]
id: PREFER:8000001
name: is fermentation experiment of
def: "x is_fermentation_experiment_of y iff x is a fermentation experiment, y is a precision fermentation process, and x is part of y." []
domain: PREFER:0000003 ! fermentation experiment
range: PREFER:9000003 ! precision fermentation process
is_transitive: true
is_a: BFO:0000050 ! part of

[Typedef]
id: PREFER:8000002
name: is fermentation run of
def: "x is_fermentation_experiment_of y iff x is a fermentation run, y is a precision fermentation process, and x is part of y." []
domain: PREFER:0000004 ! fermentation run
range: PREFER:9000003 ! precision fermentation process
is_transitive: true
is_a: BFO:0000050 ! part of
inverse_of: PREFER:8000003 ! has fermentation run

[Typedef]
id: PREFER:8000003
name: has fermentation run
def: "inverse of is fermentation run of" []
is_transitive: true
is_a: BFO:0000051 ! has part

[Typedef]
id: PREFER:8000004
name: has medium ingredient
def: "inverse of is medium ingredient of" []
is_a: BFO:0000051 ! has part
inverse_of: PREFER:8000005 ! is medium ingredient of

[Typedef]
id: PREFER:8000005
name: is medium ingredient of
def: "x is_medium_ingredient_of y iff x is a chemical entity, y is a assay medium, and x is part of y." []
domain: CHEBI:24431 ! chemical entity
range: PREFER:0000011 ! fermentation medium
is_a: BFO:0000050 ! part of

[Typedef]
id: PREFER:8000006
name: uses bioreactor
def: "x uses bioreactor y iff x is a process, y is a bioreactor, and x is somewhat used or involved in y." []
domain: BFO:0000015 ! process
range: PREFER:0000014 ! bioreactor
is_a: RO:0000057 ! has participant
inverse_of: PREFER:8000007 ! bioreactor used in

[Typedef]
id: PREFER:8000007
name: bioreactor used in
def: "inverse of uses bioreactor" []
is_a: RO:0000056 ! participates in

[Typedef]
id: PREFER:8000008
name: has bioreactor scale
def: "x has_bioreactor_scale y iff x is a bioreactor and y is the scale that the bioreactor supports." []
domain: PREFER:0000014 ! bioreactor
range: PREFER:0000185 ! bioreactor scale
is_a: RO:0000086 ! has quality
inverse_of: PREFER:8000009 ! is bioreactor scale of

[Typedef]
id: PREFER:8000009
name: is bioreactor scale of
def: "inverse of has bioreactor scale." []
is_a: RO:0000080 ! quality of

[Typedef]
id: PREFER:8000010
name: has fermentation culture type
def: "x has fermentation culture type y iff x is a fermentation culture and y is the fermentation type of x." []
domain: PREFER:0000010 ! fermentation culture
range: PREFER:0000200 ! fermentation culture role
inverse_of: PREFER:8000014 ! is fermentation culture type of

[Typedef]
id: PREFER:8000011
name: has cultivation condition
def: "x has cultivation condition y iff x is a process and y is the condition of the cultivation in x." []
domain: BFO:0000015 ! process
range: PREFER:0000008 ! cultivation condition

[Typedef]
id: PREFER:8000012
name: has data acquisition quality
def: "x has data acquisition quality y iff x is data and y is the mode in which x is acquired." []
domain: IAO:0000030 ! information content entity
range: PREFER:0000150 ! data acquisition quality
is_a: RO:0000086 ! has quality

[Typedef]
id: PREFER:8000013
name: has feed profile type
def: "x has feed profile type y iff x is a feed and y is the type of feed profile used in x." []
domain: PREFER:0000037 ! feed medium cultivation condition
range: PREFER:0000189 ! feed profile type control variable

[Typedef]
id: PREFER:8000014
name: is fermentation culture type of
def: "inverse of has fermentation culture type" []
is_a: IAO:0000136 ! is about

[Typedef]
id: PREFER:8000015
name: cultures cell
def: "x cultures_cell y iff x is a process and y is a cell that x cultures." []
domain: BFO:0000015 ! process
range: CL:0000000 ! cell

[Typedef]
id: PREFER:8000016
name: has collected
def: "x has_collected y iff x is a process and y is a material that is collected as part of the process x." []
domain: BFO:0000015 ! process
range: BFO:0000040 ! material entity

[Typedef]
id: PREFER:8000017
name: has measured compound
def: "x has_measured_compound y iff x is a process and y is a chemical entity that is being or will be measured." []
domain: BFO:0000015 ! process
range: CHEBI:24431 ! chemical entity

[Typedef]
id: PREFER:8000018
name: has operational mode
def: "x has_operational_mode y iff x is a bioreactor and y is an operational mode in which the bioreactor is operating in." []

[Typedef]
id: PREFER:8000020
name: setpoint of
def: "x is setpoint_of y iff x and y are information content entities, and x is a specified numerical value or target parameter that defines the desired state or threshold that y is designed to regulate, maintain, or reference." []
domain: IAO:0000030 ! information content entity
range: IAO:0000030 ! information content entity
inverse_of: PREFER:8000030 ! has setpoint

[Typedef]
id: PREFER:8000021
name: has denominator unit
def: "x has_denominator_unit y iff x and y are units, and x is ratio unit where y is the denominator of it." []
comment: Not using RO:0020203 as range/domain does not fit with modelling.

[Typedef]
id: PREFER:8000022
name: has numerator unit
def: "x has_numerator_unit y iff x and y are units, and x is ratio unit where y is the numerator of it." []
comment: Not using RO:0020202 as range/domain does not fit with modelling.

[Typedef]
id: PREFER:8000030
name: has setpoint
def: "Inverse of setpoint of." []
domain: IAO:0000030 ! information content entity
range: IAO:0000030 ! information content entity

[Typedef]
id: RO:0000052
name: characteristic of
def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
is_functional: true
is_a: RO:0002314 ! characteristic of part of
inverse_of: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000053
name: has characteristic
def: "Inverse of characteristic_of" []
range: BFO:0000020 ! specifically dependent continuant
is_inverse_functional: true

[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
domain: BFO:0000002 ! continuant
range: BFO:0000003 ! occurrent
inverse_of: RO:0000057 ! has participant

[Typedef]
id: RO:0000057
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
xref: RO:0000057
domain: BFO:0000003 ! occurrent
range: BFO:0000002 ! continuant
holds_over_chain: BFO:0000051 RO:0000057

[Typedef]
id: RO:0000058
name: is concretized as
def: "A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes." []
domain: BFO:0000031 ! generically dependent continuant
range: BFO:0000020 ! specifically dependent continuant
inverse_of: RO:0000059 ! concretizes

[Typedef]
id: RO:0000059
name: concretizes
def: "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." []
domain: BFO:0000020 ! specifically dependent continuant
range: BFO:0000031 ! generically dependent continuant

[Typedef]
id: RO:0000079
name: function of
def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
domain: BFO:0000034 ! function
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000085 ! has function

[Typedef]
id: RO:0000080
name: quality of
def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000086 ! has quality

[Typedef]
id: RO:0000081
name: role of
def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000087 ! has role

[Typedef]
id: RO:0000085
name: has function
def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000034 ! function
is_a: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000086
name: has quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
range: BFO:0000019 ! quality
is_a: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000087
name: has role
namespace: chebi_ontology
def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" []
xref: RO:0000087
domain: BFO:0000004 ! independent continuant
range: BFO:0000023 ! role
is_a: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000091
name: has disposition
def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000016 ! disposition
is_a: RO:0000053 ! has characteristic
inverse_of: RO:0000092 ! disposition of

[Typedef]
id: RO:0000092
name: disposition of
def: "inverse of has disposition" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
is_a: RO:0000052 ! characteristic of

[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
holds_over_chain: BFO:0000050 BFO:0000050
holds_over_chain: BFO:0000051 RO:0002131
is_symmetric: true
is_a: RO:0002323 ! mereotopologically related to
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002162
name: in taxon
def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." []
comment: Connects a biological entity to its taxon of origin.
synonym: "life cycle stage of" NARROW []
range: COB:0000022
holds_over_chain: RO:0002131 RO:0002162
is_a: RO:0002320 ! evolutionarily related to

[Typedef]
id: RO:0002314
name: characteristic of part of
def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." []
is_a: RO:0002502 ! depends on
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002320
name: evolutionarily related to
def: "A relationship that holds via some environmental process" []

[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []

[Typedef]
id: RO:0002350
name: member of
def: "is member of is a mereological relation between a item and a collection." []
is_a: BFO:0000050 ! part of
inverse_of: RO:0002351 ! has member

[Typedef]
id: RO:0002351
name: has member
def: "has member is a mereological relation between a collection and an item." []
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002502
name: depends on

[Typedef]
id: RO:0010001
name: generically depends on
def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." []
synonym: "g-depends on" EXACT []
domain: BFO:0000031 ! generically dependent continuant
range: BFO:0000004 ! independent continuant
holds_over_chain: RO:0000052 RO:0000058
inverse_of: RO:0010002 ! is carrier of

[Typedef]
id: RO:0010002
name: is carrier of
def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000031 ! generically dependent continuant
holds_over_chain: RO:0000059 RO:0000053

[Typedef]
id: RO:0015012
name: reciprocal of
comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.

[Typedef]
id: RO:0020105
name: is anatomical entity
def: "This property only applies to anatomical entities." []
property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
domain: UBERON:0001062 ! anatomical entity