2024-08-11 Shubh Sharma Saurav Kumar Vikas Kumar Deepika Deepika Panče Panov Johannes Kruisselbrink The PBPK (Physiologically Based Pharmacokinetic) Ontology (PBPKO) describes PBPK models, parameters, compartments, and pharmacokinetic processes for pharmaceutical and environmental life-science applications. It is aligned with Basic Formal Ontology (BFO) and the Relation Ontology (RO), and integrates terms from OBO Foundry ontologies including GO, OBI, and IAO. 2026-07-15 PBPK Ontology PBPK Ontology 2026-07-15 editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative label definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 A URL for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . } never in taxon A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; owl:disjointWith [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . } mutually spatially disjoint with S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } present in taxon description Mark Miller license title has_synonym_type a core relation that holds between a part and its whole part of part of a core relation that holds between a whole and its part has part Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. preceded by x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about The inverse property of is specified input of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has specified input 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. Alan Ruttenberg PERSON:Bjoern Peters is specified input of The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has specified output 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. Alan Ruttenberg PERSON:Bjoern Peters is specified output of This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch achieves_planned_objective This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI objective_achieved_by inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple 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. inheres_in characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition disposition of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. has positive regulatory component activity has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component process directly regulated by directly negatively regulated by directly positively regulated by has effector activity ends after immediately preceded by immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y overlaps w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. capable of part of temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. has input c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. acts upstream of or within p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect 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. characteristic of part of A mereological relationship or a topological relationship mereotopologically related to c enables p iff c is capable of p and c acts to execute p. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. part of structure that is capable of c involved_in p if and only if c enables some process p', and p' is part of p involved in inverse of enables enabled by inverse of regulates regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by has member is a mereological relation between a collection and an item. has member inverse of has input input of inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly negatively regulates causally related to p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. interacts with http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly positively regulates activity of helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. causal relation between processes depends on causal relation between entities causally influenced by interaction relation helper property molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. causal relation between material entity and a process Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. enables subfunction acts upstream of or within, positive effect acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative acts upstream of, negative effect causally upstream of or within, negative effect causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. indirectly regulates X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. disposition the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril quality Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) specifically dependent continuant John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. role site The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. generically dependent continuant the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. function a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. material entity immaterial entity Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. Nuclear particle of charge number +1, spin ½ and rest mass of 1.007276470(12) u. proton A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. atomic nucleus A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. macromolecule A particle smaller than an atom. subatomic particle A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. atom A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. molecule A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. gross anatomical part A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome organism completely executed planned process A complex of two or more molecules that are not covalently bound. complex of molecules A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. planned process characteristic system process A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. gene product or complex activity molecular_function A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). cellular_component excretion A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological process biological_process metabolic process cellular process true kinase activity multicellular organismal process A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. protein-containing complex Any constituent part of a virion, a complete fully infectious extracellular virus particle. virion component A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. cellular anatomical entity A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. measurement unit label 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. objective specification 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 datum label Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. software data entity Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item data entity data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. directive information entity 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. dot plot 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. graph 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. algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file data format specification homogenous data collection Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert data set group:OBI homogenous data collection 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. image data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part 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. plan specification A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. histogram A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. heatmap A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. dendrogram 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. scatter plot obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. figure A collection of information content entities intended to be understood together as a whole document denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type data collection A data entity that consists of multiple data entities. Sebastian Duesing data set https://github.com/information-artifact-ontology/IAO/issues/283 https://github.com/obi-ontology/obi/issues/1877 data collection Euteleostomi Eukaryota Euarchontoglires Tetrapoda Amniota Opisthokonta Metazoa Bilateria Mammalia Vertebrata <vertebrates> Homo sapiens a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator role 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. GROUP: Role branch regulatory role a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. PERSON:Jennifer Fostel material supplier role 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. PERSON: James Malone PERSON: Monnie McGee classified data set 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. GROUP: Role Branch specimen role 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone organization A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. AR, BP, JM, MC, PRS plan A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch regulatory agency Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch manufacturer role 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. PERSON: James Malone PERSON: Monnie McGee clustered data set An information content entity representing the relationships between data items. Melanie Courtot data representational model A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. Bjoern Peters specimen collection process A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone class prediction data transformation A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. Bjoern Peters specimen collection objective 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. James Malone Ryan Brinkman support vector machine 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. James Malone decision tree induction objective A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone decision tree building data transformation a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson GenePattern software 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 James Malone Ryan Brinkman peak matching 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. James Malone k-nearest neighbors A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone CART A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson statistical model validation A person or organization that has a manufacturer role. manufacturer 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 PERSON:Helen Parkinson service provider role A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters categorical label 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. PERSON: Jessica Turner questionnaire A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl cell specimen 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). PERSON: Chris Stoeckert, Jie Zheng specimen from organism A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification An information content entity that specifies a value within a classification scheme or on a quantitative scale. PERSON:Bjoern Peters value specification A material entity that has two or more specimens as its parts. Person: Chris Stoeckert, Jie Zheng collection of specimens 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. Chris Stoeckert, Helena Ellis histologic grade according to AJCC 7th edition A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis histologic grade for ovarian tumor according to the World Health Organization 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. Chris Stoeckert, Helena Ellis pathologic primary tumor stage for colon and rectum according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic primary tumor stage for lung according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic primary tumor stage for kidney according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic primary tumor stage for ovary according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic lymph node stage for colon and rectum according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic lymph node stage for lung according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic lymph node stage for kidney according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic lymph node stage for ovary according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic distant metastases stage for colon according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic distant metastases stage for lung according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic distant metastases stage for kidney according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pathologic distant metastases stage for ovary according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis clinical tumor stage group according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis International Federation of Gynecology and Obstetrics cervical cancer stage value specification 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. Chris Stoeckert, Helena Ellis International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis performance status value specification 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. Chris Stoeckert, Helena Ellis Eastern Cooperative Oncology Group score value specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky score vaue specification A person or organization that provides material supplies to other people or organizations. Rebecca Jackson material supplier A material entity that is collected for potential use as an input upon which measurements or observations are performed. PERSON: James Malone PERSON: Philippe Rocca-Serra specimen A completely executed planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data transformation 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 Person:Helen Parkinson leave one out cross validation method 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). Elisabetta Manduchi James Malone Philippe Rocca-Serra k-means clustering 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). James Malone hierarchical clustering 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. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra dimensionality reduction 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. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra principal components analysis dimensionality reduction A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data visualization An objective specification to transformation input data into output data James Malone data transformation objective A partitioning data transformation is a data transformation that has objective partitioning. James Malone partitioning data transformation 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. Elisabetta Manduchi James Malone partitioning objective A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone class discovery data transformation 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. James Malone class discovery objective 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 class 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. James Malone class prediction objective 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. James Malone cross validation objective 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. James Malone clustered data visualization quality A data item involved in PBPK modelling. 0000-0001-8345-1349 0000-0002-9795-5967 parameter A data representation model that predicts the absorption, distribution, metabolism, and excretion (ADME) of chemical substances in biological species based on physiological principles using mathematical modelling technique. 0000-0001-8345-1349 0000-0002-9795-5967 PBPK physiologically based pharmacokinetic model A physiologically based pharmacokinetic model that contains an explicit representation of the organs most relevant to the ADME of the compound. 0000-0001-8345-1349 0000-0002-9795-5967 All organs PBPK whole body pbpk A physiologically based pharmacokinetic model that assumes tissue concentration reaches equilibrium rapidly and uptake/elimination is limited by blood flow rate. 0000-0001-8345-1349 0000-0002-9795-5967 perfusion limited model A parameter that provides the structural framework for a PBPK model and relates to the organism's physiology (e.g., body weight, organ volume, blood flow). 0000-0001-8345-1349 0000-0002-9795-5967 physiological parameter http://snomed.info/id/398060001 A physiological parameter calculated as an individual's weight (kg) divided by the square of their height (m). 0000-0001-8345-1349 0000-0002-9795-5967 BMI body mass index http://www.ebi.ac.uk/efo/EFO_0004340 A physiological parameter representing the mass or quantity of heaviness of an individual. 0000-0001-8345-1349 0000-0002-9795-5967 bw bodyweight http://purl.obolibrary.org/obo/CMO_0000012 A physiological parameter describing the distance from the bottom to the top of someone standing upright. 0000-0001-8345-1349 0000-0002-9795-5967 ht height http://purl.obolibrary.org/obo/PATO_0000119 A physiological parameter representing the total area that the surface of an object occupies. 0000-0001-8345-1349 0000-0002-9795-5967 BSA/SA surface area http://semanticscience.org/resource/SIO_001407 A parameter representing a geographic ancestral origin category assigned to a population group. 0000-0001-8345-1349 0000-0002-9795-5967 assigned race http://purl.obolibrary.org/obo/GSSO_002199 A bodily fluid flow rate parameter representing the rate of blood flow in different parts of the body 0000-0001-8345-1349 0000-0002-9795-5967 Q blood flow rate to compartment A blood flow rate parameter representing the volume of blood pumped by the heart compartment per unit of time. 0000-0001-8345-1349 0000-0002-9795-5967 CO cardiac output rate A blood flow rate parameter specifically describing the rate to the stomach compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qstomach blood flow rate to stomach The dimensionless fraction of cardiac output delivered to the stomach compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqstomach fraction of blood flow to stomach A blood flow parameter specifically describing the rate to the intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qintestine blood flow rate to intestine The dimensionless fraction of cardiac output delivered to the intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqintestine fraction of blood flow to intestine A blood flow rate parameter specifically describing the rate to the small intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qsmall intestine blood flow rate to small intestine The dimensionless fraction of cardiac output delivered to the small intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqsmallintestine fraction of blood flow to small intestine A blood flow rate parameter specifically describing the rate to the large intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qlargeintestine blood flow rate to large intestine The dimensionless fraction of cardiac output delivered to the large intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqlargeinestine fraction of blood flow to large intestine A blood flow rate parameter specifically describing the rate to the pancreas compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qpancreas blood flow rate to pancreas The dimensionless fraction of cardiac output delivered to the pancreas compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqpancreas fraction of blood flow to pancreas A blood flow rate parameter specifically describing the rate to the liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qliver blood flow rate to liver The dimensionless fraction of cardiac output delivered to the liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqliver fraction of blood flow to liver A blood flow rate parameter specifically describing the rate to the kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qkidney blood flow rate to kidney The dimensionless fraction of cardiac output delivered to the kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqkidney fraction of blood flow to kidney A blood flow rate parameter specifically describing the rate to the muscle compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qmuscle blood flow rate to muscle The dimensionless fraction of cardiac output delivered to the muscle compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqmuscle fraction of blood flow to muscle A blood flow rate parameter specifically describing the rate to the heart compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qheart blood flow rate to heart The dimensionless fraction of cardiac output delivered to the heart compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqheart fraction of blood flow to heart A blood flow rate parameter specifically describing the rate to the fat (adipose tissue) compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qfat blood flow rate to fat The dimensionless fraction of cardiac output delivered to the fat compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqfat fraction of blood flow to fat A blood flow parameter specifically describing the rate to the gonads compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qgonad blood flow rate to gonad The dimensionless fraction of cardiac output delivered to the gonad compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqgonad fraction of blood flow to gonad A blood flow rate parameter specifically describing the rate to the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qskin blood flow rate to skin The dimensionless fraction of cardiac output delivered to the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqskin fraction of blood flow to skin A blood flow rate parameter specifically describing the rate to the bone compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qbone blood flow rate to bone The dimensionless fraction of cardiac output delivered to the bone compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqbone fraction of blood flow to bone A blood flow rate parameter specifically describing the rate to the brain compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qbrain blood flow rate to brain The dimensionless fraction of cardiac output delivered to the brain compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqbrain fraction of blood flow to brain A blood flow rate parameter specifically describing the rate to the spleen compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qspleen blood flow rate to spleen The dimensionless fraction of cardiac output delivered to the spleen compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqspleen fraction of blood flow to spleen A blood flow rate parameter specifically describing the rate to the lung compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qlung blood flow rate to lung The dimensionless fraction of cardiac output delivered to the lung compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqlung fraction of blood flow to lung A blood flow rate parameter specifically describing the rate to the poorly perfused organ/tissue compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qpoorlyperfused blood flow rate to poorly perfused The dimensionless fraction of cardiac output delivered to the poorly perfused compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqpoorlyperfused fraction of blood flow to poorly perfused A blood flow rate parameter specifically describing the rate to the richly perfused organ/tissue compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qrichlyperfused blood flow rate to richly perfused The dimensionless fraction of cardiac output delivered to the richly perfused compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqrichlyperfused fraction of blood flow to richly perfused A blood flow rate parameter specifically describing the rate to the rest of body compartment (total minus specified organs). 0000-0001-8345-1349 0000-0002-9795-5967 qrestbody blood flow rate to restbody The dimensionless fraction of cardiac output delivered to the rest of the body compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqrestbody fraction of blood flow to restbody A blood flow rate parameter specifically describing the rate to the gall bladder compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qgallbladder blood flow rate to gall bladder The dimensionless fraction of cardiac output delivered to the gall bladder compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqgallbladder fraction of blood flow to gall bladder A blood flow rate parameter specifically describing the rate to the portal vein compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qportalvein blood flow rate to portal vein The dimensionless fraction of cardiac output delivered to the portal vein compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqportalvein fraction of blood flow to portal vein A blood flow rate parameter specifically describing the rate to the lymph compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qlymph blood flow rate to lymph The dimensionless fraction of cardiac output delivered to the lymph compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqlymph fraction of blood flow to lymph An output parameter representing the total amount of compound metabolized. 0000-0001-8345-1349 0000-0002-9795-5967 ametab amount of metabolized The dimensionless fraction of cardiac output delivered to the stratum corneum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 scfblood fraction of blood flow to stratum corneum A dimensionless fraction of volume defined as the exposed skin volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fskin e fraction of exposed skin A dimensionless fraction of volume defined as the unexposed skin volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fskin u fraction of unexposed skin A blood flow rate parameter representing the rate of blood flow through the arterial compartment. 0000-0001-8345-1349 0000-0002-9795-5967 arterial blood flow rate A blood flow rate parameter representing the rate of blood flow returning through the venous compartment. 0000-0001-8345-1349 0000-0002-9795-5967 venous blood flow rate A bodily fluid flow rate parameter (or physiological process measure) describing the flow rate of filtered fluid through the kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 gfr glomerular filtration rate A physiological parameter representing the volume of a specific organ or tissue. 0000-0001-8345-1349 0000-0002-9795-5967 Vorgan volume of compartment http://www.ontology-of-units-of-measure.org/resource/om-2/Volume A volume parameter representing the total volume of the stomach compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vstomach volume of stomach http://purl.obolibrary.org/obo/OBA_VT0010199 A dimensionless fraction of volume defined as the stomach volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fstomach fraction of stomach A volume parameter representing the total volume of the intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vintestine volume of intestine A dimensionless fraction of volume defined as the intestine volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fintestine fraction of intestine A volume parameter representing the total volume of the small intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vsmall intestine volume of small intestine A dimensionless fraction of volume defined as the small intestine volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fsmall intestine fraction of small intestine A volume parameter representing the total volume of the large intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vlarge intestine volume of large intestine A dimensionless fraction of volume defined as the large intestine volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 flarge intestine fraction of large intestine A volume parameter representing the total volume of the pancreas compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vpancreas volume of pancreas http://purl.obolibrary.org/obo/OBA_2050006 A dimensionless fraction of volume defined as the pancreas volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fpancreas fraction of pancreas A volume parameter representing the total volume of the liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vliver volume of liver http://purl.obolibrary.org/obo/OBA_2050033 A dimensionless fraction of volume defined as the liver volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fliver fraction of liver A volume parameter representing the total volume of the kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vkidney volume of kidney http://purl.obolibrary.org/obo/OBA_2050015 A dimensionless fraction of volume defined as the kidney volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fkidney fraction of kidney A volume parameter representing the total volume of muscle compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vmuscle volume of muscle A dimensionless fraction of volume defined as the muscle volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fmuscle fraction of muscle A volume parameter representing the total volume of the heart compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vheart volume of heart A dimensionless fraction of volume defined as the heart volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fheart fraction of heart A volume parameter representing the total volume of fat (adipose tissue) compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vfat volume of fat A dimensionless fraction of volume defined as the fat volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 ffat fraction of fat A volume parameter representing the total volume of the gonad compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vgonad volume of gonad A dimensionless fraction of volume defined as the gonad volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fgonad fraction of gonad A volume parameter representing the total volume of the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vskin volume of skin A dimensionless fraction of volume defined as the skin volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fskin fraction of skin A volume parameter representing the total volume of bone compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vbone volume of bone A dimensionless fraction of volume defined as the bone volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fbone fraction of bone A volume parameter representing the total volume of the brain compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vbrain volume of brain http://purl.obolibrary.org/obo/OBA_2050009 A dimensionless fraction of volume defined as the brain volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fbrain fraction of brain A volume parameter representing the total volume of the spleen compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vspleen volume of spleen http://purl.obolibrary.org/obo/OBA_2050204 A dimensionless fraction of volume defined as the spleen volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fspleen fraction of spleen A volume parameter representing the total volume of the lung compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vlung volume of lung http://purl.obolibrary.org/obo/OBA_VT0001942 A dimensionless fraction of volume defined as the lung volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 flung fraction of lung A volume parameter representing the total volume of the poorly perfused compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vpoorly perfused volume of poorly perfused A dimensionless fraction of volume defined as the poorly perfused compartment volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fpoorly perfused fraction of poorly perfused A volume parameter representing the total volume of the richly perfused compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vrichly perfused volume of richly perfused A dimensionless fraction of volume defined as the richly perfused compartment volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 frichly perfused fraction of richly perfused A volume parameter representing the total volume of plasma compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vplasma volume of plasma A dimensionless fraction of volume defined as the plasma volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fplasma fraction of plasma A volume parameter representing the total volume of the rest of body compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vrest body volume of rest body A dimensionless fraction of volume defined as the rest of body volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 frest body fraction of rest body A volume parameter representing the total volume of stratum corneum compartment with respect to blood/plasma. 0000-0001-8345-1349 0000-0002-9795-5967 scvblood volume of stratum corneum with respect to blood A volume parameter representing the total volume of blood compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vblood volume of blood http://purl.obolibrary.org/obo/OBA_0003648 A volume parameter representing the total volume of the exposed skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vskin e volume of exposed skin A surface area parameter representing the fraction of skin surface area actually exposed. 0000-0001-8345-1349 0000-0002-9795-5967 fsa exposed fraction of surface area exposed A volume parameter representing the total volume of the unexposed skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vskin u volume of unexposed skin A volume parameter representing the total volume of the exposed stratum corneum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vskin sc e volume of stratum corneum exposed A volume parameter representing the total volume of the unexposed stratum corneum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vskin sc u volume of unexposed stratum corneum A dimensionless fraction of volume defined as the alveolar volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 falv fraction alveolar volume A volume parameter representing the total volume of the gall bladder compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vgall bladder volume of gall bladder A dimensionless fraction of volume defined as the gall bladder volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fgall bladder fraction of gall bladder A volume parameter representing the total volume of the portal vein compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vportal vein volume of portal vein A dimensionless fraction of volume defined as the portal vein volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fportal vein fraction of portal vein A volume parameter representing the total volume of lymph compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vlymph volume of lymph A dimensionless fraction of volume defined as the lymph volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 flymph fraction of lymph A volume parameter representing the total volume of the arterial compartment. 0000-0001-8345-1349 0000-0002-9795-5967 arterial volume http://purl.bioontology.org/ontology/LNC/LP430862-5 A volume parameter representing the total volume of the venous compartment. 0000-0001-8345-1349 0000-0002-9795-5967 venous volume A parameter relating to the physical and chemical properties of a compound (e.g., MW, lipophilicity, solubility, pKa). 0000-0001-8345-1349 0000-0002-9795-5967 physicochemical parameter A physicochemical parameter representing the sum of the weights of all atoms in a molecule. 0000-0001-8345-1349 0000-0002-9795-5967 MW molecular weight A physicochemical parameter representing the affinity or tendency of a compound to dissolve in lipids or hydrophobic environments. 0000-0001-8345-1349 0000-0002-9795-5967 lipophillicity A physicochemical parameter representing the logarithm of the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium, specifically describing lipophilicity (LogD). 0000-0001-8345-1349 0000-0002-9795-5967 Log D distribution coefficient A physicochemical parameter representing the ratio of a dissolved compound in a two-phase system (often used interchangeably with partition coefficient). 0000-0001-8345-1349 0000-0002-9795-5967 dissolution in two phase system A physicochemical parameter representing the 10-based logarithm of a compound's solubility (typically in mol/L). 0000-0001-8345-1349 0000-0002-9795-5967 log S logarithmic solubility http://purl.bioontology.org/ontology/MESH/D012995 A physicochemical parameter representing the solubility of a compound specifically in water. 0000-0001-8345-1349 0000-0002-9795-5967 water solubility A physicochemical parameter representing the negative base-10 logarithm (pKa) of the acid dissociation constant (Ka). 0000-0001-8345-1349 0000-0002-9795-5967 pka acid dissociation constant A physicochemical parameter representing the negative base-10 logarithm (pKb) of the base dissociation constant (Kb). 0000-0001-8345-1349 0000-0002-9795-5967 pKb pK(b) pK(B) affinity constant, Base dissociation constant basic dissociation constant A physicochemical parameter representing the electrical charge of a molecule at physiological pH. 0000-0001-8345-1349 0000-0002-9795-5967 physiological charge A physicochemical parameter representing the integer number of hydrogen bond acceptors in a molecular entity. 0000-0001-8345-1349 0000-0002-9795-5967 A hydrogen acceptor count http://purl.obolibrary.org/obo/CHEBI_13193 A physicochemical parameter representing the integer number of hydrogen bond donors in a molecular entity. 0000-0001-8345-1349 0000-0002-9795-5967 hydrogen donor count http://purl.obolibrary.org/obo/CHEBI_17499 A physicochemical parameter representing the integer count of rotatable bonds in a molecular entity. 0000-0001-8345-1349 0000-0002-9795-5967 rotatable bond count A parameter that is compound-dependent and relates to biological interactions or transformations (e.g., clearance, binding, partition coefficients). 0000-0001-8345-1349 0000-0002-9795-5967 biochemical parameter A biological process by which a compound moves from its site of administration into the systemic circulation or a target tissue. 0000-0001-8345-1349 0000-0002-9795-5967 A absorption http://purl.obolibrary.org/obo/ExO_0000058 An absorption rate constant parameter representing the rate constant for the movement of a compound from the gut to systemic circulation or another compartment. 0000-0001-8345-1349 0000-0002-9795-5967 Kac gut absorption rate constant gut An absorption rate constant parameter representing the movement of a compound from the intestine to systemic circulation or another compartment. 0000-0001-8345-1349 0000-0002-9795-5967 Kac intestine absorption rate constant intestine A biochemical parameter representing the rate at which the stomach empties its contents into the small intestine. 0000-0001-8345-1349 0000-0002-9795-5967 ge gastric emptying rate http://snomed.info/id/40117008 A biological process involving recycling of compounds through the liver via biliary excretion, intestinal reabsorption, portal circulation return, and re-excretion. 0000-0001-8345-1349 0000-0002-9795-5967 EHR enterohepatic recirculation http://purl.bioontology.org/ontology/MESH/D004764 A biochemical parameter representing the surface area-normalized transcellular permeability of the intestinal wall for a compound. 0000-0001-8345-1349 0000-0002-9795-5967 specific intestinal permeability http://www.ebi.ac.uk/efo/EFO_0011031 A biological process describing the movement of a compound from systemic circulation to various organs/tissues. 0000-0001-8345-1349 0000-0002-9795-5967 distribution process A biochemical parameter representing the apparent volume into which a compound distributes in the body relative to its plasma concentration. 0000-0001-8345-1349 0000-0002-9795-5967 Vd volume of distribution A distribution process (or molecular function) where substances bind to proteins or related compounds. 0000-0001-8345-1349 0000-0002-9795-5967 protein binding mediated distributiion process http://purl.obolibrary.org/obo/GO_0005515 A biochemical parameter representing the fraction of a compound that is not bound (e.g., to proteins). 0000-0001-8345-1349 0000-0002-9795-5967 FU unbound fraction An unbound fraction parameter specifically for the gut compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fugut fraction unbound gut An unbound fraction parameter specifically for the stomach compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fustomach fraction unbound stomach An unbound fraction parameter specifically for the intestine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fuintestine fraction unbound intestine An unbound fraction parameter specifically for the pancreas compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fupancreas fraction unbound pancreas An unbound fraction parameter specifically for the liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fuliver fraction unbound liver An unbound fraction parameter specifically for the kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fukidney fraction unbound kidney An unbound fraction parameter specifically for the muscle compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fumuscle fraction unbound muscle An unbound fraction parameter specifically for the heart compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fuheart fraction unbound heart An unbound fraction parameter specifically for the fat (adipose) compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fufat fraction unbound fat An unbound fraction parameter specifically for the gonad compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fugonad fraction unbound gonad An unbound fraction parameter specifically for the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fuskin fraction unbound skin An unbound fraction parameter specifically for the bone compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fubone fraction unbound bone An unbound fraction parameter specifically for the spleen compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fuspleen fraction unbound spleen An unbound fraction parameter specifically for the lung compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fulung fraction unbound lung An unbound fraction parameter specifically within enterocytes. 0000-0001-8345-1349 0000-0002-9795-5967 fuenterocytes fraction unbound enterocytes A biochemical parameter representing the ratio of the concentration of a compound in a particular tissue to its concentration in plasma/blood at equilibrium. 0000-0001-8345-1349 0000-0002-9795-5967 Kp partition coefficient A partition coefficient representing the ratio of compound concentration in gut to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 gut plasma pc gut plasma partition coefficient A partition coefficient representing the ratio of compound concentration in stomach to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 stomach plasma pc stomach plasma partition coefficient A partition coefficient representing the ratio of compound concentration in intestine to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 intestine plasma pc intestine plasma partition coefficient A partition coefficient representing the ratio of compound concentration in pancreas to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 pancreas plasma pc pancreas plasma partition coefficient A partition coefficient representing the ratio of compound concentration in liver to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 liver plasma pc liver plasma partition coefficient A partition coefficient representing the ratio of compound concentration in kidney to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 kidney plasma pc kidney plasma partition coefficient A partition coefficient representing the ratio of compound concentration in muscle to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 muscle plasma pc muscle plasma partition coefficient A partition coefficient representing the ratio of compound concentration in heart to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 heart plasma pc heart plasma partition coefficient A partition coefficient representing the ratio of compound concentration in fat (adipose tissue) to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 fat plasma pc fat plasma partition coefficient A partition coefficient representing the ratio of compound concentration in gonads to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 gonads plasma pc gonad plasma partition coefficient A partition coefficient representing the ratio of compound concentration in skin to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 skin plasma pc skin plasma partition coefficient A partition coefficient representing the ratio of compound concentration in bone to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 bone plasma pc bone plasma partition coefficient A partition coefficient representing the ratio of compound concentration in spleen to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 spleen plasma pc spleen plasma partition coefficient A partition coefficient representing the ratio of compound concentration in lung to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 lung plasma pc lung plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the lumped richly perfused compartment to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 rich perfused plasma pc rich perfused plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the lumped poorly perfused compartment to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 poor perfused plasma pc poor perfused plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the stratum corneum to the rest of the skin. 0000-0001-8345-1349 0000-0002-9795-5967 skin sc pc skin stratum corneum partition coefficient A partition coefficient representing the ratio of compound concentration in air to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 air plasma pc air plasma partition coefficient A diffusion coefficient representing the diffusion of a compound across the skin. 0000-0001-8345-1349 0000-0002-9795-5967 kp sc skin diffusion coefficient A material entity representing distribution-related protein (most abundant in human plasma) that binds various compounds. 0000-0001-8345-1349 0000-0002-9795-5967 HSA human serum albumin http://purl.bioontology.org/ontology/LNC/LP62267-7 A biochemical parameter representing the ratio of compound concentration in whole blood to that in plasma. 0000-0001-8345-1349 0000-0002-9795-5967 bp blood:plasma ratio A biochemical parameter quantifying enzymatic reaction velocity (kcat), representing the maximum number of substrate molecules converted per active site per unit time. 0000-0001-8345-1349 0000-0002-9795-5967 kcat catalytic rate constant A metabolism process involving the conversion of exogenous substances to more polar metabolites, often via oxidation, reduction, or hydrolysis (e.g., by CYPs). 0000-0001-8345-1349 0000-0002-9795-5967 phase I metabolism A metabolism process involving the conjugation of phase I products (or parent compounds) to hydrophilic moieties to facilitate excretion. 0000-0001-8345-1349 phase II A metabolism/transport process involving the further processing and excretion of conjugated metabolites (often involving efflux transporters). 0000-0001-8345-1349 0000-0002-9795-5967 phase III A metabolism process occurring at a specific location (e.g., liver, gut wall) after administration but before reaching systemic circulation, reducing the concentration of active compound. 0000-0001-8345-1349 0000-0002-9795-5967 first pass metabolism A maximum rate (Vmax) of an enzyme catalysed reaction for a compound in the intestine when the enzyme is saturated with substrate. 0000-0001-8345-1349 0000-0002-9795-5967 vmax intestine maximum rate in intestine Michaelis constant representing the substrate concentration at which the reaction rate in the intestine is half of Vmax (Km). 0000-0001-8345-1349 0000-0002-9795-5967 km intestine Michaelis constant intestine A maximum rate (Vmax) of an enzyme catalysed reaction for a compound in the liver when the enzyme is saturated with substrate. 0000-0001-8345-1349 0000-0002-9795-5967 vmax liver maximum rate in liver Michaelis constant representing the substrate concentration at which the reaction rate in the liver is half of Vmax (Km). 0000-0001-8345-1349 0000-0002-9795-5967 km liver Michaelis constant liver A metabolism process specifically occurring within the gut. 0000-0001-8345-1349 0000-0002-9795-5967 gut metabolism A biochemical parameter (Kd) measuring the affinity of a compound for its binding partner (e.g., receptor, protein). 0000-0001-8345-1349 0000-0002-9795-5967 kd dissociation constant A material entity representing protein responsible for the import or export of compounds across cell membranes. 0000-0001-8345-1349 0000-0002-9795-5967 transporter http://purl.obolibrary.org/obo/TXPO_0003638 A transporter family (Organic Anion Transporting Polypeptides) involved in transporting organic anions. 0000-0001-8345-1349 0000-0002-9795-5967 oatp http://purl.obolibrary.org/obo/TXPO_0000272 A transporter (ATP-binding cassette subfamily C member 3) involved in bile metabolism and transport. 0000-0001-8345-1349 0000-0002-9795-5967 abcc3 http://purl.obolibrary.org/obo/OGG_3000008714 A transporter (ATP-binding cassette subfamily C member 2) involved in transporting various molecules across cell membranes. 0000-0001-8345-1349 0000-0002-9795-5967 abcc2 http://purl.obolibrary.org/obo/OGG_3000001244 A biochemical parameter (kdeg) representing the rate constant for the degradation of a metabolizing enzyme or transporter. 0000-0001-8345-1349 0000-0002-9795-5967 kdeg degradation rate constant A biochemical parameter (Ki) representing the inhibition constant for a specific enzyme or transporter interaction. 0000-0001-8345-1349 0000-0002-9795-5967 ki inhibition constant An excretion process involving the elimination of compounds and metabolites primarily through urine via the kidneys. 0000-0001-8345-1349 0000-0002-9795-5967 renal excretion An excretion process involving the elimination of compounds and metabolites via the liver (often into bile). 0000-0001-8345-1349 0000-0002-9795-5967 hepatic excretion An excretion process involving the elimination of compounds and metabolites through feces. 0000-0001-8345-1349 0000-0002-9795-5967 fecal excretion An excretion process involving the elimination of volatile compounds and metabolites through respiration. 0000-0001-8345-1349 0000-0002-9795-5967 exhalation http://purl.bioontology.org/ontology/MESH/D045853 An excretion process involving the elimination of compounds and metabolites through sweat. 0000-0001-8345-1349 0000-0002-9795-5967 sweat excretion An excretion process involving the elimination and deposition of compounds and metabolites into hair. 0000-0001-8345-1349 0000-0002-9795-5967 hair excretion A biochemical parameter representing the volume of biological fluid cleared of a compound per unit time. 0000-0001-8345-1349 0000-0002-9795-5967 cl clearance rate A clearance rate specifically quantifying elimination via feces. 0000-0001-8345-1349 0000-0002-9795-5967 fecal clearance rate A clearance rate specifically quantifying elimination via sweat. 0000-0001-8345-1349 0000-0002-9795-5967 sweat clearance rate A clearance rate specifically quantifying elimination via urine. 0000-0001-8345-1349 0000-0002-9795-5967 urinary clearance rate A clearance rate specifically quantifying elimination via bile. 0000-0001-8345-1349 0000-0002-9795-5967 biliary clearance rate A clearance rate specifically quantifying elimination via the liver (metabolism and/or biliary excretion). 0000-0001-8345-1349 0000-0002-9795-5967 hepatic clearance rate A clearance rate representing the inherent ability of an organ or tissue to eliminate a compound, independent of blood flow or binding. 0000-0001-8345-1349 0000-0002-9795-5967 clint intrinsic clearance rate A biochemical parameter representing the rate constant for elimination via fecal excretion. 0000-0001-8345-1349 0000-0002-9795-5967 fecal elimination rate constant A biochemical parameter representing the rate constant for elimination via renal (urinary) excretion. 0000-0001-8345-1349 0000-0002-9795-5967 renal elimination rate constant An elimination process involving the irreversible transfer of compound or metabolites from plasma to bile via hepatocytes. 0000-0001-8345-1349 0000-0002-9795-5967 biliary elimination A parameter designating the body part or method through which exposure is introduced. 0000-0001-8345-1349 0000-0002-9795-5967 route of exposure A route of exposure via the mouth. 0000-0001-8345-1349 0000-0002-9795-5967 oral exposure A route of exposure via the skin. 0000-0001-8345-1349 0000-0002-9795-5967 dermal exposure A route of exposure via inhalation into the lungs. 0000-0001-8345-1349 0000-0002-9795-5967 inhalation exposure A route of exposure involving rapid injection directly into a vein. 0000-0001-8345-1349 0000-0002-9795-5967 IVB intravenous bolus exposure A route of exposure involving continuous administration directly into a vein over time. 0000-0001-8345-1349 0000-0002-9795-5967 IVI intravenous infusion exposure A route of exposure involving injection into a muscle. 0000-0001-8345-1349 0000-0002-9795-5967 intramuscular exposure A route of exposure involving administration directly into an artery. 0000-0001-8345-1349 0000-0002-9795-5967 intraarterial exposure A route of exposure involving administration into the spinal canal. 0000-0001-8345-1349 0000-0002-9795-5967 intrathecal exposure A route of exposure involving administration under the skin. 0000-0001-8345-1349 0000-0002-9795-5967 subcutaneous exposure A route of exposure via the nasal passages. 0000-0001-8345-1349 0000-0002-9795-5967 nasal exposure A route of exposure involving absorption through the skin, typically from a patch. 0000-0001-8345-1349 0000-0002-9795-5967 transdermal exposure A route of exposure via the eye. 0000-0001-8345-1349 0000-0002-9795-5967 ocular exposure A parameter representing a result or prediction generated by the PBPK model. 0000-0001-8345-1349 0000-0002-9795-5967 output parameter An output parameter representing the highest concentration (Cmax) of a compound achieved after exposure. 0000-0001-8345-1349 0000-0002-9795-5967 Cmax peak concentration An output parameter representing the maximum concentration (Cmax,ss) achieved at steady state during repeated dosing. 0000-0001-8345-1349 0000-0002-9795-5967 cmaxss maximum steady state concentration An output parameter representing the time (Tmax) required to reach the peak concentration. 0000-0001-8345-1349 0000-0002-9795-5967 tmax maximum time An output parameter representing the integral of the concentration-time curve (AUC), indicating total exposure. 0000-0001-8345-1349 0000-0002-9795-5967 AUC area under curve An area under curve parameter calculated from time zero to a specific time point t (AUC0-t). 0000-0001-8345-1349 0000-0002-9795-5967 auc 0 to t area under curve 0 to t An area under curve parameter calculated from time zero to the time of the last measurable concentration (AUClast). 0000-0001-8345-1349 0000-0002-9795-5967 auclast area under curve last An area under curve parameter extrapolated from time zero to infinity (AUC0-inf), representing total exposure after a single dose. 0000-0001-8345-1349 0000-0002-9795-5967 auc 0 infinity area under curve 0 to infinity An output parameter calculated as the integral of the product of time and concentration versus time (AUMC). 0000-0001-8345-1349 0000-0002-9795-5967 aumc area under moment curve An output parameter representing the average time a compound resides in the body (MRT). 0000-0001-8345-1349 0000-0002-9795-5967 MRT mean residence time An output parameter representing the time required for the compound concentration to decrease by half (t1/2). 0000-0001-8345-1349 0000-0002-9795-5967 t1/2 half-life An output parameter representing the rate and extent to which an active compound is absorbed and becomes available at the site of action or systemic circulation. 0000-0001-8345-1349 0000-0002-9795-5967 f bioavailability A bioavailability parameter comparing the rate and extent of absorption of a test compound to a reference compound. 0000-0001-8345-1349 0000-0002-9795-5967 frel relative bioavailability An output parameter representing the average time for a compound to be absorbed into systemic circulation (MAT). 0000-0001-8345-1349 0000-0002-9795-5967 MAT mean absorption time An output parameter representing the average time for a compound to dissolve in the body (MDT). 0000-0001-8345-1349 0000-0002-9795-5967 MDT mean dissolution time An output parameter indicating comparable bioavailability between test and reference formulations under similar conditions. 0000-0001-8345-1349 0000-0002-9795-5967 be bioequivalence A bioavailability parameter comparing the amount reaching systemic circulation after non-IV administration to the amount available after IV administration. 0000-0001-8345-1349 0000-0002-9795-5967 fabs absolute bioavailability An elimination process phase describing the period where removal of the compound from the body predominates. 0000-0001-8345-1349 0000-0002-9795-5967 elimination phase An absorption process phase describing the period where the compound moves from the administration site into systemic circulation. 0000-0001-8345-1349 0000-0002-9795-5967 absorption phase The amount of compound in the urine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 aurine amount in urine The amount of compound in the feces compartment. 0000-0001-8345-1349 0000-0002-9795-5967 afeces amount in feces An output parameter representing the total amount of compound excreted in urine over a specific time period. 0000-0001-8345-1349 0000-0002-9795-5967 cumulative amount in urine An output parameter representing the total amount of compound excreted in feces over a specific time period. 0000-0001-8345-1349 0000-0002-9795-5967 cumulative amount in feces An area under curve parameter calculated over a dosing interval at steady state (AUCss). 0000-0001-8345-1349 0000-0002-9795-5967 aucss steady state area under curve An output parameter representing the minimum concentration of a compound in a specific organ after exposure. 0000-0001-8345-1349 0000-0002-9795-5967 min organ concentration An output parameter representing the maximum concentration of a compound in a specific organ after exposure. 0000-0001-8345-1349 0000-0002-9795-5967 max organ concentration An output parameter representing the median concentration of a compound in a specific organ after exposure. 0000-0001-8345-1349 0000-0002-9795-5967 median organ concentration A plasma concentration parameter representing the 2.5th percentile of the plasma concentration distribution in a population simulation. 0000-0001-8345-1349 0000-0002-9795-5967 percentile 2.5 cplasma A plasma concentration parameter representing the 97.5th percentile of the plasma concentration distribution in a population simulation. 0000-0001-8345-1349 0000-0002-9795-5967 percentile 97.5 cplasma An output parameter (or exposure limit) estimating the amount of a substance that can be ingested daily over a lifetime without appreciable health risk (TDI). 0000-0001-8345-1349 0000-0002-9795-5967 tdi tolerable daily intake An output parameter estimating the amount of compound exposure based on internal body measurements. 0000-0001-8345-1349 0000-0002-9795-5967 reconstructed exposure An output parameter estimating the amount of a compound consumed daily (EDI). 0000-0001-8345-1349 0000-0002-9795-5967 edi estimated daily intake An output parameter representing the concentration of a chemical (or metabolite) in a biological medium consistent with exposure guidance values (BE). 0000-0001-8345-1349 0000-0002-9795-5967 be biomonitoring equivalent An output parameter (or exposure limit) estimating the daily oral or dermal exposure likely to be without appreciable risk over a lifetime (RfD). 0000-0001-8345-1349 0000-0002-9795-5967 RfD reference dose An output parameter (or exposure limit) estimating the amount of a substance in food/water that can be consumed daily without appreciable health risk (ADI). 0000-0001-8345-1349 0000-0002-9795-5967 adi acceptable daily intake A data set containing the physiological parameters representing a standard human, often defined by specific characteristics like 70 kg body weight. 0000-0001-8345-1349 0000-0002-9795-5967 reference human data set An output parameter representing the total concentration of a compound in a specified biological matrix. 0000-0001-8345-1349 0000-0002-9795-5967 biological matrix concentration The total concentration of compound in the hair compartment. 0000-0001-8345-1349 0000-0002-9795-5967 chair concentration in hair A biological matrix concentration specifically representing the total concentration of compound in the nail compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cnail concentration in nail A biological matrix concentration specifically representing the total concentration of compound in the teeth compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cteeth concentration in teeth The total concentration of compound in the blood compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cblood concentration in blood A biological matrix concentration specifically representing the total concentration of compound in the urine compartment. 0000-0001-8345-1349 0000-0002-9795-5967 curine concentration in urine A physiologically based pharmacokinetic model that considers the permeability across membranes as a limiting factor for compound distribution. 0000-0001-8345-1349 0000-0002-9795-5967 permeability limited pbpk Maximum rate (Vmax) of transport via a basolateral transporter, measured in vitro. 0000-0001-8345-1349 0000-0002-9795-5967 vmax baso in vitro maximum rate of basolateral transporter in vitro Michaelis constant representing the substrate concentration at half-maximal velocity (Km) for a basolateral transporter. 0000-0001-8345-1349 0000-0002-9795-5967 km baso Michaelis constant baso A maximum rate (Vmax) of an enzyme catalysed reaction for a compound across the apical membrane of an organ, measured in vitro, when the enzyme is saturated with substrate. 0000-0001-8345-1349 0000-0002-9795-5967 vmax apical in vitro maximum rate of apical transporter in vitro Michaelis constant representing the substrate concentration at half-maximal velocity (Km) for an apical transporter. 0000-0001-8345-1349 0000-0002-9795-5967 km apical Michaelis constant apical A biochemical parameter (kin) describing the rate constant for compound movement into a cell or compartment. 0000-0001-8345-1349 0000-0002-9795-5967 kiff influx constant A biochemical parameter (kefflux) describing the rate constant for compound movement out of a cell or compartment. 0000-0001-8345-1349 0000-0002-9795-5967 keffluxc efflux rate constant A physiological parameter representing the volume occupied by plasma within a tissue or the body. 0000-0001-8345-1349 0000-0002-9795-5967 plasma space A compartment representing the endosomal space within cells. 0000-0001-8345-1349 0000-0002-9795-5967 endosomal space compartment A physiological parameter representing the fluid-filled space between blood vessels and cells. 0000-0001-8345-1349 0000-0002-9795-5967 interstitial space A biochemical parameter (Peff) representing the rate at which a compound passes through a biological barrier (e.g., intestinal wall). 0000-0001-8345-1349 0000-0002-9795-5967 peff effective permeability A physiologically based pharmacokinetic model approach used to characterize interindividual variability within a population. 0000-0001-8345-1349 0000-0002-9795-5967 population pbpk A physiologically based pharmacokinetic model approach primarily based on fitting observed clinical data, often empirical. 0000-0001-8345-1349 0000-0002-9795-5967 top-down pbpk A physiologically based pharmacokinetic model approach built mechanistically using in vitro and physiological data. 0000-0001-8345-1349 0000-0002-9795-5967 bottom-up pbpk A physiologically based pharmacokinetic model that treats the entire body as a single, kinetically homogenous unit (central compartment). 0000-0001-8345-1349 0000-0002-9795-5967 one-compartment pbpk A compartment in a multi-compartment model representing plasma and highly perfused tissues where distribution is rapid. 0000-0001-8345-1349 0000-0002-9795-5967 central compartment A compartment in a multi-compartment model representing tissues where compound distribution is slower compared to the central compartment. 0000-0001-8345-1349 0000-0002-9795-5967 peripheral compartment A biological process involving the irreversible removal of a compound from the body, encompassing metabolism and excretion. 0000-0001-8345-1349 0000-0002-9795-5967 elimination An elimination process that follows first-order kinetics (rate proportional to concentration). 0000-0001-8345-1349 0000-0002-9795-5967 linear elimination An elimination process that does not follow first-order kinetics (e.g., saturable processes). 0000-0001-8345-1349 0000-0002-9795-5967 non-linear elimination A physiological parameter representing distinct phases of an individual's life (e.g., infant, adult, geriatric). 0000-0001-8345-1349 0000-0002-9795-5967 lifestage http://purl.obolibrary.org/obo/ExO_0000037 A lifestage parameter representing the unborn offspring from the postembryonic stage until birth. 0000-0001-8345-1349 0000-0002-9795-5967 fetus lifestage A lifestage parameter representing a very young child, typically under one year of age. 0000-0001-8345-1349 0000-0002-9795-5967 Inf infant lifestage A lifestage parameter representing a young child, typically between one and three years old. 0000-0001-8345-1349 0000-0002-9795-5967 Tdl toddler lifestage A lifestage parameter representing individuals typically between 3 and 11 years old. 0000-0001-8345-1349 0000-0002-9795-5967 child lifestage http://purl.obolibrary.org/obo/ExO_0000119 A lifestage parameter representing individuals typically between eleven and fifteen years old. 0000-0001-8345-1349 0000-0002-9795-5967 teenager lifestage A lifestage parameter representing the transitional stage between teenager and adulthood (approx. 15-18 years). 0000-0001-8345-1349 0000-0002-9795-5967 adolescent lifestage A lifestage parameter representing individuals typically from eighteen to thirty years old. 0000-0001-8345-1349 0000-0002-9795-5967 adult lifestage http://purl.obolibrary.org/obo/UBERON_0007023 A lifestage parameter representing individuals typically from thirty to forty-five years old. 0000-0001-8345-1349 0000-0002-9795-5967 middle age lifestage A lifestage parameter representing individuals typically from forty-five to sixty years old (or older, definitions vary). 0000-0001-8345-1349 0000-0002-9795-5967 old age lifestage http://purl.obolibrary.org/obo/UBERON_0007222 A lifestage parameter representing individuals typically below fifteen years of age. 0000-0001-8345-1349 0000-0002-9795-5967 pediatric lifestage A lifestage parameter representing older adults, often considered 60/65 years and older. 0000-0001-8345-1349 0000-0002-9795-5967 geriatric lifestage A physiologically based pharmacokinetic model specifically built to predict compound concentrations in the brain. 0000-0001-8345-1349 0000-0002-9795-5967 brain pbpk A volume parameter representing the total volume of cerebrospinal fluid (CSF) compartment in the spinal region. 0000-0001-8345-1349 0000-0002-9795-5967 spinal csf volume cerebrospinal fluid volume A volume parameter representing the total volume of cerebrospinal fluid (CSF) compartment in the cranial region. 0000-0001-8345-1349 0000-0002-9795-5967 cranial csf volume cranial cerebrospinal fluid volume A physiological parameter representing the mass of the brain. 0000-0001-8345-1349 0000-0002-9795-5967 brain mass http://purl.obolibrary.org/obo/OBA_VT0002176 A barrier compartment representing the blood-brain barrier (BBB). 0000-0001-8345-1349 0000-0002-9795-5967 bbb cpt blood brain barrier compartment A bodily fluid flow rate parameter representing the flow rate of cerebrospinal fluid (CSF) compartment in the spinal region. 0000-0001-8345-1349 0000-0002-9795-5967 spinal csf flow spinal cerebrospinal fluid flow rate A bodily fluid flow rate parameter representing the flow rate of cerebrospinal fluid (CSF) compartment in the cranial region. 0000-0001-8345-1349 0000-0002-9795-5967 cranial cerebrospinal fluid flow rate A barrier compartment representing the blood-cerebrospinal fluid barrier (BCSFB). 0000-0001-8345-1349 0000-0002-9795-5967 bc csf compartment blood cerebrospinal fluid compartment A volume parameter representing the total volume of the hippocampus compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vhippocampus volume of hippocampus A volume parameter representing the total volume of the frontal cortex compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vfrontal cortex volume of frontal cortex A volume parameter representing the total volume of the cerebrum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vcerebrum volume of cerebrum A volume parameter representing the total volume of the cerebellum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vcerebellum volume of cerebellum A blood flow rate parameter specifically describing the rate to the hippocampus compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qhippocampus blood flow rate to hippocampus A blood flow rate parameter specifically describing the rate to the frontal cortex compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qfrontalcortex blood flow rate to frontal cortex A blood flow rate parameter specifically describing the rate to the cerebrum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qcerebrum blood flow rate to cerebrum A blood flow rate parameter specifically describing the rate to the cerebellum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qcerebellum blood flow rate to cerebellum A partition coefficient representing the ratio of compound concentration in the hippocampus to the overall brain. 0000-0001-8345-1349 0000-0002-9795-5967 hippocampus brain pc hippocampus brain partition coefficient A partition coefficient representing the ratio of compound concentration in the cerebrum to the overall brain. 0000-0001-8345-1349 0000-0002-9795-5967 cerebrum brain pc cerebrum brain partition coefficient A partition coefficient representing the ratio of compound concentration in the cerebellum to the overall brain. 0000-0001-8345-1349 0000-0002-9795-5967 cerebellum brain pc cerebellum brain partition coefficient A partition coefficient representing the ratio of compound concentration in the frontal cortex to the overall brain. 0000-0001-8345-1349 0000-0002-9795-5967 frontalcortex brain pc frontalcortex brain partition coefficient Apparent permeability of a compound specifically between the cerebrum and the rest of the brain. 0000-0001-8345-1349 0000-0002-9795-5967 papp cerebrum brain apparent permeability cerebrum to rest of brain Apparent permeability of a compound specifically between the cerebellum and the rest of the brain. 0000-0001-8345-1349 0000-0002-9795-5967 papp cerebellum brain apparent permeability cerebellum to rest of brain Apparent permeability of a compound specifically between the hippocampus and the rest of the brain. 0000-0001-8345-1349 0000-0002-9795-5967 papp hippocampus brain apparent permeability hippocampus to rest of brain Apparent permeability of a compound specifically between the cortex and the rest of the brain. 0000-0001-8345-1349 0000-0002-9795-5967 papp cortex brain apparent permeability cortex to rest of brain A physiologically based pharmacokinetic model specifically built to predict compound concentrations during pregnancy. 0000-0001-8345-1349 0000-0002-9795-5967 pregnant pbpk A volume parameter representing the total volume of the placental compartment for fetus. 0000-0001-8345-1349 0000-0002-9795-5967 fetoplacental volume A volume parameter representing the total volume of the fetus. 0000-0001-8345-1349 0000-0002-9795-5967 vfetus volume of fetus A volume parameter representing the total volume of the placental compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vplacenta volume of placenta A volume parameter representing the total volume of the amniotic fluid compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vaf volume of amniotic fluid http://purl.obolibrary.org/obo/VT_0004020 A volume parameter representing the total volume of the fetal liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vliver fetus volume of liver fetus A volume parameter representing the total volume of the fetal brain compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vbrainfetus volume of brain fetus A volume parameter representing the total volume of the fetal kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vkidneyfetus volume of kidney fetus A volume parameter representing the total volume of the rest of body compartment within the fetus. 0000-0001-8345-1349 0000-0002-9795-5967 vrest body fetus volume of rest body fetus A blood flow rate parameter representing the rate of blood flow between the fetus and the placenta compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fetoplacental blood flow rate A blood flow rate parameter representing the volume of blood pumped by the fetal heart compartment per unit time. 0000-0001-8345-1349 0000-0002-9795-5967 fco fetal cardiac output rate A blood flow rate parameter specifically describing the rate to the fetal liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qliverfetus blood flow rate to liverfetus A blood flow rate parameter specifically describing the rate to the fetal kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qkidneyfetus blood flow rate to kidneyfetus A blood flow rate parameter specifically describing the rate to the fetal brain compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qbrainfetus blood flow rate to brain fetus A blood flow rate parameter specifically describing the rate to the rest of body compartment within the fetus. 0000-0001-8345-1349 0000-0002-9795-5967 qrestbodyfetus blood flow rate to restbody fetus A physiological parameter representing the age of a pregnancy, typically measured in weeks. 0000-0001-8345-1349 0000-0002-9795-5967 ga gestational age A physiological parameter representing the specific week of gestation. 0000-0001-8345-1349 0000-0002-9795-5967 gw gestational week A maximum rate (Vmax) of an enzyme catalysed reaction for a compound in fetus when the enzyme is saturated with substrate. 0000-0001-8345-1349 0000-0002-9795-5967 vmax fetus maximum rate in fetus A biochemical parameter representing the rate at which a compound transfers from maternal circulation to amniotic fluid. 0000-0001-8345-1349 0000-0002-9795-5967 atc amniotic transfer coefficient A partition coefficient representing the ratio of compound concentration in the fetal liver to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 liverfetus plasma pc liverfetus plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the fetal brain to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 brainfetus plasma pc brainfetus plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the fetal kidney to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 kidneyfetus plasma pc kidneyfetus plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the fetal rest of body compartment to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 restbody plasma pc restbodyfetus plasma partition coefficient A physiologically based pharmacokinetic model specifically built to predict compound concentrations within the kidney compartments. 0000-0001-8345-1349 0000-0002-9795-5967 kidney pbpk A kidney compartment representing the Bowman's capsule. 0000-0001-8345-1349 0000-0002-9795-5967 Bowman's capsule compartment A kidney compartment representing the filtrate within the nephron. 0000-0001-8345-1349 0000-0002-9795-5967 filtrate compartment A kidney compartment representing the proximal tubule of the nephron. 0000-0001-8345-1349 0000-0002-9795-5967 proximal tubule compartment http://purl.obolibrary.org/obo/UBERON_0004134 A kidney compartment representing the loop of Henle within the nephron. 0000-0001-8345-1349 0000-0002-9795-5967 loop of Henle compartment http://purl.obolibrary.org/obo/UBERON_0001288 A kidney compartment representing the distal tubule of the nephron. 0000-0001-8345-1349 0000-0002-9795-5967 distal tubule compartment http://purl.obolibrary.org/obo/UBERON_0004135 A kidney compartment representing the collecting duct system. 0000-0001-8345-1349 0000-0002-9795-5967 collecting duct compartment A compartment representing the urinary bladder. 0000-0001-8345-1349 0000-0002-9795-5967 bladder compartment http://purl.obolibrary.org/obo/UBERON_0001232 A physiologically based pharmacokinetic model specifically built to predict compound concentrations within the lung compartments. 0000-0001-8345-1349 0000-0002-9795-5967 lung pbpk A compartment representing the extrathoracic region (head, neck, upper respiratory tract). 0000-0001-8345-1349 0000-0002-9795-5967 extrathoracic compartment A compartment representing the thoracic region (chest). 0000-0001-8345-1349 0000-0002-9795-5967 thoracic compartment A lung compartment representing the bronchioles. 0000-0001-8345-1349 0000-0002-9795-5967 bronchiolar compartment A lung compartment representing the alveoli. 0000-0001-8345-1349 0000-0002-9795-5967 alveolar compartment A physiologically based pharmacokinetic model specifically built to predict compound concentrations within the gut compartments. 0000-0001-8345-1349 0000-0002-9795-5967 gut pbpk The dimensionless fraction of cardiac output delivered to the duodenum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqduodenum fraction of blood flow to duodenum The dimensionless fraction of cardiac output delivered to the jejunum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqjejunum fraction of blood flow to jejunum The dimensionless fraction of cardiac output delivered to the ileum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqileum fraction of blood flow to ileum The dimensionless fraction of cardiac output delivered to the colon compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqcolon fraction of blood flow to colon The dimensionless fraction of cardiac output delivered to the cecum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqcecum fraction of blood flow to cecum A blood flow rate parameter specifically describing the rate to the duodenum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qduodenum blood flow rate to duodenum A blood flow rate parameter specifically describing the rate to the jejunum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qjejunum blood flow rate to jejunum A blood flow rate parameter specifically describing the rate to the ileum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qileum blood flow rate to ileum A blood flow rate parameter specifically describing the rate to the colon compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qcolon blood flow rate to colon A blood flow rate parameter specifically describing the rate to the cecum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qcecum blood flow rate to cecum A dimensionless fraction of volume defined as the duodenum volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fduodenum fraction of duodenum A dimensionless fraction of volume defined as the jejunum volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fjejunum fraction of jejunum A dimensionless fraction of volume defined as the ileum volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fileum fraction of ileum A dimensionless fraction of volume defined as the colon volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fcolon fraction of colon A dimensionless fraction of volume defined as the cecum volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fcecum fraction of cecum A volume parameter representing the total volume of the duodenum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vduodenum volume of duodenum A volume parameter representing the total volume of the jejunum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vjejunum volume of jejunum A volume parameter representing the total volume of the ileum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vileum volume of ileum A volume parameter representing the total volume of the colon compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vcolon volume of colon A volume parameter representing the total volume of the cecum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vcecum volume of cecum A biochemical parameter representing the ratio of molecules solubilized due to bile salt presence. 0000-0001-8345-1349 0000-0002-9795-5967 bile salt effect solubilization ratio A biochemical parameter representing the average time for a compound to precipitate under specific conditions (e.g., in the GI tract). 0000-0001-8345-1349 0000-0002-9795-5967 mean precipitation time A physicochemical parameter representing the amount of substance diffusing across a unit area per unit time under a unit concentration gradient. 0000-0001-8345-1349 0000-0002-9795-5967 D diffusion coefficient A biochemical/physical parameter representing the mass per unit volume of particles (e.g., of the administered compound). 0000-0001-8345-1349 0000-0002-9795-5967 ps particle density A biochemical/physical parameter representing the radius of particles (e.g., of the administered compound). 0000-0001-8345-1349 0000-0002-9795-5967 particle radius A biochemical parameter representing the time required for a compound to move through the intestine. 0000-0001-8345-1349 0000-0002-9795-5967 itt intestinal transit time A physiologically based pharmacokinetic model specifically built to predict compound concentrations during lactation, including transfer into milk. 0000-0001-8345-1349 0000-0002-9795-5967 lactational pbpk A biochemical parameter representing the ratio of compound concentration in milk to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 milk plasma ratio An unbound fraction parameter specifically for milk. 0000-0001-8345-1349 0000-0002-9795-5967 fumilk fraction unbound milk The total concentration of compound in the milk compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cmilk concentration in milk A physiological parameter representing the daily volume of milk ingested (e.g., by an infant). 0000-0001-8345-1349 0000-0002-9795-5967 daily milk intake A biochemical parameter representing the pH of milk. 0000-0001-8345-1349 0000-0002-9795-5967 phmilk A barrier compartment representing the physiological barrier separating blood and milk in lactating species. 0000-0001-8345-1349 0000-0002-9795-5967 bmb compartment blood milk barrier compartment A partition coefficient representing the ratio of compound concentration in milk to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 milk plasma pc milk plasma partition coefficient A data representation model component representing a distinct physiological space (organ, tissue, fluid) where ADME processes occur. 0000-0001-8345-1349 0000-0002-9795-5967 compartment A lung compartment specifically representing the air within the alveoli. 0000-0001-8345-1349 0000-0002-9795-5967 alveolar air compartment A compartment representing the lumped remainder of the body not explicitly modeled as separate organs/tissues. 0000-0001-8345-1349 0000-0002-9795-5967 rest of body compartment A compartment representing the plasma specifically within the arterial blood. 0000-0001-8345-1349 0000-0002-9795-5967 arterial plasma A compartment representing the plasma specifically within the venous blood. 0000-0001-8345-1349 0000-0002-9795-5967 venous plasma compartment A compartment representing lumped tissues with high blood flow relative to their volume. 0000-0001-8345-1349 0000-0002-9795-5967 richly perfused tissue compartment A compartment representing lumped tissues with low blood flow relative to their volume. 0000-0001-8345-1349 0000-0002-9795-5967 poorly perfused tissue compartment A skin compartment representing the viable layers of skin not directly exposed to the applied compound. 0000-0001-8345-1349 0000-0002-9795-5967 viable unexposed skin compartment A skin compartment representing the viable layers of skin directly exposed to the applied compound. 0000-0001-8345-1349 0000-0002-9795-5967 viable exposed skin compartment A stratum corneum compartment representing the portion not directly exposed to the applied compound. 0000-0001-8345-1349 0000-0002-9795-5967 skin unexposed stratum corneum A stratum corneum compartment representing the portion directly exposed to the applied compound. 0000-0001-8345-1349 0000-0002-9795-5967 skin exposed stratum corneum compartment A compartment representing adipose (fat) tissue. 0000-0001-8345-1349 0000-0002-9795-5967 adipose compartment A large intestine compartment representing the anal canal. 0000-0001-8345-1349 0000-0002-9795-5967 anal canal compartment A large intestine compartment representing the appendix. 0000-0001-8345-1349 0000-0002-9795-5967 appendix compartment http://purl.obolibrary.org/obo/UBERON_0001154 A large intestine compartment representing the ascending colon. 0000-0001-8345-1349 0000-0002-9795-5967 ascending colon compartment http://purl.obolibrary.org/obo/UBERON_0001156 A compartment representing the entirety of the blood (including plasma and cells). 0000-0001-8345-1349 0000-0002-9795-5967 blood compartment http://purl.obolibrary.org/obo/UBERON_0000178 A compartment representing the bone marrow. 0000-0001-8345-1349 0000-0002-9795-5967 bone marrow compartment http://purl.obolibrary.org/obo/UBERON_0002371 A compartment representing the brain. 0000-0001-8345-1349 0000-0002-9795-5967 brain compartment http://purl.obolibrary.org/obo/UBERON_0000955 A large intestine compartment representing the cecum. 0000-0001-8345-1349 0000-0002-9795-5967 cecum compartment http://purl.obolibrary.org/obo/UBERON_0001153 A large intestine compartment representing the descending colon. 0000-0001-8345-1349 0000-0002-9795-5967 descending colon compartment http://purl.obolibrary.org/obo/UBERON_0001158 A skin compartment representing the dermis layer. 0000-0001-8345-1349 0000-0002-9795-5967 dermis compartment http://purl.obolibrary.org/obo/UBERON_0002067 A compartment representing the skin. 0000-0001-8345-1349 0000-0002-9795-5967 skin compartment http://purl.obolibrary.org/obo/UBERON_0002097 A small intestine compartment representing the duodenum. 0000-0001-8345-1349 0000-0002-9795-5967 duodenum compartment http://purl.obolibrary.org/obo/UBERON_0002114 A digestive system compartment representing the small intestine. 0000-0001-8345-1349 0000-0002-9795-5967 small intestine compartment http://purl.obolibrary.org/obo/UBERON_0002108 A compartment representing endocrine glands. 0000-0001-8345-1349 0000-0002-9795-5967 endocrine gland compartment http://purl.obolibrary.org/obo/UBERON_0002368 A digestive system compartment representing the large intestine. 0000-0001-8345-1349 0000-0002-9795-5967 large intestine compartment http://purl.obolibrary.org/obo/UBERON_0000059 A skin compartment representing the epidermis layer. 0000-0001-8345-1349 0000-0002-9795-5967 epidermis compartment http://purl.obolibrary.org/obo/UBERON_0001003 A digestive system compartment representing the gall bladder. 0000-0001-8345-1349 0000-0002-9795-5967 gall bladder compartment http://purl.obolibrary.org/obo/UBERON_0002110 A digestive system compartment representing the gut (general term, often synonymous with intestine or GI tract). 0000-0001-8345-1349 0000-0002-9795-5967 gut compartment A digestive system compartment representing the lumen (opening) within the gut. 0000-0001-8345-1349 0000-0002-9795-5967 gut lumen compartment A compartment representing hair. 0000-0001-8345-1349 0000-0002-9795-5967 hair compartment http://purl.obolibrary.org/obo/UBERON_8420000 A compartment representing the heart. 0000-0001-8345-1349 0000-0002-9795-5967 heart compartment http://purl.obolibrary.org/obo/UBERON_0000948 A small intestine compartment representing the ileum. 0000-0001-8345-1349 0000-0002-9795-5967 ileum compartment http://purl.obolibrary.org/obo/UBERON_0002116 A small intestine compartment representing the jejunum. 0000-0001-8345-1349 0000-0002-9795-5967 jejunum compartment http://purl.obolibrary.org/obo/UBERON_0002115 A compartment representing the mammary gland. 0000-0001-8345-1349 0000-0002-9795-5967 mammary gland compartment http://purl.obolibrary.org/obo/UBERON_0001911 A compartment representing muscle tissue. 0000-0001-8345-1349 0000-0002-9795-5967 muscle compartment http://purl.obolibrary.org/obo/UBERON_0005090 A compartment representing nails. 0000-0001-8345-1349 0000-0002-9795-5967 nail compartment http://purl.obolibrary.org/obo/UBERON_0001705 A compartment representing the pancreas. 0000-0001-8345-1349 0000-0002-9795-5967 pancreas compartment http://purl.obolibrary.org/obo/UBERON_0001264 A barrier compartment representing the placental barrier separating maternal and fetal circulation. 0000-0001-8345-1349 0000-0002-9795-5967 placental barrier compartment A compartment representing blood plasma. 0000-0001-8345-1349 0000-0002-9795-5967 plasma compartment A large intestine compartment representing the rectum. 0000-0001-8345-1349 0000-0002-9795-5967 rectum compartment http://purl.obolibrary.org/obo/UBERON_0001052 A compartment representing reproductive organs (gonads). 0000-0001-8345-1349 0000-0002-9795-5967 reproductive compartment A large intestine compartment representing the sigmoid colon. 0000-0001-8345-1349 0000-0002-9795-5967 sigmoid colon compartment http://purl.obolibrary.org/obo/UBERON_0001159 A compartment representing the spleen. 0000-0001-8345-1349 0000-0002-9795-5967 spleen compartment http://purl.obolibrary.org/obo/UBERON_0002106 A skin compartment representing the stratum corneum layer. 0000-0001-8345-1349 0000-0002-9795-5967 stratum corneum compartment http://purl.obolibrary.org/obo/UBERON_0002027 A large intestine compartment representing the transverse colon. 0000-0001-8345-1349 0000-0002-9795-5967 transverse colon compartment http://purl.obolibrary.org/obo/UBERON_0001157 A compartment representing a physiological barrier limiting compound movement. 0000-0001-8345-1349 0000-0002-9795-5967 barrier compartment The amount of compound in the gut compartment. 0000-0001-8345-1349 0000-0002-9795-5967 agut amount in gut The amount of compound in the liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 aliver amount in liver The amount of compound in the kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 akidney amount in kidney The amount of compound in the filtrate compartment. 0000-0001-8345-1349 0000-0002-9795-5967 afiltrate amount in filtrate The amount of compound in the hypothetical delay compartment. 0000-0001-8345-1349 0000-0002-9795-5967 adelay amount in delay The amount of compound in the rest of the body compartment. 0000-0001-8345-1349 0000-0002-9795-5967 arestbody amount in restbody The amount of compound in the plasma compartment. 0000-0001-8345-1349 0000-0002-9795-5967 aplasma amount in plasma The amount of compound in the brain compartment. 0000-0001-8345-1349 0000-0002-9795-5967 abrain amount in brain The amount of compound in the lung compartment. 0000-0001-8345-1349 0000-0002-9795-5967 alung amount in lung The amount of compound in the bone marrow compartment. 0000-0001-8345-1349 0000-0002-9795-5967 abm amount in bone marrow The amount of compound in the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 askin amount in skin The amount of compound in the mammary gland compartment. 0000-0001-8345-1349 0000-0002-9795-5967 amam amount in mammary gland A dimensionless fraction of volume defined as the filtrate volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 ffiltrate fraction of filtrate A dimensionless fraction of volume defined as the gut volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fgut fraction of gut A dimensionless fraction of volume defined as the mammary gland volume divided per unit of total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fmam fraction of mammary gland The dimensionless fraction of cardiac output delivered to the filtrate compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqfiltrate fraction of blood flow to filtrate The dimensionless fraction of cardiac output delivered to the bone marrow compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqbm fraction of blood flow to bone marrow The dimensionless fraction of cardiac output delivered to the gut compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqgut fraction of blood flow to gut The dimensionless fraction of cardiac output delivered to the mammary gland compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fqmam fraction of blood flow to mammary gland A partition coefficient representing the ratio of compound concentration in the brain to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 brain plasma pc brain plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the mammary gland to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 mam plasma pc mammary gland plasma partition coefficient A partition coefficient representing the ratio of compound concentration in the rest of body compartment to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 restbody plasma pc restbody plasma partition coefficient A partition coefficient representing the ratio of compound concentration in a generic tissue to plasma. 0000-0001-8345-1349 0000-0002-9795-5967 kt tissue plasma partition coefficient A biochemical parameter (rate constant) representing the rate at which a compound is cleared via urine, often scaled by body weight. 0000-0001-8345-1349 0000-0002-9795-5967 kurine c urinary rate constant A physiological parameter representing the period of lifespan (typically in years) for which the model is simulated. 0000-0001-8345-1349 0000-0002-9795-5967 age in PBPK model A volume parameter representing the total volume of the filtrate compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vfiltrate volume of filtrate A volume parameter representing the total volume of the bone marrow compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vbm volume of bone marrow A volume parameter representing the total volume of the gut compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vgut volume of gut A volume parameter representing the total volume of the mammary gland compartment. 0000-0001-8345-1349 0000-0002-9795-5967 vmam volume of mammary gland A volume parameter representing the check for total mass balance of all compartments (sum of organ volumes should equal body volume/weight equivalent, depending on units). 0000-0001-8345-1349 0000-0002-9795-5967 vmass bal volume of mass balance A volume parameter representing the total volume of red blood cells in whole blood. 0000-0001-8345-1349 0000-0002-9795-5967 vhct hematocrit volume A blood flow rate parameter representing the cardiac output specifically related to plasma flow. 0000-0001-8345-1349 0000-0002-9795-5967 qcplasma cardiac output rate of plasma A blood flow rate parameter specifically describing the rate to the filtrate compartment (representing glomerular filtration). 0000-0001-8345-1349 0000-0002-9795-5967 qfiltrate blood flow rate to filtrate A blood flow parameter specifically describing the rate to the bone marrow compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qbm blood flow rate to bone marrow A blood flow rate parameter specifically describing the rate to the gut compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qgut blood flow rate to gut A blood flow rate parameter specifically describing the rate to the mammary gland compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qmam blood flow rate to mammary gland A blood flow rate parameter representing the check for total blood flow mass balance of all the compartments (sum of organ flows should equal cardiac output). 0000-0001-8345-1349 0000-0002-9795-5967 qmassbal blood flow rate for mass balance A biochemical parameter representing the rate at which a compound is cleared via urine. 0000-0001-8345-1349 0000-0002-9795-5967 kurine urinary rate A biochemical parameter (Tm) representing the maximum rate of tubular resorption (e.g., in the kidney). 0000-0001-8345-1349 0000-0002-9795-5967 tmc resorption maximum A biochemical parameter or process representing the resorption of a compound (e.g., tubular resorption). 0000-0001-8345-1349 0000-0002-9795-5967 tm resorption A partition coefficient (Koa) representing the ratio of compound concentration in octanol to air at equilibrium. 0000-0001-8345-1349 0000-0002-9795-5967 koa octanol air partition coefficient The total concentration of compound in the gut compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cgut concentration in gut The total concentration of compound in the liver compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cliver concentration in liver The total concentration of compound in the brain compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cbrain concentration in brain The total concentration of compound in the kidney compartment. 0000-0001-8345-1349 0000-0002-9795-5967 ckidney concentration in kidney The total concentration of compound in the filtrate compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cfiltrate concentration in filtrate The total concentration of compound in the lung compartment. 0000-0001-8345-1349 0000-0002-9795-5967 clung concentration in lung The total concentration of compound in the fat compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cfat concentration in fat The total concentration of compound in the bone marrow compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cbm concentration in bone marrow The total concentration of compound in the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cksin concentration in skin The total concentration of compound in the mammary gland compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cmam concentration in mammary gland The total concentration of compound in the rest of body compartment. 0000-0001-8345-1349 0000-0002-9795-5967 crestbody concentration in restbody The total concentration of compound in the plasma compartment. 0000-0001-8345-1349 0000-0002-9795-5967 cplasma, cplasma_total concentration in plasma The amount of compound in the fat compartment. 0000-0001-8345-1349 0000-0002-9795-5967 afat amount in fat A parameter representing the time duration over which the model simulation runs. 0000-0001-8345-1349 0000-0002-9795-5967 PBPK model simulation time A compartment representing the arterial blood. 0000-0001-8345-1349 0000-0002-9795-5967 arterial blood compartment http://purl.obolibrary.org/obo/UBERON_0013755 A compartment representing the digestive system or parts thereof. 0000-0001-8345-1349 0000-0002-9795-5967 digestive system compartment http://purl.obolibrary.org/obo/UBERON_0001007 A compartment representing material eliminated from the body (e.g., urine, feces). 0000-0001-8345-1349 0000-0002-9795-5967 excreta compartment http://purl.obolibrary.org/obo/UBERON_0000174 An excreta compartment specifically representing feces. 0000-0001-8345-1349 0000-0002-9795-5967 feces compartment http://purl.obolibrary.org/obo/UBERON_0001988 An excreta compartment specifically representing urine. 0000-0001-8345-1349 0000-0002-9795-5967 urine compartment http://purl.obolibrary.org/obo/UBERON_0001088 A compartment representing the kidney(s). 0000-0001-8345-1349 0000-0002-9795-5967 kidney compartment http://purl.obolibrary.org/obo/UBERON_0002113 A compartment representing the liver. 0000-0001-8345-1349 0000-0002-9795-5967 liver compartment http://purl.obolibrary.org/obo/UBERON_0002107 A compartment representing the lung(s). 0000-0001-8345-1349 0000-0002-9795-5967 lung compartment http://purl.obolibrary.org/obo/UBERON_0002048 A compartment representing the venous blood. 0000-0001-8345-1349 0000-0002-9795-5967 venous blood compartment http://purl.obolibrary.org/obo/UBERON_0013756 A blood flow rate to skin parameter specifically describing the rate to the unexposed portion of the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qskinu blood flow rate to unexposed skin A blood flow rate to skin parameter specifically describing the rate to the exposed portion of the skin compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qskine blood flow rate to exposed skin A blood flow rate to skin parameter specifically describing the rate to the unexposed stratum corneum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qskinscu blood flow rate to skin stratum corneum unexposed A blood flow rate to skin parameter specifically describing the rate to the exposed stratum corneum compartment. 0000-0001-8345-1349 0000-0002-9795-5967 qskinsce blood flow rate to skin stratum corneum exposed A digestive system compartment representing the stomach. 0000-0001-8345-1349 0000-0002-9795-5967 stomach compartment http://purl.obolibrary.org/obo/UBERON_0000945 A partition coefficient representing the ratio of compound concentration in bone to blood. 0000-0001-8345-1349 0000-0002-9795-5967 bone blood pc bone blood partition coefficient A partition coefficient representing the ratio of compound concentration in air to blood. 0000-0001-8345-1349 0000-0002-9795-5967 air blood pc air blood partition coefficient A partition coefficient representing the ratio of compound concentration in brain to blood. 0000-0001-8345-1349 0000-0002-9795-5967 brain blood pc brain blood partition coefficient A partition coefficient representing the ratio of compound concentration in the fetal brain to blood. 0000-0001-8345-1349 0000-0002-9795-5967 brainfetus blood pc brainfetus blood partition coefficient A partition coefficient representing the ratio of compound concentration in gonads to blood. 0000-0001-8345-1349 0000-0002-9795-5967 gonad blood pc gonad blood partition coefficient A partition coefficient representing the ratio of compound concentration in the gut to blood. 0000-0001-8345-1349 0000-0002-9795-5967 gut blood pc gut blood partition coefficient A partition coefficient representing the ratio of compound concentration in the heart to blood. 0000-0001-8345-1349 0000-0002-9795-5967 heart blood pc heart blood partition coefficient A partition coefficient representing the ratio of compound concentration in the intestine to blood. 0000-0001-8345-1349 0000-0002-9795-5967 intestine blood pc intestine blood partition coefficient A partition coefficient representing the ratio of compound concentration in the kidney to blood. 0000-0001-8345-1349 0000-0002-9795-5967 kidney blood pc kidney blood partition coefficient A partition coefficient representing the ratio of compound concentration in the fetal kidney to blood. 0000-0001-8345-1349 0000-0002-9795-5967 kidneyfetus blood pc kidneyfetus blood partition coefficient A partition coefficient representing the ratio of compound concentration in the liver to blood. 0000-0001-8345-1349 0000-0002-9795-5967 liver blood pc liver blood partition coefficient A partition coefficient representing the ratio of compound concentration in the fetal liver to blood. 0000-0001-8345-1349 0000-0002-9795-5967 liverfetus blood pc liverfetus blood partition coefficient A partition coefficient representing the ratio of compound concentration in the lung to blood. 0000-0001-8345-1349 0000-0002-9795-5967 lung blood pc lung blood partition coefficient A partition coefficient representing the ratio of compound concentration in the mammary gland to blood. 0000-0001-8345-1349 0000-0002-9795-5967 mam blood pc mammary gland blood partition coefficient A partition coefficient representing the ratio of compound concentration in milk to blood. 0000-0001-8345-1349 0000-0002-9795-5967 milk blood pc milk blood partition coefficient A partition coefficient representing the ratio of compound concentration in muscle to blood. 0000-0001-8345-1349 0000-0002-9795-5967 muscle blood pc muscle blood partition coefficient A partition coefficient representing the ratio of compound concentration in the pancreas to blood. 0000-0001-8345-1349 0000-0002-9795-5967 pancreas blood pc pancreas blood partition coefficient A partition coefficient representing the ratio of compound concentration in the poorly perfused compartment to blood. 0000-0001-8345-1349 0000-0002-9795-5967 poor perfused blood pc poor perfused blood partition coefficient A partition coefficient representing the ratio of compound concentration in the rest of body compartment to blood. 0000-0001-8345-1349 0000-0002-9795-5967 restbody blood pc restbody blood partition coefficient A partition coefficient representing the ratio of compound concentration in the fetal rest of body compartment to blood. 0000-0001-8345-1349 0000-0002-9795-5967 restbodyfetus blood pc restbodyfetus blood partition coefficient A partition coefficient representing the ratio of compound concentration in the richly perfused compartment to blood. 0000-0001-8345-1349 0000-0002-9795-5967 rich perfused blood pc rich perfused blood partition coefficient A partition coefficient representing the ratio of compound concentration in the skin to blood. 0000-0001-8345-1349 0000-0002-9795-5967 skin blood pc skin blood partition coefficient A partition coefficient representing the ratio of compound concentration in the spleen to blood. 0000-0001-8345-1349 0000-0002-9795-5967 spleen blood pc spleen blood partition coefficient A partition coefficient representing the ratio of compound concentration in the stomach to blood. 0000-0001-8345-1349 0000-0002-9795-5967 stomach blood pc stomach blood partition coefficient An unbound fraction parameter specifically for plasma. 0000-0001-8345-1349 0000-0002-9795-5967 fuplasma fraction unbound plasma A maximum rate (Vmax) of an enzyme catalysed reaction for a compound across the apical membrane of an organ when the enzyme is saturated with substrate. 0000-0001-8345-1349 0000-0002-9795-5967 Vmax apical maximum rate of apical transporter Maximum rate (Vmax) of transport via a basolateral transporter. 0000-0001-8345-1349 0000-0002-9795-5967 vmax baso maximum rate of basolateral transporter A physiological parameter representing the dimensionless fraction computed by dividing the volume of the compartment by the total body weight. 0000-0001-8345-1349 0000-0002-9795-5967 fraction of volume of compartment A physiological parameter representing dimensionless fraction of cardiac output delivered to a compartment. 0000-0001-8345-1349 0000-0002-9795-5967 fraction of blood flow to a compartment A biochemical parameter representing the apparent permeability of a compound specifically between the compartments. 0000-0001-8345-1349 0000-0002-9795-5967 apparent permeability A biochemical parameter representing Vmax of the enzymatic activity 0000-0001-8345-1349 0000-0002-9795-5967 maximum rate An output parameter representing the amount of chemical specifically in the compartment 0000-0001-8345-1349 0000-0002-9795-5967 amount of compound in compartment An output parameter representing the total concentration of compound in the compartment. 0000-0001-8345-1349 0000-0002-9795-5967 concentration of compound in compartment A part of brain compartment representing the hippocampus region of the brain 0000-0001-8345-1349 0000-0002-9795-5967 hippocampus compartment A part of brain compartment representing the cerebrum region of the brain 0000-0001-8345-1349 0000-0002-9795-5967 cerebrum compartment A part of brain compartment representing the cerebellum region of the brain 0000-0001-8345-1349 0000-0002-9795-5967 cerebellum compartment http://purl.obolibrary.org/obo/UBERON_0002037 A part of brain compartment representing the frontal cortex region of the brain 0000-0001-8345-1349 0000-0002-9795-5967 frontal cortex compartment http://purl.obolibrary.org/obo/UBERON_0001870 A part of brain compartment representing the cerebrospinal fluid region of the brain 0000-0001-8345-1349 0000-0002-9795-5967 cerebrospinal fluid compartment http://purl.obolibrary.org/obo/UBERON_0001359 An unbound fraction parameter specifically for the blood compartment. 0000-0003-1673-5725 fublood fraction unbound blood The amount of compound in the blood compartment. 0000-0003-1673-5725 ablood amount in blood An unbound fraction parameter specifically for the rest of the body compartment. 0000-0003-1673-5725 furestbody fraction unbound restbody A skin compartment representing the exposed part of the skin to the chemical via dermal contact. 0000-0003-1673-5725 exposed skin compartment A skin compartment representing the unexposed part of the skin to the chemical such as regions covered by clothing or occluded areas like the inner arms. 0000-0003-1673-5725 unexposed skin compartment A dimensionless fraction of volume defined as the arterial plasma volume divided per unit of total body weight. 0000-0003-1673-5725 farterialplasma fraction of arterial plasma volume A dimensionless fraction of volume defined as the venous plasma volume divided per unit of total body weight. 0000-0003-1673-5725 fvenousplasma fraction of venous plasma volume The amount of compound in the richly perfused tissue compartment. 0000-0003-1673-5725 arichlyperfused amount in richly perfused tissue The amount of compound in the poorly perfused tissue compartment. 0000-0003-1673-5725 apoorlyperfused amount in poorly perfused tissue The amount of compound in the arterial blood compartment. 0000-0003-1673-5725 aarterialblood amount in arterial blood The amount of compound in the venous blood compartment. 0000-0003-1673-5725 avenousblood amount in venous blood The amount of compound in the alveolar air compartment. 0000-0003-1673-5725 aalveolar amount in alveolar air A compartment representing the red blood cells of the body. 0000-0003-1673-5725 red blood cell compartment A physiological parameter representing the thickness of the skin compartment 0000-0003-1673-5725 skin thickness A physiological parameter representing the rate of fluid flow to a particular compartment. 0000-0001-8345-1349 0000-0002-9795-5967 bodily fluid flow rate parameter The amount of chemical in viable epidermis of unexposed skin 0000-0003-1673-5725 askin_u amount in viable epidermis of unexposed skin The amount of chemical in viable epidermis of exposed skin 0000-0003-1673-5725 askin_e amount in viable epidermis of exposed skin The amount of chemical in skin stratum corneum of unexposed skin 0000-0003-1673-5725 askin_sc_u amount in skin stratum corneum of unexposed skin The amount of chemical in skin stratum corneum of exposed skin 0000-0003-1673-5725 askin_sc_e amount in skin stratum corneum of exposed skin An absorption rate constant parameter representing dermal absorption rate flux through unexposed skin 0000-0003-1673-5725 fs_u dermal absorption rate unexposed skin An absorption rate constant parameter representing dermal absorption rate flux through exposed skin 0000-0003-1673-5725 fs_e dermal absorption rate exposed skin A skin thickness parameter representing the thickness of stratum corneum. 0000-0003-1673-5725 height_sc Thickness_SC thickness stratum corneum A skin thickness parameter representing the thickness of viable epidermis. 0000-0003-1673-5725 height_vs thickness_ve thickness viable epidermis A partition coefficient representing the ratio of compound concentration in fat to blood. 0000-0003-1673-5725 fat blood pc PCFat fat blood partition coefficient A biochemical parameter representing the diffusion rate of the chemical 0000-0003-1673-5725 diffusion rate A diffusion rate parameter representing diffusion rate of the chemical across the skin 0000-0003-1673-5725 diffusion rate skin A diffusion rate skin parameter representing diffusion rate from stratum corneum to viable epidermis 0000-0003-1673-5725 kp_sc_vs diffusion rate stratum corneum viable epidermis A parameter being used in the model but does not belong to specific parameter subclass 0000-0003-1673-5725 miscellaneous parameter A flag indicating for Michaelis-Menten or linear metabolism equation being used in the model 0000-0003-1673-5725 Michaelis A dimensionless fraction of volume defined as the arterial blood volume divided per unit of total body weight. 0000-0003-1673-5725 farterialblood scvart fraction of arterial blood volume 0000-0001-8893-1587 0000-0002-0280-0111 pgp 0000-0001-8893-1587 0000-0002-0280-0111 mrp2 0000-0001-8893-1587 0000-0002-0280-0111 mrp4 0000-0001-8893-1587 0000-0002-0280-0111 bcrp 0000-0001-8893-1587 0000-0002-0280-0111 nctp 0000-0001-8893-1587 0000-0002-0280-0111 oct1 0000-0001-8893-1587 0000-0002-0280-0111 oat1 0000-0001-8893-1587 0000-0002-0280-0111 oat3 0000-0001-8893-1587 0000-0002-0280-0111 oat4 A compartment representing the bile storage 0000-0002-6705-835X bile compartment A compartment representing the colon 0000-0002-6705-835X colon compartment A compartment representing the small intestinal tissue 0000-0002-6705-835X small intestine tissue compartment A compartment representing the whole intestinal tissue 0000-0002-6705-835X intestinal tissue compartment A compartment with grouped organs that are exclusively perfused via the portal vein (i.e.: Stomach, small and large intestine, spleen) 0000-0002-6705-835X portal vein perfused tissue comparment A part of kidney compartment in the model representing glomerulus in the body 0000-0001-8345-1349 0000-0002-9795-5967 gfr compartment glomerulus compartment http://purl.obolibrary.org/obo/UBERON_0000074 A compartment representing menstrual plasma 0009-0001-7071-8646 menstrual plasma compartment A compartment representing rest of the lumen of kidney. 0009-0001-7071-8646 kidney rest lumen compartment A compartment representing rest of the tissue of kidney. 0009-0001-7071-8646 kidney proximal tubule tissue compartment A compartment representing vascular and interstitial space of the liver. 0009-0001-7071-8646 liver extracellular compartment A compartment representing intracellular space of the liver. 0009-0001-7071-8646 liver intracellular space compartment A digestive system compartment representing the gastro-intestinal tract 0000-0002-7534-0937 gastro intestinal tract compartment A compartment representing gonads. 0000-0002-7534-0937 gonad compartment The absorption rate constant parameter representing the intrinsic rate of the chemical release from stomach to lumen or the jejunum segment 0000-0002-6705-835X kstoC intrinsic gastric emptying rate The absorption rate constant parameter representing the intrinsic absorption rate from the gut or any intestinal segment to the liver or the portal vein 0000-0002-6705-835X kabsC intrinsic absorption rate The absorption rate constant parameter representing the intrinsic absorption rate of a chemical from the stomach to the gut tissue or any intestinal segment 0000-0002-6705-835X k0C intrinsic stomach uptake rate The absorption rate constant parameter representing the absorption rate from stomach to gut tissue or any intestine segment 0000-0002-6705-835X k0 stomach uptake rate 0000-0002-6705-835X intrinsic fecal excretion rate 0000-0002-6705-835X fecal excretion rate 0000-0002-6705-835X intrinsic biliary clearance rate 0000-0002-6705-835X kinetic emptying rate from jejunum lumen to ileum lumen 0000-0002-6705-835X kinetic emptying rate from ileum lumen to large intestine lumen 0000-0002-6705-835X kinetic absorption rate from jejunum lumen to intestinal tissue 0000-0002-6705-835X kinetic absorption rate from ileum lumen to intestinal tissue 0000-0002-6705-835X kinetic absorption rate from large intestinal lumen to intestinal tissue 0000-0002-6705-835X effective Caco-2 permeability 0000-0002-6705-835X apparent Caco-2 permeability 0000-0002-6705-835X kinetic emptying rate between intestinal segments 0000-0002-6705-835X Hill dissociation constant 0000-0002-6705-835X Hill coefficient 0000-0002-6705-835X intrinsic absorption rate of metabilite 0000-0002-6705-835X absorption rate of metabolite 0000-0002-6705-835X intrinsic enterohepatic recirculation rate constant 0000-0002-6705-835X enterohepatic recirculation rate constant 0000-0002-6705-835X intrinsic reabsorption rate constant 0000-0002-6705-835X reabsorption rate constant 0000-0002-6705-835X maximum capacity of binding sites in red cells 0000-0002-6705-835X half-saturation concentration of chemical for binding by sites in red cells 0000-0002-6705-835X metabolism rate constant in liver 0000-0002-6705-835X metabolism rate constant in intestinal tissue 0000-0002-6705-835X red blood cells partition coefficient follicle permeability coefficient partition coeffcient of stratum corneum to viable epidermis partition coeffcient of viable epidermis to blood partition coeffcient of stratum corneum to skin surface depot partition coeffcient of follicle to skin surface depot octanol water partition coefficient medium polymer partition coefficient medium air partition coefficient medium mitochondria partition coefficient medium lysosomes partition coefficient medium intracellular water partition coefficient medium microsomes partition coefficient medium other organelles partition coefficient medium albumin partition coefficient abiotic degradation rate in medium acidic phospholipid association constant abiotic degradation rate in air maximum metabolic rate linear metabolic rate cell radius cell replication time cell fraction of proteins cell fraction of lipids cell fraction of intracellular water cell fraction of mitochondria cell fraction of lysosomes cell fraction of microsomes fraction of neutral lipids in the FBS fraction of albumin in the FBS culture area top well diameter well depth plate wall thickness culture medium pH fraction of serum in total media FBS pH initial number of cells nominal concentration of medium volume of medium fraction of FBS iin the medium ionized fraction in the medium fraction unbound in the medium fraction unbound in the FBS fraction unbound in the cell A biochemical parameter representing the rate constant at which a compound is absorbed into systemic circulation or a target compartment from the site of administration 0000-0001-8345-1349 0000-0002-6705-835X 0000-0002-9795-5967 ka absorption rate constant An unbound fraction parameter specifically for the kidney proximal tubule. 0009-0001-7071-8646 fraction unbound kidney proximal tubule A bodily fluid flow rate parameter specifically describing the flow of plasma to a compartment. 0000-0002-6705-835X qplasma plasma flow rate A plasma flow rate parameter specifically describing the rate to the stomach compartment. 0000-0002-6705-835X plasma flow rate to stomach A plasma flow rate parameter specifically describing the rate to the intestine compartment. 0000-0002-6705-835X plasma flow rate to intestine A plasma flow rate parameter specifically describing the rate to the small intestine compartment. 0000-0002-6705-835X plasma flow rate to small intestine A plasma flow rate parameter specifically describing the rate to the large intestine compartment. 0000-0002-6705-835X plasma flow rate to large intestine A plasma flow rate parameter specifically describing the rate to the pancreas compartment. 0000-0002-6705-835X plasma flow rate to pancreas A plasma flow rate parameter specifically describing the rate to the liver compartment. 0000-0002-6705-835X plasma flow rate to liver A plasma flow rate parameter specifically describing the rate to the kidney compartment. 0000-0002-6705-835X plasma flow rate to kidney A plasma flow rate parameter specifically describing the rate to the muscle compartment. 0000-0002-6705-835X plasma flow rate to muscle A plasma flow rate parameter specifically describing the rate to the heart compartment. 0000-0002-6705-835X plasma flow rate to heart A plasma flow rate parameter specifically describing the rate to the fat compartment. 0000-0002-6705-835X qfat_p plasma flow rate to fat A plasma flow rate parameter specifically describing the rate to the gonad compartment. 0000-0002-6705-835X plasma flow rate to gonad A plasma flow rate parameter specifically describing the rate to the skin compartment. 0000-0002-6705-835X plasma flow rate to skin A plasma flow rate parameter specifically describing the rate to the bone compartment. 0000-0002-6705-835X qbone_p plasma flow rate to bone A plasma flow rate parameter specifically describing the rate to the brain compartment. 0000-0002-6705-835X qbrain_p plasma flow rate to brain A plasma flow rate parameter specifically describing the rate to the spleen compartment. 0000-0002-6705-835X plasma flow rate to spleen A plasma flow rate parameter specifically describing the rate to the lung compartment. 0000-0002-6705-835X plasma flow rate to lung A plasma flow rate parameter specifically describing the rate to the poorly perfused compartment. 0000-0002-6705-835X plasma flow rate to poorly perfused A plasma flow rate parameter specifically describing the rate to the richly perfused compartment. 0000-0002-6705-835X plasma flow rate to richly perfused A plasma flow rate parameter specifically describing the rate to the rest of the body compartment. 0000-0002-6705-835X plasma flow rate to restbody A plasma flow rate parameter specifically describing the rate to the gall bladder compartment. 0000-0002-6705-835X plasma flow rate to gall bladder A plasma flow rate parameter specifically describing the rate to the portal vein compartment. 0000-0002-6705-835X plasma flow rate to portal vein A plasma flow rate parameter specifically describing the rate to the lymph compartment. 0000-0002-6705-835X plasma flow rate to lymph A plasma flow rate parameter specifically describing the rate to the duodenum compartment. 0000-0002-6705-835X qduodenum_p plasma flow rate to duodenum A plasma flow rate parameter specifically describing the rate to the jejunum compartment. 0000-0002-6705-835X plasma flow rate to jejunum A plasma flow rate parameter specifically describing the rate to the ileum compartment. 0000-0002-6705-835X plasma flow rate to ileum A plasma flow rate parameter specifically describing the rate to the colon compartment. 0000-0002-6705-835X qcolon_p plasma flow rate to colon A plasma flow rate parameter specifically describing the rate to the cecum compartment. 0000-0002-6705-835X qcecum_p plasma flow rate to cecum A plasma flow rate parameter specifically describing the rate to the filtrate compartment. 0000-0002-6705-835X qfiltrate_p plasma flow rate to filtrate A plasma flow parameter specifically describing the rate to the bone marrow compartment. 0000-0002-6705-835X qbm_p plasma flow rate to bone marrow A plasma flow rate parameter specifically describing the rate to the gut compartment. 0000-0002-6705-835X plasma flow rate to gut A plasma flow rate parameter specifically describing the rate to the mammary gland compartment. 0000-0002-6705-835X plasma flow rate to mammary gland A plasma flow rate parameter representing the check for total plasma flow mass balance of all the compartments (sum of organ flows should equal cardiac output). 0000-0002-6705-835X qmassbal_p plasma flow rate for mass balance A plasma flow rate parameter specifically describing the rate to the unexposed skin compartment. 0000-0002-6705-835X plasma flow rate to unexposed skin A plasma flow rate parameter specifically describing the rate to the exposed skin compartment. 0000-0002-6705-835X qskine_p plasma flow rate to exposed skin A plasma flow rate parameter specifically describing the rate to the unexposed stratum corneum compartment. 0000-0002-6705-835X plasma flow rate to skin stratum corneum unexposed A plasma flow rate parameter specifically describing the rate to the exposed stratum corneum compartment. 0000-0002-6705-835X plasma flow rate to skin stratum corneum exposed 0000-0002-6705-835X fraction of blood flow to red blood cells 0000-0002-6705-835X blood flow rate to red blood cells 0000-0002-6705-835X volumen of lumen 0000-0002-6705-835X volume of small intestine tissue 0000-0002-6705-835X volume of bile 0000-0002-6705-835X enterocyte volume 0000-0002-6705-835X hepatic vein blood flow 0000-0002-6705-835X blood flow rate to bile diameter of intestinal diameter of the jejunum lumen diameter of the ileum lumen diameter of the large intestine lumen surface area of the jejunum lumen surface area of the ileum lumen surface area of the large intestine lumen uptake fraction to blood fraction of bile in small intestine fraction of bile in liver fraction of feces volume fraction of blood volume fraction of red blood cells skin area thickness epidermis volume of exposed viable epidermis volume of follicle area of exposed skin volume of serum volume of adrenals volume of breast volume of thyroid volume of intestinal lumen volume of small intestinal lumen volume of large intestinal lumen volume of stomach lumen volume of gut intestinal tract volume of testis volume of uterus volume of skeleton volume of hair volume of urinary tract volume of skin surface depot volume of cortical bone volume of trabecular bone volume of alveolar compartment fraction of serum fraction of adrenals fraction of breast fraction of thyroid fraction of intestinal lumen fraction of small intestinal lumen fraction of large intestinal lumen fraction of stomach lumen fraction of gut intestinal tract fraction of testis fraction of uterus fraction of skeleton fraction of hair fraction of amniotic fluid fraction of urinary tract fraction of cortical bone fraction of trabecular bone fraction of the skin surface depot A dimensionless fraction of volume defined as the blood volume divided per unit of total body weight. 0009-0001-7071-8646 fraction of blood A dimensionless fraction of volume defined as the bone marrow volume divided per unit of total body weight. 0009-0001-7071-8646 fraction of bone marrow A dimensionless fraction of volume defined as the bone non perfuse volume divided per unit of total body weight. 0009-0001-7071-8646 fraction of bone non perfused A dimensionless fraction of volume defined as the adipose mass volume divided per unit of total body weight. 0009-0001-7071-8646 fraction of fat mass fraction of adipose mass A dimensionless fraction of volume defined as the intestinal tissue volume divided per unit of total body weight. 0009-0001-7071-8646 fraction of intestinal tissue A volume parameter representing the total volume of the kidney rest tissue compartment. 0009-0001-7071-8646 volume of kidney rest tissue A volume parameter representing the total volume of the kidney rest lumen compartment. 0009-0001-7071-8646 volume of kidney rest lumen A volume parameter representing the total volume of the lumen of kidney proximal tubule compartment. 0009-0001-7071-8646 volume of kidney proximal tubule lumen A volume parameter representing the total volume of the tissue of kidney proximal tubule compartment. 0009-0001-7071-8646 volume of kidney proximal tubule tissue A volume parameter representing the total volume of the vascular and interstitial spaces of liver compartment. 0009-0001-7071-8646 volume of liver extracellular A volume parameter representing the total volume of the hepatocytes in liver compartment. 0009-0001-7071-8646 volume of hepatocytes volume of liver intracellular space A volume parameter representing the total volume of the tissue of intestine compartment. 0009-0001-7071-8646 volume of intestine tissue A physicochemical parameter representing the volume of one mole of a molecule. 0000-0001-8893-1587 0000-0002-0280-0111 MV molar volume A physicochemical parameter describing the volatily of a compound 0000-0001-8893-1587 0000-0002-0280-0111 Henry Henry's law constant A physicochemical parameter describing the vapor pressure of the compound 0000-0003-1673-5725 VP vapor pressure 0000-0002-6705-835X unbound venous concentration of compound in compartment 0000-0002-6705-835X unbound concentration of compund in compartment The amount of chemical in stomach compartment. 0000-0002-6705-835X asto amount in stomach The amount of chemical in small intestine compartment 0000-0002-6705-835X asi amount in small intestine The amount of chemical in jejunum compartment. 0000-0002-6705-835X aj amount in jejunum The amount of chemical in ileum compartment. 0000-0002-6705-835X ai amount in ileum The amount of chemical in large intestine compartment. 0000-0002-6705-835X ali amount in large intestine The amount of chemical in lumen of the intestine. 0000-0002-6705-835X alumen amount in lumen The amount of chemical in segment of small intestine. 0000-0002-6705-835X asi_segment amount in small intestine segment The amount of chemical in colon compartment. 0000-0002-6705-835X acolon amount in colon The amount of chemical in bile. 0000-0002-6705-835X abile amount in bile The amount of chemical in spleen compartment 0000-0002-6705-835X aspleen amount in spleen The amount of chemical in duodenum compartment. 0000-0002-6705-835X aduo amount in duodenum The amount of chemical in intestinal tissue 0000-0002-6705-835X ait amount in intestinal tissue The amount of chemical in portal vein. 0000-0002-6705-835X apv amount in portal vein The unbound concentration of compound in the plasma compartment. 0000-0002-6705-835X cplasma_unbound unbound concentration in plasma The unbound venous concentration of compound in the liver compartment. 0000-0002-6705-835X cvliver_unbound unbound venous liver concentration The unbound venous concentration of compound in the gut compartment. 0000-0002-6705-835X cvgut_unbound unbound venous gut concentration The unbound venous concentration of compound in the brain compartment. 0000-0002-6705-835X cvbrain_unbound unbound venous brain concentration The unbound venous concentration of compound in the kidney compartment. 0000-0002-6705-835X cvkidney_unbound unbound venous kidney concentration The unbound venous concentration of compound in the filtrate compartment. 0000-0002-6705-835X cvfiltrate_unbound unbound venous filtrate concentration The unbound venous concentration of compound in the lung compartment. 0000-0002-6705-835X cvlung_unbound unbound venous lung concentration The unbound venous concentration of compound in the fat compartment. 0000-0002-6705-835X cvfat_unbound unbound venous fat concentration The unbound venous concentration of compound in the bone marrow compartment. 0000-0002-6705-835X cvbm_unbound unbound venous bone marrow concentration The unbound venous concentration of compound in the skin compartment. 0000-0002-6705-835X cvksin_unbound unbound venous skin concentration The unbound venous concentration of compound in the mammary gland compartment. 0000-0002-6705-835X cvmam_unbound unbound venous mammary gland concentration The unbound venous concentration of compound in the rest body compartment. 0000-0002-6705-835X cvrestbody_unbound unbound venous rest body concentration 0000-0002-6705-835X total venous concentration of compound in compartment The total venous concentration of compound in the liver compartment. 0000-0002-6705-835X cvliver total venous liver concentration The total venous concentration of compound in the gut compartment. 0000-0002-6705-835X cvgut total venous gut concentration The total venous concentration of compound in the kidney compartment. 0000-0002-6705-835X cvkidney total venous kidney concentration The total venous concentration of compound in the brain compartment. 0000-0002-6705-835X cvbrain total venous brain concentration The total venous concentration of compound in the filtrate compartment. 0000-0002-6705-835X cvfiltrate total venous filtrate concentration The total venous concentration of compound in the lung compartment. 0000-0002-6705-835X cvlung total venous lung concentration The total venous concentration of compound in the fat compartment. 0000-0002-6705-835X cvfat total venous fat concentration The total venous concentration of compound in the bone marrow compartment. 0000-0002-6705-835X cvbm total venous bone marrow concentration The total venous concentration of compound in the skin compartment. 0000-0002-6705-835X cvksin total venous skin concentration The total venous concentration of compound in the mammary gland compartment. 0000-0002-6705-835X cvmam total venous mammary gland concentration The total venous concentration of compound in the rest of the body compartment. 0000-0002-6705-835X cvrestbody total venous rest body concentration The concentration of chemical in stomach compartment. 0000-0002-6705-835X csto concentration in stomach The concentration of chemical in small intestine compartment. 0000-0002-6705-835X csi concentration in small intestine The concentration of chemical in jejunum compartment. 0000-0002-6705-835X cj concentration in jejunum The concentration of chemical in ileum compartment. 0000-0002-6705-835X ci concentration in ileum The concentration of chemical in large intestine compartment. 0000-0002-6705-835X cli concentration in large intestine The concentration of chemical in tissue of intestine. 0000-0002-6705-835X cit concentration in intestinal tissue The concentration of chemical in lumen of intestine. 0000-0002-6705-835X clumen concentration in lumen The concentration of chemical in bile. 0000-0002-6705-835X cbile concentration in bile The concentration of chemical in spleen compartment. 0000-0002-6705-835X cspleen concentration in spleen The concentration of chemical in feces. 0000-0002-6705-835X cfeces concentration in feces amount in skin surface depot The maximum amount of chemical in a compartment 0000-0002-6705-835X amax maximum amount amount in follicles concentration in medium concentration in cell concentration in mitochondria concentration in lysosomes concentration in microsomes concentration in intracellular water concentration in polymer concentration in air The amount of compound in the menstrual compartment. 0009-0001-7071-8646 amount in menstrual The amount of compound in the kidney rest tissue compartment. 0009-0001-7071-8646 amount in kidney rest tissue The amount of compound in the rest of kidney lumen compartment. 0009-0001-7071-8646 amount in rest of kidney lumen amount in kidney rest lumen The amount of compound in the proximal tubule tissue of kidney compartment. 0009-0001-7071-8646 amount in kidney proximal tubule tissue The amount of compound in the proximal tubule lumen of kidney compartment. 0009-0001-7071-8646 amount in kidney proximal tubule lumen The amount of compound in the intracellular spaceof liver compartment. 0009-0001-7071-8646 amount in liver intracellular The amount of compound in the extracellular space of liver compartment. 0009-0001-7071-8646 amount in liver extracellular invitro pbpk An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. amino acid chain Anatomical entity that has mass. material anatomical entity Anatomical entity that has no mass. immaterial anatomical entity Anatomical group whose component anatomical structures lie in close proximity to each other. anatomical cluster 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. anatomical entity length unit mass unit time unit temperature unit substance unit concentration unit volume unit frequency unit volumetric flow rate unit rate unit Western Australian Mulga Shrublands Ecoregion Australasia Ecoregion Tirari-Sturt Stony Desert Ecoregion Simpson Desert Region Pilbara Shrublands Ecoregion Carnarvon Xeric Shrublands Ecoregion Central Ranges Xeric Shrub Ecoregion Gibson Desert Ecoregion The Great Sandy-Tanami Desert Ecoregion Great Victoria Desert Ecoregion Nullarbor Plains Xeric Shrubland Ecoregion Afrotropical Ecoregion Succulent Karoo Ecoregion Yemen and Saudi Arabia Ecoregion Yemen, Saudi Arabia, and Oman Ecoregion Somali Montane Xeric Woodland Ecoregion Socotran Archipelago Ecoregion Red Sea Coastal Desert Ecoregion Namibian Savanna Woodland Ecoregion Namib Desert Ecoregion Nama Karoo Ecoregion Masai Xeric Grasslands and Shrublands Ecoregion Madagascar Succulent Woodlands Ecoregion Madagascar Spiny Thickets Ecoregion Kaokoveld Desert Ecoregion Kalahari Xeric Savanna Ecoregion Ile Europa and Bassas da India Ecoregion Hobyo Grassland and Shrubland Ecoregion Oman and United Arab Emirates Ecoregion Ethiopian Xeric Grasslands and Shrublands Ecoregion Eritrean Coastal Desert Ecoregion East Saharan Montane Xeric Woodland Ecoregion Oman, Yemen, and Saudi Arabia Ecoregion Aldabra Island Xeric Scrub Ecoregion Indo-Malay Ecoregion Thar Desert Northwestern Thorn Scrub Forests Stellar radiation emitted from Sol. Solar radiation example to be eventually removed example to be eventually removed failed exploratory term The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. PERSON:Alan Ruttenberg organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. placeholder removed terms merged The term has been combined with one or more other terms to create a more encompassing (merged) term. The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported The term has been replaced by a term imported from another ontology. This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. term imported term split The term has been split into two or more new terms. This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel Transformation-ML ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel ACS XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel XML RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel RDF zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel zip tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel tar FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel FCS Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel Compensation-ML Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel Gating-ML OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel OWL An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Philippe Rocca-Serra Thermo Philippe Rocca-Serra Waters Philippe Rocca-Serra BIO-RAD James Malone GenePattern hierarchical clustering Philippe Rocca-Serra Ambion Philippe Rocca-Serra Helicos Philippe Rocca-Serra Roche Philippe Rocca-Serra Illumina GenePattern PCA GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM James Malone GenePattern k-nearest neighbors GenePattern LOOCV James Malone GenePattern k-means clustering Philippe Rocca-Serra Agilent GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone GenePattern module KMeansClustering James Malone GenePattern CART GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation Philippe Rocca-Serra Li-Cor Philippe Rocca-Serra Bruker Corporation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering James Malone GenePattern SVM Philippe Rocca-Serra Applied Biosystems GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone GenePattern module PCA James Malone Ryan Brinkman GenePattern peak matching Philippe Rocca-Serra Bruker Daltonics The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan U.S. Food and Drug Administration right handed ambidexterous left handed The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. PERSON:Alan Ruttenberg PERSON:Jessica Turner Edingburgh handedness inventory Karin Breuer eBioscience Karin Breuer Cytopeia Karin Breuer Exalpha Biological Karin Breuer Apogee Flow Systems Karin Breuer Exbio Antibodies Karin Breuer Becton Dickinson (BD Biosciences) Karin Breuer Dako Cytomation Karin Breuer Millipore Karin Breuer Antigenix Karin Breuer Partec Karin Breuer Beckman Coulter Karin Breuer Advanced Instruments Inc. (AI Companies) Karin Breuer Miltenyi Biotec Karin Breuer AES Chemunex Karin Breuer Bentley Instruments Karin Breuer Invitrogen Karin Breuer Luminex Karin Breuer CytoBuoy An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis Thermo Fisher Scientific A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1: Well differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2: Moderately differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G3: Poorly differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4: Undifferentiated A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Chris Stoeckert, Helena Ellis G1 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis G2 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis G3 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Chris Stoeckert, Helena Ellis G4 (Fuhrman) A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade ovarian tumor A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 (WHO) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis pT0 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis pTis (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis pT1 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis pT2 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. Chris Stoeckert, Helena Ellis pT3 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis pT4a (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis pT4b (colon) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis pT0 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis pTis (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). Chris Stoeckert, Helena Ellis pT1 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis pT1a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. Chris Stoeckert, Helena Ellis pT1b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. Chris Stoeckert, Helena Ellis pT2 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. Chris Stoeckert, Helena Ellis pT2a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. Chris Stoeckert, Helena Ellis pT2b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. Chris Stoeckert, Helena Ellis pT3 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. Chris Stoeckert, Helena Ellis pT4 (lung) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis pT0 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis pT1 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis pT1a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. Chris Stoeckert, Helena Ellis pT1b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis pT2 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. Chris Stoeckert, Helena Ellis pT2a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. Chris Stoeckert, Helena Ellis pT2b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. Chris Stoeckert, Helena Ellis pT3 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. Chris Stoeckert, Helena Ellis pT3a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis pT3b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. Chris Stoeckert, Helena Ellis pT3c (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). Chris Stoeckert, Helena Ellis pT4 (kidney) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis pT0 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis pT1 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis pT1a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis pT1b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis pT1c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis pT2 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis pT2a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis pT2b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis pT2c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis pT3 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis pT3a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis pT3b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis pT3c (ovary) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis pN0 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis pN1 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis pN1a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis pN1b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. Chris Stoeckert, Helena Ellis pN1c (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis pN2 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis pN2a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis pN2b (colon) A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis pN0 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. Chris Stoeckert, Helena Ellis pN1 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis pN2 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). Chris Stoeckert, Helena Ellis pN3 (lung) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis pN0 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis pN1 (kidney) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis pN0 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis pN1 (ovary) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis cM0 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. Chris Stoeckert, Helena Ellis cM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis cM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. Chris Stoeckert, Helena Ellis cM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis pM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis pM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. Chris Stoeckert, Helena Ellis pM1b (colon) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis cM0 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis cM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis cM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis cM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis pM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis pM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. Chris Stoeckert, Helena Ellis pM1b (lung) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis cM0 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis cM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis pM1 (kidney) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis cM0 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. Chris Stoeckert, Helena Ellis cM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. Chris Stoeckert, Helena Ellis pM1 (ovary) A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Chris Stoeckert, Helena Ellis Occult Carcinoma (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Chris Stoeckert, Helena Ellis Stage 0 (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Chris Stoeckert, Helena Ellis Stage IIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Chris Stoeckert, Helena Ellis Stage IIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Chris Stoeckert, Helena Ellis Stage IIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Chris Stoeckert, Helena Ellis Stage IIIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Chris Stoeckert, Helena Ellis Stage IIIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Chris Stoeckert, Helena Ellis Stage IIIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Chris Stoeckert, Helena Ellis Stage IVA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Chris Stoeckert, Helena Ellis Stage IVB (AJCC 7th) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Chris Stoeckert, Helena Ellis Stage IA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Chris Stoeckert, Helena Ellis Stage IA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Chris Stoeckert, Helena Ellis Stage IA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Chris Stoeckert, Helena Ellis Stage IB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Chris Stoeckert, Helena Ellis Stage IIIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Chris Stoeckert, Helena Ellis Stage IIIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Chris Stoeckert, Helena Ellis Stage 3 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Chris Stoeckert, Helena Ellis Stage 3C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Chris Stoeckert, Helena Ellis Stage Unknown (FIGO) An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. Chris Stoeckert, Helena Ellis 3: symptomatic in bed more than 50% of the day but not bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. Chris Stoeckert, Helena Ellis 2: symptomatic but in bed less than 50% of the day An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis 4: bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis 0: asymptomatic An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis 1: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis 100: asymptomatic A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis 80-90: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. Chris Stoeckert, Helena Ellis 60-70: symptomatic but in bed less than 50% of the day A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. Chris Stoeckert, Helena Ellis 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden An organization that is developing and selling nanopore sequencing products and is based in the UK. James A. Overton Oxford Nanopore Technologies An organization that manufactures mosquito traps and other mosquito control products. John Judkins BioGents A manufacturer of rapid point-of-care assay devices. John Judkins ORCID:0000-0001-6595-0902 Abbott A manufacturer of in vitro diagnostic assay kits in India. John Judkins ORCID:0000-0001-6595-0902 J. Mitra A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. John Judkins ORCID:0000-0001-6595-0902 InBios The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 out of scope The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). https://github.com/information-artifact-ontology/ontology-metadata/issues/136 domain entity does not exist A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. meter A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kilogram A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. second A length unit which is equal to one hundredth of a meter or 10^[-2] m. centimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. millimeter A length unit which is equal to one millionth of a meter or 10^[-6] m. micrometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nanometer A length unit which is equal to 10 [-10] m. angstrom A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. gram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. milligram A mass unit which is equal to one millionth of a gram or 10^[-6] g. microgram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. nanogram A mass unit which is equal to 10^[-12] g. picogram A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. degree Celsius A time unit which is equal to 60 seconds. minute A time unit which is equal to 3600 seconds or 60 minutes. hour A time unit which is equal to 24 hours. day A time unit which is equal to 7 days. week A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year A substance unit equal to a millionth of a mol or 10^[-6] mol. micromole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nanomole A substance unit equal to 10^[-12] mol. picomole A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). molar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. millimolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. micromolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nanomolar A unit of molarity which is equal to 10^[-12] M. picomolar A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cubic centimeter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. milliliter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. liter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter A volume unit which is equal to one millionth of a liter or 10^[-6] L. microliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nanoliter A volume unit which is equal to 10^[-12] L. picoliter A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. mass percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. mass volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. volume percentage A mass unit density which is equal to mass of an object in grams divided by the volume in liters. gram per liter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. milligram per milliliter A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. milliliter per liter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. gram per deciliter A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute A rate unit which is equal to one over one nanomolar second. count per nanomolar second A rate unit which is equal to one over one molar second. count per molar second A rate unit which is equal to one over one nanomolar. count per nanomolar A rate unit which is equal to one over one molar. count per molar A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. microgram per liter inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).