Alice Nzinga Chris Stoeckert Jan-Eric Litton Jie Zheng Loreana Norlin Maria Anderberg Martin N. Fransson Mathias Brochhausen Mikael Eriksson Roxana Merino-Martinez Sanela Kjellqvist William R. Hogan The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. MIABIS_v2_accepted and UPenn Biobank ontology Ontology for BIoBanking (OBIB) 2023-04-05 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred 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 in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). 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 has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type 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 expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to 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 first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 label is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) 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. is preceded by preceded_by 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 occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process span-of spanOf [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) has temporal occupant history-of historyOf [copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001 b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001 history of has-history hasHistory b has_history c iff c history_of b [XXX-001 [copied from inverse property 'history of'] b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001 has history A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2. 'is subordinate authority of' Domain: governing organization Range: governing organization Formal properties: transitive, anti-symmetric, irreflexive Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2. is subordinate authority of has measurement unit label This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.. Mathias Brochhausen designates p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context. Mathias Brochhausen is designated by results_in A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Person: Jie Zheng, Chris Stoeckert Penn Group has maximum capacity A relation that relates a container to a measurement datum that specifies the actual amount of material in the container. Person: Jie Zheng, Chris Stoeckert Penn Group has actual load Mathias Brochhausen This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. owns a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a. Mathias Brochhausen Mathias Brochhausen A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl administrates a is contact information for b, if a is a information content entity, b is a human being or an organization and a identifies a physical location or electronic resource that allows to initiate communication with a. Mathias Brochhausen is contact information about a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. is owned by provides_service_consumer_with The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization has disposition to bind A relationship between two material entitites that each have disposition to form a complex with the other. This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other IEDB has disposition to bind has organization member Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng has organization member specifies value of A relation between a value specification and an entity which the specification is about. specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification Mathias Brochhausen obsolete owns true Mathias Brochhausen obsolete administrates true Mathias Brochhausen obsolete is contact information about true Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204. obsolete is owned by true BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. is-aggregate-of true 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 Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. 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 participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically 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. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary 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 temporally related to inverse of starts with starts 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. consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. produces has output p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). results in developmental progression of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) results in formation of 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 A relationship that holds between entities participating in some developmental process (GO:0032502) developmentally related to An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has input input of inverse of has output output of relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. 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 '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. influences (processual) causally upstream of or within 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 causally upstream of or within, negative effect DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. DEPRECATED inheres in true DEPRECATED bearer of true http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y RO lacks_part has measurement value has specified numeric value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified numeric value has specified value A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value A measurement datum that is the output of counting. Mathias Brochhausen A measurement datum that is the output of counting. count count The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting The planned process of finding the number of elements in a finite set of objects. counting age structure data set A data set consisting of measurements of age organized in age brackets. A data set consisting of measurements of age organized in age brackets. age data in age brackets data set An identifier curated by ORCID, Inc. to denote some academic author. Matthew Diller William R. Hogan An identifier curated by ORCID, Inc. to denote some academic author. http://purl.obolibrary.org/obo/IAO_0000708 orcId ORCID true entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process 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]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] r-quality RelationalQuality 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. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) A monocarboxylic acid amide resulting from the formal condensation of the aryl amino group of N-phenyl-1-(2-phenylethyl)piperidin-4-amine with propanoic acid. N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide fentanyl A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group. ETHANOL Ethanol ethanol ethanol Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. Peptide peptides peptide An aldehyde resulting from the formal oxidation of methanol. FORMALDEHYDE Formaldehyde formaldehyde formaldehyde High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. Deoxyribonucleic acid deoxyribonucleic acids deoxyribonucleic acid A nitrogen oxide consisting of linear unsymmetrical molecules with formula N2O. While it is the most used gaseous anaesthetic in the world, its major commercial use, due to its solubility under pressure in vegetable fats combined with its non-toxicity in low concentrations, is as an aerosol spray propellant and aerating agent for canisters of 'whipped' cream. Dinitrogen oxide dinitrogen oxide oxidodinitrogen(N--N) dinitrogen oxide A morphinane alkaloid that is a highly potent opiate analgesic psychoactive drug. Morphine acts directly on the central nervous system (CNS) to relieve pain but has a high potential for addiction, with tolerance and both physical and psychological dependence developing rapidly. Morphine is the most abundant opiate found in Papaver somniferum (the opium poppy). 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol Morphine morphine A racemate composed of equimolar amounts of (R)- and (S)-nicotine. rac-3-(1-methylpyrrolidin-2-yl)pyridine nicotine Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity molecular entity xylene xylene A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. Alcohol alcohols alcohol A racemate composed of equimolar amounts of dextrobupivacaine and levobupivacaine. Used (in the form of its hydrochloride hydrate) as a local anaesthetic. Bupivacaine rac-1-butyl-N-(2,6-dimethylphenyl)piperidine-2-carboxamide bupivacaine A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom atom A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acids nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid ribonucleic acids ribonucleic acid 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 macromolecule Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene. Steroid steroids steroid A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. opioid analgesic A central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. sedative Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. local anaesthetic local anaesthetic Substance which produces loss of feeling or sensation. anaesthetic anaesthetic inhalation anaesthetic intravenous anaesthetic A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). (ethane-1,2-diyldinitrilo)tetraacetate EDTA(4-) A phenol resulting from the formal substitution of the hydrogen at the 2 position of 1,3-diisopropylbenzene by a hydroxy group. 2,6-bis(propan-2-yl)phenol Propofol propofol An organofluorine compound that is haloperidol in which the hydroxy group has been eliminated with the introduction of a double bond in the piperidine ring, and the 4-chlorophenyl group has been replaced by a benzimidazol-2-on-1-yl group. It is used in the management of chemotherapy-induced nausea and vomiting, and in conjunction with an opioid analgesic such as fentanyl to maintain the patient in a calm state of neuroleptanalgesia with indifference to surroundings but still able to cooperate with the surgeon. 1-{1-[4-(4-fluorophenyl)-4-oxobutyl]-1,2,3,6-tetrahydropyridin-4-yl}-1,3-dihydro-2H-benzimidazol-2-one droperidol The ethyl ester of 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylic acid. It is an intravenous general anaesthetic with no analgesic activity. Etomidate ethyl 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylate etomidate A 1,4-benzodiazepinone that is 1,3-dihydro-2H-1,4-benzodiazepin-2-one substituted by a chloro group at position 7, a methyl group at position 1 and a phenyl group at position 5. 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one Diazepam diazepam Any compound used for the purpose of preserving biological tissues from decay in such a way as to allow for the preparation of thin, stained sections for subsequent histological study. fixative A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors. antiemetic A drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis. muscle relaxant A 1,4-benzodiazepinone compound having a methyl substituent at the 1-position, a hydroxy substituent at the 3-position, a 2-chlorophenyl group at the 5-position and a chloro substituent at the 7-position. 7-chloro-5-(2-chlorophenyl)-3-hydroxy-1-methyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one Lormetazepam lormetazepam The trisodium salt of citric acid. trisodium 2-hydroxypropane-1,2,3-tricarboxylate sodium citrate A morphinane alkaloid that is a hydrogenated ketone derivative of morphine. A semi-synthetic drug, it is a centrally acting pain medication of the opioid class. 3-hydroxy-17-methyl-4,5alpha-epoxymorphinan-6-one Hydromorphone hydromorphone 2-chloro-2-difluoromethoxy-1,1,1-trifluoroethane Isoflurane isoflurane A member of the class of cyclohexanones in which one of the hydrogens at position 2 is substituted by a 2-chlorophenyl group, while the other is substituted by a methylamino group. 2-(2-chlorophenyl)-2-(methylamino)cyclohexanone KETAMINE Ketamine ketamine A chloride salt in which the negative charge of the chloride ions is balanced by succinylcholine dications. 2,2'-[(1,4-dioxobutane-1,4-diyl)bis(oxy)]bis(N,N,N-trimethylethanaminium) dichloride succinylcholine chloride (anhydrous) The monocarboxylic acid amide resulting from the formal condensation of N,N-diethylglycine with 2,6-dimethylaniline. Lidocaine N-(2,6-dimethylphenyl)-N(2),N(2)-diethylglycinamide lidocaine Any substance which is used to neutralise stomach acidity. antacid A piperidinecarboxylate ester that is piperidine which is substituted by a methyl group at position 1 and by phenyl and ethoxycarbonyl groups at position 4. It is an analgesic which is used for the treatment of moderate to severe pain, including postoperative pain and labour pain. ethyl 1-methyl-4-phenylpiperidine-4-carboxylate pethidine The sodium salt of methohexital. sodium 5-(hex-3-yn-2-yl)-1-methyl-4,6-dioxo-5-(prop-2-en-1-yl)-1,4,5,6-tetrahydropyrimidin-2-olate methohexital sodium Ondansetron Ondansetron A steroid ester in which a 5alpha-androstane skeleton is C-3alpha- and C-17beta-disubstituted with acetoxy groups and 2beta- and 16beta-disubstituted with 1-methylpiperidinium-1-yl groups. It is a non-depolarizing curare-mimetic muscle relaxant. 3alpha,17beta-diacetoxy-2beta,16beta-bis(1-methylpiperidinium-1-yl)-5alpha-androstane Pancuronium pancuronium A benzoate ester, formally the result of esterification of 4-aminobenzoic acid with 2-diethylaminoethanol but formed experimentally by reaction of ethyl 4-aminobenzoate with 2-diethylaminoethanol. 2-(diethylamino)ethyl 4-aminobenzoate Procaine procaine A member of the class of furans used to treat peptic ulcer disease (PUD) and gastroesophageal reflux disease. (E)-N-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)sulfanyl]ethyl}-N'-methyl-2-nitroethene-1,1-diamine ranitidine An organic sodium salt having thiopental(1-) as the counter-ion. sodium 5-ethyl-4,6-dioxo-5-(pentan-2-yl)-1,4,5,6-tetrahydropyrimidine-2-thiolate thiopental sodium A 5alpha-androstane compound having 3alpha-acetoxy-, 17beta-acetoxy-, 2beta-piperidino- and 16beta-N-methylpiperidinium substituents. (2beta,3alpha,5alpha,16beta,17beta)-3,17-diacetoxy-16-(1-methylpiperidinium-1-yl)-2-(piperidin-1-yl)androstane vecuronium A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. continuous cell line cell permanent cell line cell immortal cell line cell He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. permanent cell line immortal cell line 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 cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. primary cultured cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). native cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. reticulocyte A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. experimentally modified cell in vitro An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. leukocyte A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. cell in vitro Paraffin A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. environmental material A specimen barcode is a specimen identification number formatted as an optical machine-readable representation. specimen barcode Left renal cortex Cortex of left kidney Wall of distal ileum Wall of distal part of ileum Paries anterior (vagina) Anterior wall of vagina Paries posterior (vagina) Posterior wall of vagina Right tibial nerve Left tibial nerve Right frontal lobe cortex Cortex of right frontal lobe Right leg Left leg Right leg skin Skin of right leg Left leg skin Skin of left leg Left posterior tibial artery Spatial association relationship which describes the containment, adjacency and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate. Anatomical location Right mammary gland Mucosa of abdominal part of esophagus Muscularis mucosae of abdominal part of esophagus Right hemisphere of cerebellum a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority Amanda Hicks William R. Hogan subnational entity A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region. Amanda Hicks William R. Hogan Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. But otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom). geopolitical dependency geographical entity of astronomical body A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface). Mathias Brochhausen Matt Diller William R. Hogan Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc. Generally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought. But the intent is definitely for this class to NOT subsume organism universally. Human beings are contained within, but not part of, the Earth, for example. Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc. We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn). So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities. We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond. Thus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc. geographical entity A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. François Modave Mathias Brochhausen Matt Diller William R. Hogan geographical region A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states. William R. Hogan de facto sovereign state de facto state nation nation state http://en.wikipedia.org/wiki/Sovereign_state Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam". sovereign state An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization". Amanda Hicks IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class. governmental organization Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response 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 A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. immunoglobulin complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. protein-containing complex Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data ancestry category Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. Asian Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations Hispanic or Latin American Japanese Chinese American Indian African American European American conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral 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 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set image 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. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI 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 plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts, 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. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity document title Textual characteristics of traditional and Open Access scientific journals are similar A textual entity that names a document PERSON: Lawrence Hunter document title figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document running title A shorter version of a document title PERSON: Lawrence Hunter running title A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum 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 A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 postal address email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. A planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. Justin Whorton PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls https://github.com/information-artifact-ontology/IAO/issues/237 centrally registered identifier registry time stamped measurement datum An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. Mathias Brochhausen postal code identifier An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. Justin Whorton Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Mathias Brochhausen Mathias Brochhausen dubbing process A personal name is a proper name identifying an individual person. Mathias Brochhausen http://en.wikipedia.org/wiki/Personal_name Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name) personal name A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name Mathias Brochhausen http://en.wikipedia.org/wiki/Given_name given name A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. Mathias Brochhausen http://en.wikipedia.org/wiki/Family_name family name A document that denotes some identity and is concretized by the bearer of some credential role. Amanda Hicks identity document A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents. Amanda Hicks is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities? documented identity I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database. Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit). Amanda Hicks authentication A role that inheres in a concretization of an identity document and is realized by an authentication process. Amanda Hicks credential role ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred. informed consent document informed consent form An informed consent form that has been filled with all required contents. completely filled informed consent form An informed consent form that has been partially filled with required contents. partially filled informed consent form A planned process of making the decision of the competent authorities in form of a letter, document, or verbal or electronic form, that confirms that somebody has permission to do something or be somewhere, e.g. to realize a given project. permission act of authorizing A document that is the output of an authorization process. obsolete authorization document A role that represents the eligibility of a candidate according to a study protocol. eligibility of candidate participation A role inhering in a participant who meets all eligibility criteria defined within a study protocol. candidate eligible for study role A role inhering in a participant who does not meet all eligibility criteria defined within the study protocol. candidate ineligible for study role A disposition to initiate processes that result in a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell pathogenicity A pathogenic disposition is realized in processes that create a disorder. The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. pathogenic disposition An organism that is experiencing pregnancy-induced or pathologic immunosuppression. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppressed organism A material entity with a pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen A process that attenuates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppression An immunosuppression process which arises as the result of a disorder. Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition. Albert Goldfain Alexander Diehl Lindsay Cowell pathologic immunosuppression A disposition whose realization negatively regulates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppressive disposition An immunosuppression induced by progesterone and other factors upregulated in pregnant women. Albert Goldfain Alexander Diehl Lindsay Cowell pregnancy-induced immunosuppression An immunosuppressed organism that is a human experiencing HIV-based immunosuppression. Alex Diehl Lindsay Cowell NCI BBRB immunosuppressed human experiencing HIV-based immunosuppression An immunosuppressed organism that is a human experiencing chronic systemic steroid use-based immunosuppression. Alex Diehl Lindsay Cowell NCI BBRB immunosuppressed human experiencing chronic systemic steroid use-based immunosuppression A pathologically immunosuppressed organism that is a human experiencing drug-based immunosuppression. Alex Diehl Lindsay Cowell NCI BBRB immunosuppressed human experiencing drug-based immunosuppression due to organ transplant Viruses Herpesviridae Cytomegalovirus Epstein Barr virus Epstein-Barr virus Epstein-Barr virus EBV Human herpesvirus 4 Human herpesvirus type 4 Human gammaherpesvirus 4 Human hepatitis B virus hepatitis B virus (HBV) hepatitis B virus HBV hepatitis B virus, HBV human hepatitis B virus HBV Hepatitis B virus Hepatitis C virus hepatitis C virus HCV human hepatitis C virus human hepatitis C virus HCV human hepatitis virus C HCV post-transfusion hepatitis non A non B virus Hepacivirus C Lentivirinae Lentivirus human immunodeficiency virus 1 HIV-1 human immunodeficiency virus HIV-1 human immunodeficiency virus type 1 HIV 1 human immunodeficiency virus type 1 HIV1 human immunodeficiency virus type 1, HIV-1 human immunodeficiency virus type I HIV-1 human immunodeficiency virus type-1 HIV-1 human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 1 HIV type 2 Human immunodeficiency virus type 2 Human immunodeficiency virus-2 human immunodeficiency virus type 2 HIV-2 human immunodeficiency virus type 2, HIV-2 Human immunodeficiency virus 2 bony vertebrates Euteleostomi eubacteria Bacteria Archaea eucaryotes eukaryotes Eukaryota Euarchontoglires tetrapods Tetrapoda amniotes Amniota Opisthokonta Bilateria HIV-1 group O mammals Mammalia Vertebrata vertebrates Vertebrata <vertebrates> human Homo sapiens The method by which conception or impregnation is prevented. This may be achieved through the use of devices, drugs or surgery. BCMETHOD Birth Control Method Birth Control Method A rare, cytologically high grade carcinoma that arises from the renal parenchyma. It is characterized by the presence of prominently dilated cystic spaces in a bland, fibrotic stroma. The lining cells have large irregular nuclei with prominent nucleoli and abundant eosinophilic cytoplasm. Necrosis and mitotic figures are not present. It rarely metastasizes. Tubulocystic Renal Cell Cancer Tubulocystic Renal Cell Carcinoma Tubulocystic renal cell carcinoma Tubulocystic Renal Cell Carcinoma Denotes a person whose ancestry is in any of the countries of the central part of the African continent: Burundi, the Central African Republic, Chad, the Democratic Republic of the Congo, and Rwanda. Central African Central African Denotes a person whose ancestry is in any of the countries of the northern part of the African continent: Algeria, Egypt, Libya, Morocco, Sudan, Tunisia, and Western Sahara. North African North African Denotes a person whose ancestry is in the country of South Africa. South African South African Denotes a person whose ancestry is in any of the Asian countries south of China, east of India, west of New Guinea and north of Australia. SOUTHEAST ASIAN Southeast Asian Southeast Asian Denotes a person whose ancestry is in any of the Asian countries between the Caspian Sea in the west, China in the east, Afghanistan in the south, and Russia in the north. CENTRAL ASIAN Central Asian Central Asian Denotes a person whose ancestry is in the country or continent of Australia. Australian Australian Denotes a person whose ancestry is in the country of New Zealand. New Zealander New Zealander Denotes a person whose ancestry is in the countries of Scandinavia: Denmark, Norway and Sweden. Finland and Iceland are generally included as part of the Scandinavian region. Scandinavian Scandinavian A collection of ethnic geographical categories including Australian and New Zealander. Australian/New Zealand Australian/New Zealand Ethnicity Australian/New Zealand Ethnicity An indicator that a person previously received radiation treatment for the same condition. Prior RT Prior Radiation Prior Radiation Therapy Prior Radiotherapy previously irradiated previously_irradiated Prior Radiation Therapy Any therapy that is administered to augment or stimulate other treatment modalities or to minimize or prevent disease recurrence subsequent to the main treatment plan. AJ-Adjuvant Therapy Adjuvant Therapy adjunct therapy adjunctive therapy adjuvant therapy Adjuvant Therapy Originally, therapeutic administration of serum or gamma globulin containing preformed antibodies produced by another individual; currently, immunotherapy includes nonspecific systemic stimulation, adjuvants, active specific immunotherapy, and adoptive immunotherapy. New forms of immunotherapy include the use of monoclonal antibodies. This approach has been widely adopted by cancer specialists, often in cases which fail to respond to other treatment. Immunotherapy aims to boost immune system function, as with the administration of interferons and interleukin-2, or to attack cancerous cells directly, as with the injection of monoclonal antibodies. Various immunotherapeutic techniques have also been employed among AIDS patients. In addition, a number of alternative medical practices are claimed to enhance immune function, and various over-the-counter substances (e.g., goldenseal, lysine have gained popularity for this supposed property. Prior Immunotherapy Prior Immunotherapy Previous chemotherapy administered as treatment for this cancer. Prior Chemotherapy Prior Chemotherapy Regimens Prior Chemotherapy An indication that an individual has been previously treated with hormonal therapy. Prior Hormone Therapy prior hormonal therapy Prior Hormone Therapy Any intervention for management of a malignant neoplasm. Cancer Therapeutic Procedure Cancer Therapy Cancer Treatment Malignant Neoplasm Therapy Malignant Neoplasm Treatment anticancer therapy Cancer Therapeutic Procedure A group of renal cell carcinomas characterized by the presence of different translocations involving the chromosome Xp11.2. These translocations result in the creation of gene fusions involving the TFE3 gene. Patients are usually children and young adults. Morphologically, the malignant epithelial cells form papillary patterns. Renal Cell Cancer Associated with Xp11.2 Translocations/TFE3 Gene Fusions Renal Cell Carcinoma Associated with Xp11.2 Translocations/TFE3 Gene Fusions TFE3-Rearranged Renal Cell Carcinoma Xp11.2 Translocation-Related Renal Cell Carcinoma tRCC Renal Cell Carcinoma Associated with Xp11.2 Translocations/TFE3 Gene Fusions A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others. Smoking History Tobacco Smoking History Tobacco Smoking History A neoplasm of low malignant potential arising from the ovary. It is characterized by the proliferation of neoplastic mucinous epithelial cells that resemble intestinal epithelial cells. There is no evidence of stromal invasion. Borderline Ovarian Mucinous Tumor, Intestinal Type Borderline Ovarian Mucinous Tumor, Intestinal Type A neoplasm of low malignant potential arising from the ovary. It is characterized by the proliferation of neoplastic epithelial cells that resemble endocervical epithelial cells. There is no evidence of stromal invasion. Borderline Ovarian Mucinous Tumor, Endocervical-Like Borderline Ovarian Mucinous Tumor, Endocervical-Like An epithelial neoplasm with low malignant potential affecting the ovary. It is characterized by the presence of clear or hobnail cells. In some cases, the cells may display nuclear atypia and prominent nucleoli. When such cells are present, they remain confined to the glands. There is no evidence of stromal invasion. Borderline Ovarian Clear Cell Neoplasm Borderline Ovarian Clear Cell Tumor Clear cell cystic tumor of borderline malignancy Borderline Ovarian Clear Cell Tumor An ovarian epithelial neoplasm that resembles the transitional cell neoplasms found in the urinary tract. It is characterized by the presence of atypia and absence of stromal invasion. Borderline Ovarian Transitional Cell Neoplasm Borderline Ovarian Transitional Cell Tumor Borderline Ovarian Transitional Cell Tumor Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka. SOUTH ASIAN South Asian South Asians South Asian Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere. EUROPEAN European European An aggressive carcinoma arising from the ovary. Most patients present with advanced disease. Microscopically, it is characterized by significant cytologic atypia, increased mitotic activity, and necrosis. The prognosis is usually poor. Anaplastic Carcinoma of Ovary Anaplastic Carcinoma of the Ovary Anaplastic Ovarian Carcinoma Ovarian Undifferentiated Carcinoma Undifferentiated Carcinoma of Ovary Undifferentiated Carcinoma of the Ovary Undifferentiated Ovarian Cancer Undifferentiated Ovarian Carcinoma Ovarian Undifferentiated Carcinoma A morphologic variant of squamous cell lung carcinoma characterized by the presence of papillary structures. Lung Squamous Cell Carcinoma, Papillary Variant Squamous Cell Lung Carcinoma, Papillary Variant Lung Squamous Cell Carcinoma, Papillary Variant A morphologic variant of squamous cell lung carcinoma characterized by the presence of clear cells. Lung Squamous Cell Carcinoma, Clear Cell Variant Squamous Cell Lung Carcinoma, Clear Cell Variant Lung Squamous Cell Carcinoma, Clear Cell Variant A poorly differentiated morphologic variant of squamous cell lung carcinoma characterized by the presence of small tumor cells with focal squamous differentiation. Lung Squamous Cell Carcinoma, Small Cell Variant Squamous Cell Lung Carcinoma, Small Cell Variant Lung Squamous Cell Carcinoma, Small Cell Variant A morphologic variant of lung adenocarcinoma characterized by the presence of mucin pools containing islands of well differentiated adenocarcinoma cells. Lung Colloid Adenocarcinoma Lung Mucinous Cystadenocarcinoma Lung Mucinous Cystic Tumor of Borderline Malignancy Mucinous cystic tumor of borderline malignancy Lung Colloid Adenocarcinoma A morphologic variant of lung adenocarcinoma characterized by the presence of signet ring cells. Lung Signet Ring Cell Carcinoma Lung Signet-Ring Cell Carcinoma Lung Signet Ring Cell Carcinoma A low grade serous epithelial neoplasm arising from the ovary. It is characterized by an atypical proliferation of serous-type epithelial cells without evidence of stromal invasion. It is often asymptomatic but rarely it may present with abdominal pain or abdominal enlargement due to rupture or torsion. Borderline Ovarian Serous Neoplasm Borderline Ovarian Serous Tumor Borderline Serous Neoplasm of Ovary Borderline Serous Neoplasm of the Ovary Borderline Serous Tumor of Ovary Borderline Serous Tumor of the Ovary Ovarian Serous Neoplasm of Low Malignant Potential Ovarian Serous Tumor of Low Malignant Potential Proliferating Ovarian Serous Neoplasm Proliferating Ovarian Serous Tumor Proliferating Serous Neoplasm of Ovary Proliferating Serous Neoplasm of the Ovary Proliferating Serous Tumor of Ovary Proliferating Serous Tumor of the Ovary Serous Neoplasm of Ovary with Low Malignant Potential Serous Neoplasm of the Ovary with Low Malignant Potential Serous Ovarian Neoplasm of Low Malignant Potential Serous Ovarian Tumor of Low Malignant Potential Serous Tumor of Ovary with Low Malignant Potential Serous Tumor of the Ovary with Low Malignant Potential Borderline Ovarian Serous Tumor A morphologic variant of lung adenocarcinoma characterized by the presence of polygonal malignant cells forming sheets. Acinar, papillary, micropapillary, or lepidic growth patterns are absent. If the tumor is 100 percent solid, intracellular mucin should be present in at least five tumor cells in each of two high-power fields and confirmed with mucin immunohistochemical stains. Tumors formerly classified as large cell carcinomas expressing pneumocyte immunohistochemical markers, even if intracellular mucin is absent, are now included in this category. Lung Solid Adenocarcinoma with Mucin Pulmonary Solid Adenocarcinoma with Mucin Solid Adenocarcinoma of Lung with Mucin Solid Adenocarcinoma of the Lung with Mucin Solid Lung Adenocarcinoma Solid adenocarcinoma Solid Lung Adenocarcinoma An invasive malignant epithelial tumor that arises from the colon. There is no morphologic, immunophenotypic, or molecular biological evidence of glandular or squamous differentiation. Carcinoma Simplex of the Colon. Colon Anaplastic Carcinoma Colon Undifferentiated Carcinoma Undifferentiated Carcinoma of Colon Undifferentiated Carcinoma of the Colon Undifferentiated Colon Cancer Undifferentiated Colonic Carcinoma Colon Undifferentiated Carcinoma A low grade, non-invasive ovarian epithelial neoplasm characterized by the presence of atypical neoplastic serous and mucinous cells. Borderline Ovarian Seromucinous Tumor/Atypical Proliferative Ovarian Seromucinous Tumor Borderline Ovarian Seromucinous Tumor/Atypical Proliferative Ovarian Seromucinous Tumor A quantification of lifetime tobacco exposure defined as (number of cigarettes smoked per day x number of years smoked)/20. One pack-year is smoking 20 cigarettes a day for one year. Pack Year Pack Year: The number of cigarettes smoked per day times the number of years smoked divided by 20 (the number of cigarettes in a pack) Pack-Year pack year pack years smoked pack_years_smoked {Pack Year} Pack Year Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe. MEDITERRANEAN Mediterranean Mediterranean Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France. WESTERN EUROPEAN Western European Western European Denotes a person having origins in any of the countries of Eastern Europe such as Czechoslovakia, Poland, Croatia, Hungary, Slovenia, Former Soviet Union, or Finland. It also includes persons who call themselves Gypsies from this region. EASTERN EUROPEAN Eastern European Eastern European Denotes a person having origins in the region of southwest Asia, between the India subcontinent and Europe, including Kuwait, Turkey, Lebanon, Israel, Iraq, Iran, Jordan, Saudi Arabia, lands east of Pakistan or the other countries of the Arabian Peninsula. Also includes people of Jewish ethnicity including Sephardic and Ashkenazic. MIDDLE EASTERN Middle Eastern Middle Eastern An epithelial neoplasm that arises from the ovary characterized by the presence of glandular or cystic spaces which contain atypical glandular epithelial cells resembling endometrial cells. The surrounding ovarian stroma is often fibrotic. There is no evidence of stromal invasion. Borderline Endometrioid Neoplasm of Ovary Borderline Endometrioid Neoplasm of the Ovary Borderline Endometrioid Tumor of Ovary Borderline Endometrioid Tumor of the Ovary Borderline Ovarian Endometrioid Neoplasm Borderline Ovarian Endometrioid Tumor Borderline Ovarian Endometrioid Tumor/Atypical Proliferative Ovarian Endometrioid Tumor EBT/APET Endometrioid Neoplasm of Low Malignant Potential Endometrioid Neoplasm with Proliferating Activity, Ovarian Endometrioid Tumor of Low Malignant Potential Endometrioid Tumor with Proliferating Activity, Ovarian Endometrioid tumor of low malignant potential Low Malignant Potential Endometrioid Neoplasm of Ovary Low Malignant Potential Endometrioid Neoplasm of the Ovary Low Malignant Potential Endometrioid Tumor of Ovary Low Malignant Potential Endometrioid Tumor of the Ovary Low Malignant Potential Ovarian Endometrioid Neoplasm Low Malignant Potential Ovarian Endometrioid Tumor Ovarian Endometrioid Borderline Neoplasm Ovarian Endometrioid Borderline Tumor Ovarian Endometrioid Neoplasm of Low Malignant Potential Ovarian Endometrioid Neoplasm with Proliferating Activity Ovarian Endometrioid Tumor of Low Malignant Potential Ovarian Endometrioid Tumor with Proliferating Activity Proliferating Endometrioid Neoplasm of Ovary Proliferating Endometrioid Neoplasm of the Ovary Proliferating Endometrioid Tumor of Ovary Proliferating Endometrioid Tumor of the Ovary Proliferating Ovarian Endometrioid Neoplasm Proliferating Ovarian Endometrioid Tumor Borderline Ovarian Endometrioid Tumor/Atypical Proliferative Ovarian Endometrioid Tumor A description of an individual's current and past experience with alcoholic beverage consumption. Alcohol History Alcohol Use Alcohol Use History alcohol history alcohol_history Alcohol Use History A surgery that is a surgical procedure to remove all or part of your colon. colectomy A textual entity providing information about a biobank and that is written in English. Mathias Brochhausen biobank description biobank description in english A proper name that refers to a sample collection. Mathias Brochhausen sample collection identifier A device that is part of a freezer and consists of a solid horizontal surface to keep material in the freezer on a flat surface. Person: Jie Zheng, Chris Stoeckert Penn Group freezer shelf A planned process that gets rid of a material that is no longer useful or desirable. Person: Jie Zheng, Chris Stoeckert Penn Group discarding A worker role of recruiting human subjects to partcipate in a clinical investigation in which data about human subject is collected. Person: Jie Zheng, Chris Stoeckert Penn Group human subject recuiter role A device that is intended to hold cryovials. Person: Jie Zheng, Chris Stoeckert Penn Group cryovial box A container that is used for discarded material. Person: Jie Zheng, Chris Stoeckert Penn Group trash container A device that is part of a freezer for keeping material in the freezer in a defined position and prevents movement. Person: Jie Zheng, Chris Stoeckert Penn Group freezer rack A device that is designed to contain blood spot cards. Person: Jie Zheng, Chris Stoeckert Penn Group blood spot card box A questionnaire that comprises a set of questions about patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by a recruiter based on an Electronic Medical Record (EMR). Person: Jie Zheng, Chris Stoeckert Penn Group data confirm questionnaire A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare. Person: Jie Zheng, Chris Stoeckert Penn Group form filling A patient questionnaire which has been filled out by a patient. Person: Jie Zheng, Chris Stoeckert Penn Group filled patient questionnaire A questionnaire that comprises a set of demographic and medical questions about a patient which will be filled by the patient or their legally authorized representative. Person: Jie Zheng, Chris Stoeckert Penn Group patient questionnaire A collection packet which contains a container with a specimen and a form filled with information about the collected specimen and specimen source. Person: Jie Zheng, Chris Stoeckert Penn Group collection packet with specimen and information material A material to be added role that is born by a chemical entity which is added into a blood collection containter to optimize specific blood component(s) preservation and/or separation. Person: Jie Zheng, Chris Stoeckert Penn Group blood additive role A worker role that performs the practical hands-on work in laboratories and is realized during study design execution. Person: Jie Zheng, Chris Stoeckert Penn Group lab technician role A collection packet which contains a container with a specimen. Person: Jie Zheng, Chris Stoeckert Penn Group collection packet with specimen A collection packet which contains an empty container that will be used for holding a specimen. Person: Jie Zheng, Chris Stoeckert Penn Group collection packet with empty container A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease. Person: Chris Stoeckert, Jie Zheng Penn Group obsolete medication role true A data confirm questionnaire which has been filled out by a human subject recruiter. Person: Jie Zheng, Chris Stoeckert Penn Group filled data confirm questionnaire A material entity used for specimen collection. It can contain a container to hold a specimen and material (e.g. paper) carrying information about the specimen and the specimen source (e.g. patient). Person: Jie Zheng, Chris Stoeckert Penn Group collection packet A material entity that is bearer of a medication role. Person: Chris Stoeckert, Jie Zheng Penn Group medication material A device that is designed to collect, ship and store blood specimens in an easy and inexpensive way. Person: Jie Zheng, Chris Stoeckert Penn Group blood spot card A test tube that designed to store materials at very low temperatures. Person: Jie Zheng, Chris Stoeckert Penn Group cryovial A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Vacutainer vacutainer A planned process for receiving specimens such as into a laboratory. Person: Jie Zheng, Chris Stoeckert Penn Group specimen receiving An adding a material entity into a target process where a collected specimen is added to a specimen container. (note, not used for other specimen process that produce new specimens) Person: Jie Zheng, Chris Stoeckert Penn Group adding specimen into a container An adding specimen into a container process that spots the blood from an organism on the blood spot card. Person: Jie Zheng, Chris Stoeckert Penn Group blood spotting A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Buffy_coat buffy coat specimen A blood specimen that is located on a blood spot card. Person: Jie Zheng, Chris Stoeckert Penn Group A specimen that located in a blood spot card via blood spotting process. blood specimen on blood spot card A collection packet which contains a container without a specimen and an unfilled form that will be used to fill in information about specimen to be collected. Person: Jie Zheng, Chris Stoeckert Penn Group collection packet with empty container and unfilled information material A duration time of smoking about how long a person has been smoking regularly. (better to have criteria of regularly mean, such as smoke everyday) Person: Jie Zheng, Chris Stoeckert Penn Group duration time of smoking regularly An average value of use of cigarettes per day. Person: Jie Zheng, Chris Stoeckert Penn Group average daily use of cigarette datum A processed material that contains nicotine in the form of a transdermal patch which releases nicotine into the body through the skin. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Nicotine_patch nicotine patch A processed material which is a small cylinder of finely cut tobacco leaves rolled in thin paper for smoking. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Cigarette cigarette A processed material contains nicotine in a form of a chewing gum or a candy-like tablet. It delivers nicotine to the body via absorption by the tissues of the mouth. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Nicotine_gum nicotine gum or lozenge A processed material which is a tightly-rolled bundle of dried and fermented tobacco that is ignited so that its smoke may be drawn into the mouth. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Cigar cigar A processed material which is a kind of smokeless tobacco product consumed by placing a portion of the tobacco between the cheek and gum or upper lip teeth and chewing. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Chewing_tobacco chewing tobacco A processed material that contains nicotine. Person: Jie Zheng, Chris Stoeckert nicotine product Penn Group nicotine material A device made to allow the user to inhale or taste smoke or vapor derived from the burning or vaporization of some substance. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Smoking_pipe smoking pipe A processed material that vaporizes a liquid solution containing nicotine and simulates tobacco smoking by producing an aerosol that resembles smoke. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Electronic_cigarette nicotine e-cigarette A time measurement datum which is the start date of a smoking behavior. Person: Jie Zheng, Chris Stoeckert Penn Group smoking start date A smoking behavior that uses a smoking pipe to inhale or taste tobacco material. Person: Jie Zheng, Chris Stoeckert Penn Group pipe smoking behavior A time measurement datum about how long a person has been smoking. Person: Jie Zheng, Chris Stoeckert Penn Group duration time of smoking A time measurement datum which is the end date of a smoking behavior. Person: Jie Zheng, Chris Stoeckert Penn Group smoking end date A processed material which is made from tobacco for smoking tobacco using a pipe. Person: Jie Zheng, Chris Stoeckert Penn Group pipe tobacco A Eukaryota that is within the genus Nicotiana of the Solanaceae (nightshade) family. Person: Jie Zheng, Chris Stoeckert Penn Group tobacco A processed material that is made from tobacco. Typically, tobacco material is meant to be used as a source of nicotine as tobacco contains a higher concentration of nicotine than most other plants. Person: Jie Zheng, Chris Stoeckert tobacco product Penn Group tobacco material An anatomical location that is just below (1 cm) the site of surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB Location below resection adjacent to tissue for PAXgene fixation. An anatomical location that is adjacent to the site where tissue was collected and subjected to fixation. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB Location adjacent to tissue fixation A time measurement datum that states the duration during which a specimen was submerged in fixative. more general than time in formalin Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time in fixative measurement A collection from organism that occurs after the organism is dead. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB postmortem collecting specimen from organism A collecting specimen from organism that occurs during the process of organ donation. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB collecting specimen from organism during organ donation A temperature measurement assay to obtain the body temperature of an organism through placement of a thermometer in an internal cavity or organ. Person: Chris Stoeckert, Helena Ellis, Jie Zheng core body temperature OBIB NCI BBRB internal body temperature measurement assay An internal body temperature measurement assay where the thermometer is placed in the rectum. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB rectal temperature measurement assay An internal body temperature measurement assay where the thermometer is placed in an organ. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB organ temperature measurement assay An internal body temperature measurement assay where the temperature probe interfaces with the anesthesia vent monitor. Typically the thermometer is a rectal probe with a wire and connector that hooks up to the ekg/pulse ox/co2 monitor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB anesthesia probe temperature measurement assay An identifier that refers to a collection packet used in a specimen collection process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Kit ID OBIB NCI BBRB collection packet identifier A role which inheres in a person and is realized in the dissection of a body for anatomical instruction or pathological examination. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://medical-dictionary.thefreedictionary.com/prosector NCI BBRB prosector role A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations. Person: Chris Stoeckert, Helena Ellis, Jie Zheng SOP https://en.wikipedia.org/wiki/Standard_operating_procedure NCI BBRB standard operating procedure A standard operating procedure for the transportation of specimens. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB specimen transport SOP A standard operating procedure for collecting specimens from organism. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB tissue procurement SOP A standard operating procedure for properly and completely filling out a case report form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng CRF completion protocol OBIB NCI BBRB case report form completion SOP A textual entity that is a short communication to provide advisory or informative matter about a standard operating procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://www.merriam-webster.com/dictionary/memorandum NCI BBRB SOP memorandum A protocol that provides deviations or changes to part of an existing standard operating procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB SOP adjustment A date of specimen collection for the first collection of blood from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB first blood draw date A date of specimen collection for the first collection of a tissue from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB first tissue removed date A data item that reports the calendar date when the data collected on a form was verified. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB date of form data verification A data item that reports the time of day when a blood specimen was collected. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB blood draw time A blood draw time for the first collection of a blood specimen from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB first blood draw time A time of surgical removal of specimen for the first removal of tissue from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB first tissue removed time A data item that reports the time of day when a clamp or ligature was applied to an organ for specimen collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of surgical ligature for specimen collection A planned process to assess the correctness of data entered on a form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB form data verification process A planned process to stop blood flow for an organ during a surgical procedure using a clamp or ligature. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB surgical ligature process An organization at which the process of collecting a specimen from an organism occurred. Person: Chris Stoeckert, Helena Ellis, Jie Zheng biospecimen source site tissue source site OBIB NCI BBRB organization conducting specimen collection from organism specimen collected with GTEx Pink Kit A specimen from organism that is collected with a collection packet that is designed to collect specimens of a particular type for a particular purpose. Person: Chris Stoeckert, Helena Ellis, Jie Zheng specimen collected with specific kit OBIB NCI BBRB specimen collected with specific collection packet A categorical value specification that is used to record the destruction of an organism cells or tissues by the organisms' own enzymes or processes with nominal categories ranging from none to severe. Add instances 0-non, 1-slight, 2-moderate, 3-severe Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB autolysis value specification follow up needed for Pathology Resource Center identified issue for Postmortem/Organ Procurement Tissue Collection A data item that is an indicator of whether further followup on a specimen collection issue is required. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB followup required for specimen collection issue resolution of Pathology Resource Center identified issue for Postmortem/Organ Procurement Tissue Collection A data item that is an indicator of whether a specimen collection issue is resolved. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB resolved specimen collection issue A comment from tissue procurement that is an explanation as to why frozen specimens were not collected. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB reason for not collecting frozen specimens A comment from tissue procurement made in regards to the resolution of an issue with the tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on resolved specimen collection issue A data item indicating whether the body of the specimen donor was refrigerated after death but prior to specimen collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen donor body refrigerated indicator A time measurement datum that states the duration during which the specimen donor's body was refrigerated. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time donor body refrigerated measurement A life-death temporal boundary marked by the irreversible end of all brain activity (including involuntary activity necessary to sustain life). Person: Chris Stoeckert, Helena Ellis, Jie Zheng brain death NCI BBRB, OBIB NCI BBRB cessation of brain activity death A life-death temporal boundary marked by the natural cessation of cardiac activity. Person: Chris Stoeckert, Helena Ellis, Jie Zheng cardiac death NCI BBRB, OBIB NCI BBRB cessation of cardiac activity death A data item that indicates the amount of a serum analyte is at a level above a threshold considered to be present. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB positive serological assay result A data item that indicates the amount of a serum analyte is at a level below a threshold considered to be present. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB negative serological assay result A data item that indicates the amount of a serum analyte is approximately at a threshold considered to be present and therefore can not be confidently scored as positive or negative. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB indeterminate serological assay result An information content entity that is about the status of an assay and indicates that the assay has not been started or completed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB non-performance of an assay A date of specimen collection on which the surgery was performed during which the specimen was collected. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date of surgical removal of specimen A planned process to administer sedation drugs intravenously prior to surgery in order to induce total or partial loss of sensation especially tactile sensation and pain. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB preoperative intravenous administration of sedative A planned process to administer opioid analgesics intravenously prior to surgery in order to induce total or partial loss of sensation especially tactile sensation and pain. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB preoperative intravenous administration of opioid analgesic A planned process to administer antiemetic agents intravenously prior to surgery to prevent nausea or vomiting. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB preoperative intravenous administration of antiemetic A planned process to administer antacid intravenously prior to surgery in order to relieve and reduce the symptoms of ulcers in the stomach and upper small intestine. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB preoperative intravenous administration of antacid A planned process to administer medication intravenously prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB preoperative intravenous administration of medication administered prior to organ removal A planned process to administer anaesthetic to a restricted or localized area in order to produce a loss of feeling. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of local anaesthetic epidural administration prior to organ removal A planned process to administer anaesthetic to a restricted area or part of the body in order to produce a loss of feeling. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of regional anaesthetic administered prior to organ removal A planned process to administer anaesthetic within or into a vein or veins in order to produce a loss of feeling. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of intravenous anaesthetic administered prior to organ removal A planned process to administer opioid analgesics intravenously in order to induce total or partial loss of sensation especially tactile sensation and pain. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB intravenous administration of opioid analgesic administered prior to organ removal A planned process to administer muscle relaxant intravenously in order to relax skeletal muscles and reduce muscle contraction. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB intravenous administration of muscle relaxant administered prior to organ removal A planned process to administer anaesthetic in the form of a gas aerosol or fine powder via the respiratory tract usually by oral or nasal inhalation for local or systemic effect. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of inhalation anaesthetic A planned process to administer anaesthetic in order to produce a loss of feeling. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of anaesthetic A planned process to administer insulin during a surgical procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of insulin during surgery A planned process to administer steroid during a surgical procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of steroid during surgery A planned process to administer antimicrobial agent(s) during a surgical procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of antimicrobial agent during surgery A planned process to administer medication(s) during a surgical procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB administration of medication during surgery A data item that reports the time of day at which the first incision is made during surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time of first surgical incision A surgical procedure in which the anus, rectum, and sigmoid colon are removed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://my.clevelandclinic.org/health/articles/laparoscopic-abdominoperineal-resection-basic-surgical-steps NCI BBRB abdominoperineal resection A colectomy that is the surgical removal of the left side of the large intestine. Person: Chris Stoeckert, Helena Ellis, Jie Zheng left colectomy http://emedicine.medscape.com/article/1965606-overview NCI BBRB left hemicolectomy A colectomy that is the surgical removal of the sigmoid colon. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://emedicine.medscape.com/article/1965606-overview NCI BBRB sigmoid colectomy A colectomy that involves removing the cecum, the ascending colon, the hepatic flexure (where the ascending colon joins the transverse colon), the first one-third of the transverse colon, and part of the terminal ileum, along with fat and lymph nodes. Person: Chris Stoeckert, Helena Ellis, Jie Zheng right colectomy http://emedicine.medscape.com/article/1535001-overview NCI BBRB right hemicolectomy A colectomy that is complete resection of the colon Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Colectomy NCI BBRB subtotal colectomy A colectomy that is resection of part of the colon or a resection of all of the colon without complete resection of the colon Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Colectomy NCI BBRB total colectomy A colectomy that is resection of the transverse colon along with the middle colic vessels and its mesentery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://ether.stanford.edu/abdominal_surgery_rotation/documents/Colon%20surgeries%20vm%20071512.pdf NCI BBRB transverse colectomy A surgical procedure that is done to treat cancer of the rectum in which the part of the rectum containing the cancer is removed. The remaining part of the rectum is reconnected to the colon. Person: Chris Stoeckert, Helena Ellis, Jie Zheng LAR https://www.mskcc.org/cancer-care/patient-education/about-your-low-anterior-resection-surgery NCI BBRB low anterior resection A surgical procedure to remove all or part of the rectum. It is often needed to treat rectal cancer. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.hopkinsmedicine.org/healthlibrary/test_procedures/gastroenterology/proctectomy_135,53/ NCI BBRB proctectomy A colectomy that is the surgical removal of the rectum and all or part of the colon.[ Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Proctocolectomy NCI BBRB proctocolectomy A colectomy that is the surgical removal of the rectum and sigmoid colon. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://medical-dictionary.thefreedictionary.com/rectosigmoidectomy NCI BBRB rectosigmoidectomy A data item that reports the time of day when the first clamp was applied to the vasculature of an organ for specimen collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time of first clamp for specimen removal A data item that reports the time of day when the second clamp was applied to the vasculature of an organ for specimen collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time of second clamp for specimen removal A time measurement datum of the period between organ resection and the time of first clamping perfomed in vivo. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB in vivo intraoperative ischemic period A data item on the duration of blood pressure variances of greater than 20 mmHg from a patient's pre-operative baseline from the time of anesthesia induction to 15 minutes post. Person: Chris Stoeckert, Helena Ellis, Jie Zheng BP excursions from time of anesthesia induction to 15 minutes post NCI BBRB, OBIB NCI BBRB vital sign blood pressure variance early in organ excision A data item on the duration of blood pressure variances of greater than 20 mmHg from a patient's pre-operative baseline from 15 minutes post anesthesia induction to the organ excision. Person: Chris Stoeckert, Helena Ellis, Jie Zheng BP excursions from 15 minutes post anesthesia induction to organ excision NCI BBRB, OBIB NCI BBRB vital sign blood pressure variance late in organ excision A time stamped measurement datum that is the first temperature recorded in the operating room of the specimen donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB first temperature recorded in operating room of specimen donor A time stamped measurement datum that is the second temperature recorded in the operating room of the specimen donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB second temperature recorded in operating room of specimen donor A comment from tissue procurement of the epochs of oxygen desaturation of less than 92% for more than 5 minutes prior to organ excision. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB oxygen desaturation epochs prior to organ excision description A measurement datum of the level of carbon dioxide gas at time closest to organ exiscion from the specimen donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB carbon dioxide level of specimen donor recorded at time closest to organ excision A measurement datum of the volume of albumin administered during surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB albumin volume administered intraoperatively A count of the number of units of packed red blood cells administered during surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB amount of packed red blood cells administered intraoperatively A measurement datum of the volume of platelets administered during surgery measured. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB platelet volume administered intraoperatively A count of the number of units of fresh frozen plasma administered during surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB amount of fresh frozen plasma administered intraoperatively A measurement datum of the volume of intraoperative blood loss from the specimen donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng intraoperative blood loss of specimen donor NCI BBRB, OBIB NCI BBRB specimen donor intraoperative blood loss volume measurement datum A specimen donor intraoperative blood loss volume measurement datum obtained prior to organ excision. Person: Chris Stoeckert, Helena Ellis, Jie Zheng intraoperative blood loss of specimen donor prior to organ excision NCI BBRB, OBIB NCI BBRB specimen donor intraoperative blood loss prior to organ excision volume measurement datum A specimen donor intraoperative blood loss volume measurement datum obtained at the end of surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng intraoperative blood loss of specimen donor at end of surgery NCI BBRB, OBIB NCI BBRB specimen donor intraoperative blood loss at end of surgery volume measurement datum A measurement datum of the volume of intraoperative urine excreted obtained from the specimen donor during surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng intraoperative urine volume excreted NCI BBRB, OBIB NCI BBRB specimen donor intraoperative urine excreted volume measurement datum A specimen donor intraoperative urine excreted volume measurement datum obtained during prior to organ excision. Person: Chris Stoeckert, Helena Ellis, Jie Zheng intraoperative urine volume excreted of specimen donor prior to organ excision NCI BBRB, OBIB NCI BBRB specimen donor intraoperative urine excreted prior to organ excision volume measurement datum A specimen donor intraoperative urine excreted volume measurement datum obtained at the end of surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng intraoperative urine volume excreted of specimen donor at end of surgery NCI BBRB, OBIB NCI BBRB specimen donor intraoperative urine excreted at end of surgery volume measurement datum An information content entity that is an indication of whether ascites fluid was collected from the specimen donor during organ excision. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB indicator of ascites fluid collection during surgery A measurement datum of the volume of ascites fluid collected from the specimen donor during surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB ascites fluid from specimen donor during surgery volume measurement datum A time measurement datum of the duration of fasting by the specimen donor prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB Duration of fasting by specimen donor prior to surgery A comment from tissue procurement of the pre-operative bowel preparation performed prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on donor pre-operative bowel preparation prior to surgery A comment from tissue procurement of notable events that occurred during surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on notable events during donor surgery A data item indicating the time at which the surgical specimen left the operating for delivery to the pathology gross room. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time specimen left operating room A surgical procedure with the removal of the uterus, cervix, fallopian tubes, and ovaries. This is the most common surgery done for endometrial cancer. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.webmd.com/cancer/cervical-cancer/hysterectomy-for-endometrial-cancer NCI BBRB hysterectomy with bilateral salpingo-oophorectomy A surgical procedure with the removal of the uterus, cervix, left fallopian tube, and left ovary. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB hysterectomy with left salpingo-oophorectomy A surgical procedure with the removal of the uterus, cervix, right fallopian tube, and right ovary. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB hysterectomy with right salpingo-oophorectomy A surgical procedure with the removal of both ovaries. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.mayoclinic.org/tests-procedures/oophorectomy/home/ovc-20314905 NCI BBRB bilateral oophorectomy A surgical procedure with the removal of the left ovary. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB left oophorectomy A surgical procedure with the removal of the right ovary. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB right oophorectomy A surgical procedure that removes all organs from a person's pelvic cavity including the urinary bladder, urethra, rectum, and anus. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Pelvic_exenteration NCI BBRB pelvic exenteration A surgical procedure to remove a mass (growth or tumor) on the ovary or in the pelvis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://innovativegyn.com/conditions/ovarian-cyst-and-pelvic-mass/ NCI BBRB pelvic mass excision A surgical procedure to remove both ovaries and both fallopian tubes. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=322852 NCI BBRB bilateral salpingo-oophorectomy A surgical procedure to remove the left ovary and left fallopian tube. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB left salpingo-oophorectomy A surgical procedure to remove the right ovary and right fallopian tube. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB right salpingo-oophorectomy A protocol providing the action or system by which the surgical procedure is to be performed. Person: Chris Stoeckert, Jie Zheng Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB surgical method A surgical method in which operations are performed through the abdomen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB abdominal surgical method A surgical method in which operations are performed through the vagina. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB vaginal surgical method A surgical method in which operations are performed far from their location through small incisions (usually 0.5���1.5��cm) elsewhere in the body. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Laparoscopic_surgery NCI BBRB laparoscopic surgical method Laparoscopically Assisted Vaginal Hysterectomy (LAVH) A surgical method in which operations are performed through the vagina aided by laparoscopic tools and techniques. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB laparoscopically assisted vaginal surgical method A surgical procedure in which the body of the uterus is removed but the cervix is kept intact, as compared to the more common total hysterectomy, in which the uterus, cervix and fundus (the part of the uterus above the fallopian tube openings) are removed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://www.floridahospital.com/supracervical-hysterectomy NCI BBRB supracervical hysterectomy A surgical method using very small tools attached to a robotic arm. The surgeon controls the robotic arm with a computer. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://medlineplus.gov/ency/article/007339.htm NCI BBRB robotic surgical method An information content entity that is an indication of whether pelvic washings were collected during ovarian surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB indicator of pelvic washings collected during ovarian surgery A biopsy of the left kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Kidney biopsy (left) OBIB NCI BBRB left kidney biopsy A biopsy of the right kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Kidney biopsy (right) OBIB NCI BBRB right kidney biopsy A surgical procedure to remove a mass (growth or tumor) in the left kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Kidney mass excision (left) OBIB NCI BBRB left kidney mass excision A surgical procedure to remove part of the left kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Nephrectomy (partial left) OBIB NCI BBRB left partial nephrectomy A surgical procedure to remove the entire left kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Nephrectomy (radical left) OBIB NCI BBRB left radical nephrectomy A surgical procedure that is minimally invasive to remove a patient's left renal pelvis, kidney, ureter, and bladder cuff. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Nephroureterectomy (left) https://my.clevelandclinic.org/health/articles/nephroureterectomy NCI BBRB left nephroureterectomy A surgical procedure to remove a mass (growth or tumor) in the right kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Kidney mass excision (right) OBIB NCI BBRB right kidney mass excision A surgical procedure to remove part of the right kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Nephrectomy (partial right) OBIB NCI BBRB right partial nephrectomy A surgical procedure to remove the entire right kidney. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Nephrectomy (radical right) OBIB NCI BBRB right radical nephrectomy A surgical procedure that is minimally invasive to remove a patient's right renal pelvis, kidney, ureter, and bladder cuff. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Nephroureterectomy (right) https://my.clevelandclinic.org/health/articles/nephroureterectomy NCI BBRB right nephroureterectomy A surgical method in which an incision is made using a scalpel. Open surgery is the traditional type of surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng open surgery https://www.verywell.com/open-surgery-3157124 NCI BBRB open surgical method A biopsy of the left lung. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB left lung biopsy A biopsy of the right lung. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB right lung biopsy A surgical procedure to remove one of the lobes of the left lung. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.hopkinsmedicine.org/healthlibrary/test_procedures/pulmonary/lobectomy_92,P07749/ NCI BBRB left lung lobectomy A surgical procedure to remove one of the lobes of the right lung. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.hopkinsmedicine.org/healthlibrary/test_procedures/pulmonary/lobectomy_92,P07749/ NCI BBRB right lung lobectomy A surgical procedure to remove a mass (growth or tumor) in the left lung. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB left lung mass excision A surgical procedure to remove a mass (growth or tumor) in the right lung. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB right lung mass excision A surgical procedure performed to remove an entire left lung Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.cancercenter.com/treatments/pneumonectomy/ NCI BBRB left pneumonectomy A surgical procedure performed to remove an entire right lung Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.cancercenter.com/treatments/pneumonectomy/ NCI BBRB right pneumonectomy A surgical procedure to remove a triangle-shaped slice of tissue from the left lung. It may be used to remove a tumor or some other type of tissue that requires removal and typically includes a small amount of normal tissue around it. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Wedge_resection NCI BBRB wedge resection of left lung A surgical procedure to remove a triangle-shaped slice of tissue from the right lung. It may be used to remove a tumor or some other type of tissue that requires removal and typically includes a small amount of normal tissue around it. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Wedge_resection NCI BBRB wedge resection of right lung An information content entity that is an indicator of whether pre-operative/pre-anesthesia blood samples were collected from the participant and were successfully banked in a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB indicator of collected and banked pre-operative blood specimens The reason(s) that the pre-operative/pre-anesthesia blood samples were not received in the tissue bank as per the BPV Collection and Processing SOP. A comment from tissue procurement providing a reason that the pre-operative/pre-anesthesia blood samples were not received in a biobank as per SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB reason for not banking pre-operative blood specimen A reason for not banking pre-operative blood specimen which is the blood specimen was not received in the biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB blood not received in biobank A reason for not banking pre-operative blood specimen which is a minimum amount of required pre-op blood was not drawn. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB minimum amount of required pre-op blood not drawn A reason for not banking pre-operative blood specimen which is a minimum number of aliquots was not banked. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB minimum number of aliquots not banked A reason for not banking pre-operative blood specimen which is the blood was hemolyzed or not useable. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB blood was hemolyzed or not useable BPV SOP governing receipt and dissection of surgical tissue in the Tissue Bank A standard operating procedure for the receipt and dissection of surgical tissue in a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB receipt and dissection of surgical specimen SOP Date and time tissue specimens were received in Tissue Bank from the Pathology Gross Room A data item indicating the date and time at which the specimen was received in the biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB data and time of biobank receipt of specimen A personal name that designates the person who received a specimen in the biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of biobank person receiving specimen A textual entity that states a comment or issue regarding specimen receipt or deviations from a standard operating procedure for specimen receipt. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment from specimen receipt Parent Tissue Specimen ID of required study tumor tissue received in Tissue Bank from the Pathology Gross Room A specimen ID denoting a specimen that is used to create a specimen family. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB parent specimen ID A personal name that designates the person who performed the dissection of a surgical specimen to create a specimen family. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of dissector of parent specimen A data item indicating the time that the dissection of a specimen for specimen family creation began. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB beginning time of parent specimen dissection. A data item indicating the time that the dissection of a specimen for specimen family creation ended. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB ending time of parent specimen dissection. The gross appearance of the parent sample as determined in the pathology gross room. A data item on manifestations of disease produced from macroscopic analysis of a specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Gross_pathology NCI BBRB specimen gross appearance A specimen gross appearance of a tumor manifestation. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen gross appearance of tumor A biopsy that uses a thin, hollow needle to draw cells from a body. Person: Chris Stoeckert, Helena Ellis, Jie Zheng needle biopsy http://www.mayoclinic.org/tests-procedures/needle-biopsy/basics/what-you-can-expect/prc-20012926 NCI BBRB obsolete fine needle biopsy true A biopsy that uses a hollow tube that allows extracting a core of tissue for testing. This type of needle biopsy uses a wider needle than does fine-needle aspiration. Person: Chris Stoeckert, Helena Ellis, Jie Zheng core biopsy http://www.mayoclinic.org/tests-procedures/needle-biopsy/basics/what-you-can-expect/prc-20012926 NCI BBRB obsolete core needle biopsy true A processed material that is a non-carcinogenic, non-cross-linking mixture of different alcohols, acid and a soluble organic compound that rapidly preserves morphology and all bio-molecules. Person: Chris Stoeckert, Helena Ellis, Jie Zheng PAXgene Tissue FIX http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027704 NCI BBRB PAXgene fixation reagent 10% neutral buffered formalin (4% neutral buffered formaldehyde) A processed material that is a mixture of formalin (formaldehyde), phosphates, and water used as a standard fixative for diagnostic preparations. Person: Chris Stoeckert, Helena Ellis, Jie Zheng buffered formalin http://stainsfile.info/StainsFile/prepare/fix/fixatives/formalin-buffered.htm NCI BBRB neutral buffered formalin A protocol specifying the buffer formula of the fixative in which tissue specimens are processed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Fixative formula (buffer) NCI BBRB, OBIB NCI BBRB buffer formula for specimen fixative A data item that indicates the the date determined by appropriate stability testing of the medical product, lot, batch or item after which the product may not meet the appropriate regulatory agencies requirements. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB medical product expiration date A manufacturer that produces fixatives used in specimen collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB fixative product manufacturer A manufacturer that produces materials to be sold for profit. Person: Chris Stoeckert, Helena Ellis, Jie Zheng commercial source OBIB NCI BBRB commercial manufacturer A manufacturer that produces materials internally for the internal needs of the organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng In-house source OBIB NCI BBRB in-house manufacturer A buffered formalin condition by virtue of the formalin having undergone a recycling process such as fractional distillation by temperature. Person: Chris Stoeckert, Helena Ellis, Jie Zheng recycled formalin OBIB NCI BBRB recycled buffered formalin condition A quality that inheres in buffered formalin by virtue of its usage and processing. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB buffered formalin condition A buffered formalin condition by virtue of being newly prepared with formalin that has not been previously used. Person: Chris Stoeckert, Helena Ellis, Jie Zheng fresh formalin OBIB NCI BBRB fresh buffered formalin condition A standard operating procedure for collection and processing of blood specimens. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB blood specimen collection and processing SOP An information content entity indicating whether the minimum requirement according to a standard operating procedure was met for pre-operative blood collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB minimum required pre-operative blood tubes collected An information content entity indicating whether approval was received to proceed with collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB approval to proceed with collection A health care provider role borne by a person trained to draw blood from a patient for clinical or medical testing, transfusions, donations, or research. Phlebotomists collect blood primarily by performing venipunctures. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Phlebotomy NCI BBRB phlebotomist role A health care provider role borne by a medical practitioner trained in anesthesia and perioperative medicine. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Anesthesiologist NCI BBRB anesthesiologist role A nurse role borne by a nurse who specializes in the administration of anesthesia. Person: Chris Stoeckert, Helena Ellis, Jie Zheng https://en.wikipedia.org/wiki/Nurse_anesthetist NCI BBRB nurse anesthetist role A health care provider role borne by a person whose duties are to prepare operating rooms, set up equipment and surgical tools, and assist doctors and nurses during surgeries as instructed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng O.R. technician surgical technician http://work.chron.com/become-operating-room-technician-12460.html NCI BBRB operating room technician A data item indicating the date and time when a blood specimen was collected. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Date and Time Blood Was Drawn OBIB NCI BBRB date and time of blood collection A blood specimen collection that occurs pre-operatively or pre-anesthesia relative to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng pre-operative blood draw NCI BBRB, OBIB NCI BBRB pre-operative blood specimen collection A collecting specimen from organism that results in a blood specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng blood draw OBIB NCI BBRB blood specimen collection A personal name that designates the person who performed the collection of a blood specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person performing blood draw A specimen container for collecting blood and has ethylenediaminetetraacetic acid (EDTA) as an anticoagulant. Person: Chris Stoeckert, Helena Ellis, Jie Zheng lavender top tube http://www.mayomedicallaboratories.com/customer-service/faq/specimen/collection-tubes NCI BBRB blood specimen container with EDTA A specimen container developed by PreAnalytiX that is intended to collect, anticoagulate, stabilize, transport, and store a venous whole blood sample for preparation of high quality DNA for use with molecular diagnostic test methods that require DNA. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.preanalytix.com/sites/default/files/handbooks/PAXgene%20Blood%20DNA%20Tube%20IVD%20Product%20Circular.pdf NCI BBRB PAXgene DNA vacutainer A specimen container developed by PreAnalytiX that contains a proprietary reagent for stabilization of intracellular RNA immediately upon collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.preanalytix.com/products/blood/RNA/paxgene-blood-rna-tube NCI BBRB PAXgene RNA vacutainer Volume of blood collected in milliliters A scalar measurement datum that is the output of a volume measurement assay that has a blood specimen as evaluant. need volume measurement assay from OBI first Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB blood specimen volume A blood specimen collection that is performed with a fresh needle inserted into a vein. Person: Chris Stoeckert, Helena Ellis, Jie Zheng fresh venous needle stick NCI BBRB, OBIB NCI BBRB fresh venous needle blood specimen collection A textual entity that states additional information about the blood specimen or donor that is deemed relevant for the specimen collection process. Consider generalizing label of ���comment from tissue procurement�� Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment from blood specimen collection A data item indicating the date and time at which the specimen was received in the laboratory for processing. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB data and time of laboratory receipt of specimen A personal name that designates the person who received a blood specimen in the laboratory. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of person receiving blood specimen in laboratory A scalar measurement datum that is the output of a temperature measurement assay occurring in a laboratory and performed when a blood specimen is received. need temperature measurement assay from OBI and humidity from PATO Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB temperature in lab when blood specimen was received A measurement datum that is the output of an assay of humidity occurring in a laboratory and performed when a blood specimen is received. need humidity from PATO Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB humidity in lab when blood specimen was received DNA PAXgene tube Specimen Barcode ID A specimen barcode that is associated with a vacutainer. need specimen barcode Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB vacutainer specimen barcode Time DNA PAXgene tube was frozen at -20�_C �� 2�_C A time of specimen freezing which occurred at approximately -20�_C. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of specimen freezing at approximately -20 degrees C Time DNA PAXgene tube was transferred to storage at -75�_C �� 5�_C A time of specimen freezing which occurred at -75�_ �� 5�_C. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of specimen freezing at -70 to -80 degrees C A personal name that designates the person who stored a specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of person storing specimen DNA PAXgene tube was collected and stored in accordance with the specified SOP An information content entity indicating whether the specimen was collected and stored in accordance with the specified SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen was collected and stored in accordance with the specified SOP DNA PAXgene tube storage comments A textual entity that states additional information about the blood specimen or donor that is deemed relevant for the specimen storage process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment from blood specimen storage Time plasma processing began. A data item indicating the time when a blood specimen was processed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of blood processing An identifier that specifically identifies a particular conical centrifuge tube. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Conical centrifuge Tube code NCI BBRB, OBIB NCI BBRB conical centrifuge tube identifier A blood specimen volume of blood contained in a conical centrifuge tube. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB blood specimen volume in conical centrifuge tube A specimen barcode that is associated with a blood plasma specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB blood plasma specimen barcode A scalar measurement datum that is the output of a volume measurement assay that has a blood plasma specimen as evaluant. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB blood plasma specimen volume A data item indicating the time when a blood plasma specimen was placed on dry ice. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of blood plasma specimen placement on dry ice A specimen barcode that is associated with a cryovial. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB cryovial specimen barcode A data item indicating the time when a blood plasma specimen was transferred to a freezer. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of blood plasma specimen transfer to freezer A personal name that designates the person who processed a blood specimen to generate aliquots of blood plasma specimens. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person processing blood plasma specimen aliquots A personal name that designates the person who transferred blood plasma specimens to freezer. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person transferring blood plasma specimens to freezer Plasma Processing Was Performed in Accordance With Specified SOP An information content entity indicating whether the specimen was processed in accordance with the specified SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen was processed in accordance with the specified SOP Plasma Processing Comments A textual entity that states additional information about the blood specimen or donor that is deemed relevant for specimen processing. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment from blood specimen processing An information content entity indicating whether the presence of gross hemolysis of plasma was observed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB presence of gross hemolysis of plasma observed Volume in ml of Whole Cell Pellet A scalar measurement datum that is the output of a volume measurement assay that has a cell pellet as evaluant. need volume measurement assay from OBI first Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB cell pellet volume Whole Cell Pellet Aliquot Specimen Barcode ID A specimen barcode that is associated with a cell pellet specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB cell pellet specimen barcode A data item indicating the time when processing of a blood cell pellet specimen was completed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of completion of blood cell pellet processing A data item indicating the time when the blood cell pellet specimen was transferred to storage. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of blood cell pellet transfer to storage A personal name that designates the person who performed processing of the blood cell pellet specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person processing blood cell pellet specimen A data item indicating the calendar date when a specimen was placed on dry ice for transport. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB date of specimen placement on dry ice for transport A data item indicating the time when a specimen was placed on dry ice for transport. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time of specimen placement on dry ice for transport A data item indicating the calendar date when a specimen was stored at -75_ � 5_C. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB date of specimen freezing at -70 to -80 degrees C A data item indicating the calendar date when a specimen was transported to another institution. Person: Chris Stoeckert, Helena Ellis, Jie Zheng date of specimen shipment OBIB NCI BBRB date of specimen transport A data item indicating the time when a specimen was transported to another institution. Person: Chris Stoeckert, Helena Ellis, Jie Zheng time of specimen shipment OBIB NCI BBRB time of specimen transport A role borne by an organization that is the provider of a specimen that is transported to another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng specimen shipping organization NCI BBRB, OBIB NCI BBRB specimen transporting organization A role borne by an organization that is the recipient of a specimen that is transported from another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen receiving organization A personal name that designates the person who is responsible for the transport of a specimen to another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of person responsible for specimen shipment NCI BBRB, OBIB NCI BBRB name of person responsible for specimen transport A personal name that designates the person who verified the specimen transport was according to best practice, international standards, and industry regulations as trained by the IATA. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of IATA-trained person verifying specimen shipment http://www.iata.org/training/pages/index.aspx NCI BBRB name of IATA-trained person verifying specimen transport A data item indicating the calendar date when a specimen was received after transport from another institution. Person: Chris Stoeckert, Helena Ellis, Jie Zheng date of receiving specimen shipment OBIB NCI BBRB date of receiving specimen transport A data item indicating the time when a specimen was received after transport from another institution. Person: Chris Stoeckert, Helena Ellis, Jie Zheng time of receiving specimen shipment OBIB NCI BBRB time of receiving specimen transport A scalar measurement datum that is the output of a temperature measurement assay performed on a collection packet when it is received with a specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng temperature of interior kit at time of receipt OBIB NCI BBRB temperature of specimen collection packet at time of receipt A personal name that designates the person who received the specimen that was transported from another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person receiving specimen shipment An information content entity indicating that the physical condition of a specimen upon receipt after transport was good. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB specimen shipment received in good condition An information content entity indicating that the physical condition of a specimen upon receipt after transport was poor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB specimen shipment received in poor condition A textual entity that states information about the physical integrity or wholeness of the specimen that is deemed relevant for the specimen transport process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB comment on specimen integrity after transport A data item indicating the calendar date when a specimen arrives in the gross pathology room for processing and review. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date of specimen receipt for pathologist processing A data item indicating the time when a specimen arrives in the gross pathology room for processing and review. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time of receipt for pathologist processing A personal name that designates the person who performed a quality control inspection of the specimen that is to be transported to another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of quality control inspector of specimen A personal name that designates the person who performed the data entry process for filling in a tissue recovery case report form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of data entry person for tissue recovery form A personal name that designates the person who is the leader of the team responsible for entering the tissue recovery form data. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of team leader for filling out tissue recovery form A standard operating procedure for fixation of a tissue to the state where it is completely infiltrated with a suitable histological wax and can be embedded ready for section cutting on the microtome for a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.leicabiosystems.com/pathologyleaders/an-introduction-to-specimen-processing/ NCI BBRB FFPE tissue processing SOP An information content entity that indicates whether equipment was maintained following the manufacturers recommendations. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB equipment maintained as per manufacturer recommendations A textual entity that states information about maintenance discrepancies from manufacturer recommendations. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB comment on maintenance discrepancy from manufacturer recommendations A role borne by a chemical that is realized in the formalin-fixed paraffin-embedded (FFPE) processes to remove alcohol used for specimen dehydration, remove stains, and prepare a specimen for infiltration medium. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE clearing agent role An information content entity that indicates whether duration of the alcohol stage followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of alcohol stage duration to FFPE tissue processing SOP A time measurement datum that is the result of measuring the duration of the alcohol stage in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE alcohol stage duration An information content entity that indicates whether duration of the dehydration process followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of dehydration process duration to FFPE tissue processing SOP A time measurement datum that is the result of measuring the duration of the dehydration process in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE dehydration process duration An information content entity that indicates whether temperature of the dehydration process followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of dehydration process temperature to FFPE tissue processing SOP A scalar measurement datum that is the output of a temperature measurement assay performed on a specimen in alcohol during the dehydration process in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE dehydration process temperature An information content entity that indicates whether the number of stages and replicates followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of stage and replicate numbers to FFPE tissue processing SOP A data item that indicates the number of stages and replicates in a FFPE process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB number of FFPE stages/replicates An information content entity that indicates whether the duration in clearing agent followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of duration in clearing agent to FFPE tissue processing SOP A time measurement datum that is the result of measuring the duration in clearing agent in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE clearing agent duration An information content entity that indicates whether the temperature of clearing agent followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of temperature of clearing agent to FFPE tissue processing SOP A scalar measurement datum that is the output of a temperature measurement assay performed on a specimen in clearing agent in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE clearing agent temperature An information content entity that indicates whether the paraffin impregnation method followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence to paraffin impregnation method in FFPE tissue processing SOP A protocol for the paraffin impregnation step of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE paraffin impregnation method An information content entity that indicates whether the paraffin temperature followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of paraffin temperature to FFPE tissue processing SOP A scalar measurement datum that is the output of a temperature measurement assay performed on paraffin in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE paraffin temperature A textual entity that states information relevant to tissue processing in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on FFPE tissue processing A standard operating procedure for the paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue paraffin embedding SOP A scalar measurement datum that is the output of a temperature measurement assay performed during the paraffin processing for embedding in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE paraffin processing for embedding temperature A paraffin that has not been previously used or recycled. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB fresh paraffin A scalar measurement datum that is the output of an age measurement assay performed on paraffin. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB age of paraffin A time measurement datum that is the result of measuring the total time that freshly poured blocks were cooled in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB total time FFPE freshly poured blocks were cooled A standard operating procedure for the handling, tracking, and storing of a formalin-fixed paraffin-embedded (FFPE) tissue block. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue block handling, tracking, and storage SOP An information content entity that indicates whether the FFPE tissue block storage SOP was followed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence to FFPE tissue block storage SOP discrepancies from a FFPE tissue block storage SOP. A textual entity that states information relevant to storage of a formalin-fixed paraffin-embedded (FFPE) tissue block. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on FFPE tissue block storage A textual entity that states information relevant to paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on paraffin embedding of FFPE tissue A personal name that designates the person who performed a specimen slide preparation. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Slide Prep Technician Name NCI BBRB, OBIB NCI BBRB name of specimen slide preparation technician A standard operating procedure for the preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue section preparation SOP An age that inheres in a microtome blade. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB microtome blade age A microtome blade age that indicates that the microtome blade is as new as possible. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB fresh microtome blade A protocol describing the preparation on the faced block prior to sectioning of a formalin-fixed paraffin-embedded (FFPE) tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB preparation of FFPE block face for sectioning protocol A textual entity that describes the carge on a glass slide. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Slide Charge NCI BBRB, OBIB NCI BBRB description of glass slide charge An information content entity that indicates that a glass slide has been positively charged. Person: Chris Stoeckert, Helena Ellis, Jie Zheng charged slide NCI BBRB, OBIB NCI BBRB charged glass slide indicator An information content entity that indicates that a glass slide has not been positively charged. Person: Chris Stoeckert, Helena Ellis, Jie Zheng uncharged slide NCI BBRB, OBIB NCI BBRB uncharged glass slide indicator A scalar measurement datum that is the output of a temperature measurement assay performed on a water bath used in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE water bath temperature An information content entity that indicates the frequency with which microtome maintenance is performed and recorded. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB microtome maintenance frequency A microtome maintenance frequency that indicates that microtome maintenance is performed and recorded daily. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB daily microtome maintenance A textual entity that states information about deviations from a microtome daily maintenance standard operating procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB comment on deviations from microtome daily maintenance SOP An information content entity that indicates the frequency with which water bath maintenance is performed and recorded. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB water bath maintenance frequency A water bath maintenance frequency that indicates that microtome maintenance is performed and recorded daily. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB daily water bath maintenance A textual entity that states information about deviations from a water bath daily maintenance standard operating procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB comment on deviations from water bath daily maintenance SOP A textual entity that states information relevant to preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on preparation of FFPE tissue section A standard operating procedure for the hematoxylin and eosin (H&E) staining and slide mounting of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E staining and mounting SOP A time measurement datum that is the result of measuring the duration in an oven for the hematoxylin and eosin staining of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E staining in oven duration A scalar measurement datum that is the output of a temperature measurement assay performed on a oven during a formalin-fixed paraffin-embedded (FFPE) tissue section hematoxylin and eosin (H&E) staining. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB oven temperature during FFPE tissue section H&E staining A protocol describing the deparaffinization method used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng H&E deparaffinization method NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E deparaffinization protocol A protocol describing the staining method used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng H&E staining method NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E staining protocol A protocol describing the clearing method used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng H&E clearing method NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E clearing protocol A protocol describing the method for applying a cover slip used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng H&E cover slipping method NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E cover slip protocol A planned process involving the manual performance of the FFPE tissue section H&E deparaffinization protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E deparaffinization A planned process involving the manual performance of the FFPE tissue section H&E staining protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E staining A planned process involving the manual performance of the FFPE tissue section H&E clearing protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E clearing A planned process involving the manual performance of the FFPE tissue section H&E cover slip protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E cover slipping A textual entity that states information relevant to the preparation of a formalin-fixed paraffin-embedded (FFPE) hematoxylin and eosin (H&E) stained slide. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on preparation of FFPE H&E stained slide A data item that indicates the frequency with which hematoxylin and eosin (H&E) staining equipment maintenance is performed and recorded. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB H&E staining equipment maintenance performed and recorded frequency A categorical value specification that is used to record the frequency with which hematoxylin and eosin (H&E) staining equipment maintenance is performed and recorded. Categories include daily, weekly, bi-monthly, and per SOP. Add instances: daily, weekly, bi-monthly, per SOP Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB H&E staining equipment maintenance performed and recorded frequency value specification A textual entity that states information about deviations from a hemtoxylin and eosin (H&E) equipment maintenance standard operating procedure. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB comment on deviations from H&E equipment maintenance SOP A specimen barcode associated with the specific chart (key) used to randomly assign specimens to one of several distinct experimental protocols. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen randomization key ID A role borne by personnel responsible for managing human research protocol requirements including but not limited to screening, obtaining authorization, consenting and/or enrollment activities. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Consent or Research Analyst/Coordinator role NCI BBRB, OBIB NCI BBRB manager of human research protocol requirements role A textual entity that is a notification within a clinical data repository that a specimen donor was a transplant recipient. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB transplant alert associated with specimen donor A textual entity that is a notification within a clinical data repository that specimen donor serology results include positive infectious disease data. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB serology alert associated with specimen donor A data item indicating the date and time at which the parent specimen ID was recorded. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB data and time parent specimen ID was recorded A textual entity that states additional information deemed relevant for tissue specimen processing. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on tissue specimen processing Brain Endowment Bank at Miller School of Medicine, of the University of Miami. A biobank that focuses on the special requirements of the human brain with regards to preservation, handling, and analysis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng brain bank NCI BBRB, OBIB NCI BBRB human brain biobank A biobank which receives its specimens primarily/exclusively from tissue source sites.� Activities include receipt, some processing, production of slides/images of the tissue, storage, and retrieval/shipping of materials on-demand. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Central Biospecimen Repository NCI BBRB, OBIB NCI BBRB central biobank A laboratory that specializes in acquiring human tissues and analyzing components such as DNA and RNA from them. Person: Chris Stoeckert, Helena Ellis, Jie Zheng LDACC NCI BBRB, OBIB NCI BBRB laboratory, data analysis, and coordinating center for human specimens A laboratory that performs a rigorous review of images of tissue specimens by a group of senior pathologists not involved in the specimen collection typically to evaluate and characterize the tissue (e.g., % necrosis). Person: Chris Stoeckert, Helena Ellis, Jie Zheng PRC NCI BBRB, OBIB NCI BBRB pathology research center A data item indicating the time when a specimen was placed in a container with stabilizing reagent. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time specimen place in stabilizer An identifier that specifically identifies a particular component of a collection packet. Person: Chris Stoeckert, Helena Ellis, Jie Zheng kit component ID NCI BBRB, OBIB NCI BBRB collection packet component ID A data item indicating the date and time at which a specimen was frozen by placement in liguid nitrogen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB data and time specimen was frozen in liquid nitrogen weight of frozen tumor block after freezing in liquid nitrogen A mass measurement datum that is the result of measuring the weight of a frozen tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB weight of frozen tissue specimen A protocol for the fixation step of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE fixation protocol A FFPE fixation protocol that specifies the planned delay to fixation time. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE fixation delay protocol A specimen ID that specifically identifies a particular tissue cassete used in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE tissue cassette ID A data item indicating the date and time at which the FFPE tissue cassette ID was recorded. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB data and time FFPE tissue cassette ID was recorded A data item indicating the date and time when a tissue cassette was placed in fixative as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue cassette placed in fixative A time measurement datum that is the result of measuring the duration of the the planned delay of placing the tissue cassette in fixative in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB placement of tissue cassette in FFPE fixative delay duration A data item indicating the date and time when a tissue cassette was placed in a tissue processor as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue cassette placed in processor A data item indicating the date and time when a tissue processor cycle ended as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue processor cycle ended A time in fixative measurement that states the duration during which a specimen was submerged in fixative as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time in FFPE fixative measurement A data item indicating the date and time when a tissue cassette was removed from a tissue processor as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue cassette removed from processor A data item indicating the date and time when a tissue embedding started as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue embedding started A time measurement datum that is the result of measuring the time between FFPE tissue processor cycle completion and embedding in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB measurement of time between FFPE tissue processor cycle completion and embedding A data item indicating the date and time when a tissue cassette was frozen as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue cassette was frozen A protocol for the freezing step of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng FFPE freezing method NCI BBRB, OBIB NCI BBRB FFPE freezing protocol A FFPE freezing protocol that involves the use of dry ice. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE freezing by dry ice protocol A FFPE freezing protocol that involves the use of liquid nitrogen vapor phase. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE freezing by LN2 vapor phase protocol Date/Time Tissue Cryosettes Were Transferred to Storage A data item indicating the date and time when a tissue cassette was transferred to storage after a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue cassette transferred to storage A personal name that designates the person who performed the dissection of a normal tissue adjacent to a tumor for a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of dissector of normal adjacent tissue to tumor for FFPE A specimen was processed in accordance with the specified SOP where the specified SOP is for a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen was processed in accordance with the FFPE SOP A data item indicating the date and time when a specimen tissue was fixed or frozen as part of a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date and time FFPE tissue was preserved A specimen was processed in accordance with the specified SOP where the specified SOP is for a formalin-fixed paraffin-embedded (FFPE) process and includes less than 1 hour delay in fixation and 23 hour time in fixative. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen was processed in accordance with the FFPE SOP including <1 hour delay to fixation and 23 hour time in fixative A comment from tissue procurement made in regards to all non-consent issues related to or creating a limitation on tissues that can be procured including tissue type and reason for restriction. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on procurement site restriction An identifier that specifically identifies a particular specimen image. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen image ID A textual entity that states information relevant to an image from a formalin-fixed paraffin-embedded (FFPE) slide. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on FFPE slide image A personal name that designates the person who was the submitter of a pathology case summary report. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of submitting pathologist NCI BBRB, OBIB NCI BBRB name of submitter of pathology case summary report. A data item that reports the calendar date when a pathology case summary report was submitted. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB date of submission of pathology case summary report A personal name that designates the person who served as the reviewer for quality assurance purposes of a pathology case summary report. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of reviewing pathologist NCI BBRB, OBIB NCI BBRB name of reviewer of pathology case summary report. A data item that reports the calendar date when a pathology case summary report was reviewed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB date of review of pathology case summary report A comment from tissue procurement that was submitted as feedback by a pathologist Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB pathologist submitted specimen procurement feedback The largest dimension of the tumor on the slide measured in millimeters. A length measurement datum that is the result of measuring the maximum length of a tumor specimen as presented on a slide. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB greatest tumor dimension on slide A data item that is the result of determining the percentage of cross-sectional surface area of an entire specimen slide composed of tumor focus including necrotic tumor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of cross-sectional surface area of entire slide composed of tumor focus A data item that is the result of determining the percentage of tumor nuclei by cell count of the entire specimen slide (number of tumor epithelial cell nuclei as compared to all cell nuclei). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of tumor cellularity by cell count of the entire slide. A data item that is the result of determining the percentage of cross-sectional surface area of an entire specimen slide that is composed of necrotic tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of cross-sectional surface area of entire slide composed of necrotic tissue A data item that is made up of percentages of different histology-based assessments of a tumor slide specimen that in aggregate describe the total tumor surface area (i.e. add up to 100%). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB histologic profile quantitative assessment of tumor slide specimen surface area A data item that is the result of determining the percentage of a tumor slide specimen that is viable based on surface area not including stroma. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of viable tumor slide specimen by surface area A data item that is the result of determining the percentage of a tumor slide specimen that is necrotic based on surface area. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of necrotic tumor slide specimen by surface area A data item that is the result of determining the percentage of a tumor slide specimen that is stroma based on surface area. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of tumor slide specimen stroma by surface area Percent non-cellular component consisting of mucin, hemorrhage, blood clot, etc. A data item that is the result of determining the percentage of a tumor slide specimen that is non-cellular based on surface area. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of non-cellular component of tumor slide specimen by surface area A textual entity that describes the non-cellular component of a tumor slide specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB non-cellular component of tumor slide specimen description An information content entity that is an indicator of whether the local pathology review of a formalin-fixed paraffin-embedded (FFPE) hematoxylin and eosin (H&E)-stained tumor tissue slide confirmed the histological type. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB confirmation of histologic type of FFPE H&E tumor slide This Slide Meets the Microscopic Analysis Criteria of the BPV Project of Necrosis Percentage of <20% AND Tumor Content of _50% Tumor Nuclei An information content entity that is an indicator of whether a formalin-fixed paraffin-embedded (FFPE) slide meets the microscopic analysis criteria with respect to necrosis percentage and tumor content. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE slide meets necrosis percentage and tumor content criteria A textual entity that describes findings upon review of a formalin-fixed paraffin-embedded (FFPE) slide that do not meet microscopic analysis criteria. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE slide findings that do not meet microscopic analysis criteria A textual entity that states information relevant to a review by a pathologist of a formalin-fixed paraffin-embedded (FFPE) slide. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment from pathology review of FFPE slide An information content entity that is an indicator of whether a formalin-fixed paraffin-embedded (FFPE) slide was consistent with findings of diagnostic pathology report. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE slide consistent with findings of diagnostic pathology report A textual entity that describes inconsistencies with findings of diagnostic pathology report upon review of a formalin-fixed paraffin-embedded (FFPE) slide. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE slide inconsistencies with findings of diagnostic pathology report A personal name that designates the person who served as the pathologist reviewing a specimen slide at an organization conducting specimen collection from organisms. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of reviewing pathologist at organization conducting specimen collection A data item that reports the calendar date when a formalin-fixed paraffin-embedded (FFPE) slide was reviewed by a pathologist. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB date of FFPE slide review by the pathologist A personal name that designates the person who performed the data entry process for filling in a local pathology review form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of data entry person for local pathology review form An information content entity that is an indicator of whether examination of a tissue specimen slide revealed the presence of sarcomatoid features. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB presence of sarcomatoid features on specimen slide A textual entity that describes sarcomatoid features observed on a formalin-fixed paraffin-embedded (FFPE) slide. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB sarcomatoid features observed on FFPE slide A personal name that designates the person who received a specimen in a pathology gross room from an associated operating room (OR). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of person in gross room receiving OR specimen A specimen transport SOP governing the transport of tissue from the operating room (OR) to the pathology gross room. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen transport from OR to gross room SOP An information content entity that is an indicator of whether transport of tissue from the operating room (OR) to the pathology gross room was performed in accordance with the relevant standard operating procedure (SOP). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen transport from OR to gross room was performed as per SOP A textual entity that describes issues with the transport of tissue from the operating room (OR) to the pathology gross room or deviations from the relevant standard operating procedure (SOP). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen transport from OR to gross room issues or deviations from SOP A scalar measurement datum that is the output of a temperature measurement assay occurring in a pathology gross room and performed when a specimen arrived from the operating room (OR). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB temperature in gross room when specimen arrived from OR A measurement datum that is the output of an assay of humidity occurring in a pathology gross room and performed when a specimen arrived from the operating room (OR). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB humidity in gross room when specimen arrived from OR A personal name that designates the person who performed the gross evaluation of a resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of performer of gross evaluation of resected tissue specimen A mass measurement datum that is the output of an assay to measure the weight of a resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng resected tissue weight OBIB NCI BBRB resected tissue specimen mass measurement datum An information content entity that is an indicator of whether gross appearance of disease was observed in a resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB gross appearance of disease in resected tissue A textual entity that states information relevant to gross evaluation of a resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on gross evaluation of resected tissue specimen A diagnosis that is based on the gross evaluation of a resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB gross diagnosis of resected tissue An information content entity that is an indicator of whether a photograph was taken in the pathology gross room of a resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB photograph of tissue was taken in pathology gross room A textual entity that describes the reason no photographs were taken of a resected tissue specimen in the pathology gross room. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB reason for not taking a photograph of resected tissue in pathology gross room An information content entity that is an indicator of whether pathology ink was used to mark the resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB pathology ink used on resected tissue specimen India ink A processed material that is used to mark the margin of a surgical excision of a resected tissue. It is used to evaluate whether the margin is free of tumor tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng pathology ink https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248492/ NCI BBRB ink used for marking surgical margin An information content entity that is an indicator of whether a tumor tissue specimen was released to a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB tumor tissue was released to the biobank A textual entity that describes the reason why a tumor tissue specimen was not released to a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB explanation of why tumor tissue specimen was not released to a biobank A data item that is the result of determining the percentage of gross area of necrosis of a specimen sent to a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of gross area of necrosis of a specimen sent to biobank A data item that is the result of determining the percentage of tumor content of a specimen sent to a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB percentage of tumor content of specimen sent to biobank An information content entity that is an indicator of whether a second piece of tumor was collected and released to a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB second piece of tumor tissue was collected An information content entity that is an indicator of whether the dimensions of each specimen meet the criteria specified within the relevant tissue procurement standard operating procedure (SOP). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB dimensions of each specimen meet the criteria specified within the relevant tissue procurement SOP A textual entity that states information relevant to deviations from a tissue procurement SOP with regards to specimen dimensions. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB comment on deviations in specimen dimensions from a tissue procurement SOP An information content entity that is an indicator of whether normal adjacent tissue was released to the biobank in addition to the tumor tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB normal adjacent tissue released to the biobank in addition to tumor tissue A data item indicating the time when a specimen was transferred from a pathology gross room to a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time of specimen transfer from pathology gross room to a biobank An information content entity that is about the status of a tumor and indicates that there has not been a recurrence. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB no recurrence of tumor A comment from tissue procurement that was submitted as part of a follow-up documenting donor outcome after initial specimen collection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB follow-up on donor outcome comment from tissue procurement Did the participant sign and date the informed consent for HRRC/IRB#11-279? An information content entity that is an indicator of whether the participant signed and dated a specified informed consent form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB participant signed and dated informed consent form A textual entity that states information relevant to a review to determine if requirements were met for a specimen collection from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case quality review comment NCI BBRB, OBIB NCI BBRB specimen collection quality review comment An information content entity that is an indicator of whether the minimum required pre-operative RNA and DNA PAXgene tubes were collected from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB minimum required pre-operative RNA and DNA PAXgene tubes were collected An information content entity that is an indicator of whether the desired plasma and serum aliquots were obtained from a specimen donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB desired plasma and serum aliquots were obtained An information content entity that is an indicator of whether a tumor specimen was obtained and processed with a particular FFPE fixation delay protocol to meet the top priority for tissue procurement. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB top priority tumor specimen was obtained and processed with a particular FFPE fixation delay protocol An information content entity that is an indicator of whether a tumor specimen was obtained and processed with a particular FFPE fixation delay protocol other than meeting the top priority for tissue procurement. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB additional tumor specimen was obtained and processed with a particular FFPE fixation delay protocol An information content entity that is an indicator of whether the local pathology review of a hematoxylin (H&E) slide derived from a quality control (QC) formalin-fixed paraffin-embedded (FFPE) tumor tissue was completed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB local pathology review of QC FFPE tumor tissue H&E slide was completed An information content entity that is an indicator of whether the local pathology review was consistent with the findings of the diagnostic pathology report from the site of specimen collection from a donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB local pathology review was consistent with site of tissue procurement diagnostic pathology report An information content entity that is an indicator of whether clinical data entry was completed for a specimen donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case clinical data entry was completed NCI BBRB, OBIB NCI BBRB specimen donor clinical data entry was completed Required tumor module satisfies the project criteria of necrosis percentage of less than 20% and tumor content of greater than or equal to 50% tumor cells by surface area An information content entity that is an indicator of whether the tumor specimen obtained satisfied criteria of necrosis percentage and tumor content of tumor cells by surface area. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB tumor specimen satisfied criteria of necrosis percentage and tumor content An information content entity that is an indicator of whether all requirements for an investigation were met such that a specimen from a particular donor is released for shipment. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case meets all requirements for an investigation and is released for shipment. NCI BBRB, OBIB NCI BBRB all requirements for an investigation are met enabling release of specimen for shipment. An information content entity that is an indicator of whether activity related to a particular specimen donor was stopped. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case was stopped NCI BBRB, OBIB NCI BBRB activity related to a particular specimen donor was stopped. An activity related to a particular specimen donor was stopped that is because there was not enough blood collected. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case was stopped because not enough blood collected NCI BBRB, OBIB NCI BBRB activity related to a particular specimen donor was stopped because not enough blood collected An activity related to a particular specimen donor was stopped that is because there was not enough tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case was stopped because not enough tissue NCI BBRB, OBIB NCI BBRB activity related to a particular specimen donor was stopped because not enough tissue An activity related to a particular specimen donor was stopped that is because the tissue was too necrotic. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case was stopped because tissue was too necrotic NCI BBRB, OBIB NCI BBRB activity related to a particular specimen donor was stopped because tissue was too necrotic An activity related to a particular specimen donor was stopped that is because the tissue was benign. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case was stopped because tissue was benign NCI BBRB, OBIB NCI BBRB activity related to a particular specimen donor was stopped because tissue was benign An activity related to a particular specimen donor was stopped that is because the tissue was not released to a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng case was stopped because tissue was not released to biobank NCI BBRB, OBIB NCI BBRB activity related to a particular specimen donor was stopped because tissue was not released to a biobank An authorization in which a legally authorized individual is asked to give permission for general research for post mortem specimen donation from a person they represent. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation A role borne by a person who approaches a person's legal representative and informs them of key facts about potential risks and benefits, and asks them for authorization for post-mortem specimen donation for general research for the person they legally represent. Person: Chris Stoeckert, Helena Ellis, Jie Zheng obtainer of research authorization for post-mortem specimen donation NCI BBRB, OBIB NCI BBRB research authorization obtainer role for post mortem donation of specimens from a legally authorized representative An authorization documentation that is the output of a research authorization for post mortem specimen donation. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB research authorization documentation for post mortem specimen donation An information content entity that indicates whether research authorization for post mortem specimen donation was obtained. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation was obtained A research authorization documentation for post mortem specimen donation establishing agreement for post-mortem donation and use in general research. Person: Chris Stoeckert, Helena Ellis, Jie Zheng agreed to research authorization for post mortem specimen donation NCI BBRB, OBIB NCI BBRB research authorization documentation for post mortem specimen donation that is affirmative A research authorization documentation for post mortem specimen donation establishing the lack of agreement for post-mortem donation and use in general research. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused research authorization documentation for post mortem specimen donation NCI BBRB, OBIB NCI BBRB research authorization documentation for post mortem specimen donation that is negative A research authorization documentation for post mortem specimen donation in which the reason authorization was not obtained was due to due to religious reasons. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused due to religious reasons NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained due to religious reasons A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the donors surgeon did not recommend it. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused due to surgeon's recommendation NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained due to surgeon's recommendation A research authorization documentation for post mortem specimen donation because the legally authorized representative felt pressured into making a decision. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused because legally authorized representative felt pressured NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained because legally authorized representative felt pressured A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative felt too distraught. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused because legally authorized representative too distraught NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained because legally authorized representative felt too distraught A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative needed more time to make a decision. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused because legally authorized representative needed more time to make a decision NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained because legally authorized representative needed more time to make a decision A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative was uncomfortable with the risks of the request. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused because legally authorized representative was uncomfortable with the risks NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained because legally authorized representative was uncomfortable with the risks A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative was afraid the decision might affect the surgery plans for the donor. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused because legally authorized representative was afraid the decision would affect surgery plans NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained because legally authorized representative was afraid the decision might affect the surgery plans of donor A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative did not agree with the activity of biobanking. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused because legally authorized representative did not agree with the activity of biobanking. NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained because legally authorized representative did not agree with the activity of biobanking A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative did not show up to the appointment as scheduled. Person: Chris Stoeckert, Helena Ellis, Jie Zheng refused because legally authorized representative did not show up to the appointment as scheduled. NCI BBRB, OBIB NCI BBRB research authorization for post mortem specimen donation not obtained because legally authorized representative did not show up to the appointment as scheduled A data item that indicates the calendar date on which a research protocol was approved by an Institutional Review Board related to where the research will take place. Person: Chris Stoeckert, Helena Ellis, Jie Zheng IRB approval date NCI BBRB, OBIB NCI BBRB date of research protocol approval as determined by an institutional review board A data item that indicates the calendar date on which a research protocol expires and becomes inactive as determined by an Institutional Review Board. Person: Chris Stoeckert, Helena Ellis, Jie Zheng IRB expiration date NCI BBRB, OBIB NCI BBRB date of research protocol expiration as determined by an institutional review board An centrally registered identifier symbol assigned by an Institutional Review Board (IRB) that identifies a particular protocol at a given site. Person: Chris Stoeckert, Helena Ellis, Jie Zheng protocol number at a site NCI BBRB, OBIB NCI BBRB identification number of a protocol at a particular site A data item that indicates the calendar date on which the signing of the research authorization for post mortem specimen donation by the legally authorized individual was witnessed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB date that research authorization for post mortem specimen donation was witnessed A data item that indicates the calendar date on which the receipt of the research authorization was verified by study personnel. Person: Chris Stoeckert, Helena Ellis, Jie Zheng research authorization verification date NCI BBRB, OBIB NCI BBRB date of research authorization verification A personal name that designates who performed the screening of a potential specimen donor for a research study. Person: Chris Stoeckert, Helena Ellis, Jie Zheng specimen donor screener NCI BBRB, OBIB NCI BBRB name of person screening specimen donors A personal name of an individual with research obtainer role who approaches a person's legal representative and informs them of key facts about potential risks and benefits, and asks them for authorization for post-mortem specimen donation for research for the person they legally represent. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Research authorization obtainer for post-mortem specimen donation NCI BBRB, OBIB NCI BBRB name of person obtaining authorization from legally authorized representative for post-mortem specimen donation A data item that indicates the calendar date on which a research authorization was obtained from a specimen donor's legally authorized representative. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Research authorization date NCI BBRB, OBIB NCI BBRB date on which research authorization was obtained from legally authorized representative An identifier that uniquely identifies a particular legally authorized representative in a research study. Person: Chris Stoeckert, Helena Ellis, Jie Zheng legal representative identifier NCI BBRB, OBIB NCI BBRB identifier for legally authorized representative A relationship that may be biological or legal, between the specimen donor a