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)
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
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.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative 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.
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).
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
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
imported from
For external terms/classes, the ontology from which the term was imported
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 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.
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
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
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 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
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
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.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
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"
Add as annotation triples in the granting ontology
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
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
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
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
GO ontology
has axiom id
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
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
ISA tools project (http://isa-tools.org)
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:Randi Vita, Jason Greenbaum, Bjoern Peters
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
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.
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.
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.
has broad synonym
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
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.
has related synonym
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
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
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
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
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
[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
[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
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.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
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.
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
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
is quality measured as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
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..
designates
p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
is designated by
results_in
A relation that relates a container to a measurement datum that specifies the maximum capacity of the container.
has maximum capacity
A relation that relates a container to a measurement datum that specifies the actual amount of material in the container.
has actual load
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
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.
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.
is owned by
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.
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
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
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.
is_specified_input_of
has_specified_output
The inverse property of 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.
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
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
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
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.
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.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
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
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204.
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.
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
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The 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).
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
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
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
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.
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
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
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.
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.
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.
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.
member of
has member is a mereological relation between a collection and an item.
has member
input of
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.
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.
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
DEPRECATED bearer of
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
has measurement value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
A measurement datum that is the output of counting.
count
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.
age data in age brackets data set
An identifier curated by ORCID, Inc. to denote some academic author.
ORCID
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
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
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
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
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
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
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
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
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
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
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a 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
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
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 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
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
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
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
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
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 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
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
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
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
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
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
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
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
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 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 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.
A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.
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.
An aldehyde resulting from the formal oxidation of methanol.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
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.
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).
A racemate composed of equimolar amounts of (R)- and (S)-nicotine.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
A racemate composed of equimolar amounts of dextrobupivacaine and levobupivacaine. Used (in the form of its hydrochloride hydrate) as a local anaesthetic.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A 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.
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.
A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood.
A central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety.
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.
Substance which produces loss of feeling or sensation.
A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA).
A phenol resulting from the formal substitution of the hydrogen at the 2 position of 1,3-diisopropylbenzene by a hydroxy group.
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.
The ethyl ester of 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylic acid. It is an intravenous general anaesthetic with no analgesic activity.
ethyl 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylate
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.
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.
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.
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.
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.
trisodium 2-hydroxypropane-1,2,3-tricarboxylate
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.
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.
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
The monocarboxylic acid amide resulting from the formal condensation of N,N-diethylglycine with 2,6-dimethylaniline.
Any substance which is used to neutralise stomach acidity.
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
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
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.
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.
A member of the class of furans used to treat peptic ulcer disease (PUD) and gastroesophageal reflux disease.
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
A 5alpha-androstane compound having 3alpha-acetoxy-, 17beta-acetoxy-, 2beta-piperidino- and 16beta-N-methylpiperidinium substituents.
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 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.
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).
cell line
A cell line that is expected to be capable of indefinite propagation in an vitro culture.
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.
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.
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).
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
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.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
A specimen barcode is a specimen identification number formatted as an optical machine-readable representation.
Spatial association relationship which describes the containment, adjacency and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate.
Muscularis mucosae of abdominal part of esophagus
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.
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).
Matt Diller
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
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.
de facto sovereign state
de facto state
nation
nation 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".
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.
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.
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.
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.
Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data
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.
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
American
Indian
conditional specification
A directive information entity that specifies what should happen if the trigger condition is fulfilled.
PlanAndPlannedProcess Branch
OBI branch derived
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
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.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts, 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
Clint Dowland
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
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
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.
batch 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.
2009/10/23 Alan Ruttenberg: We need to work on the definition still
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.
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
text
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
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.
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
running title
A shorter version of a document title
A scalar measurement datum that is the result of measurement of length quality
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.
Barry Smith, Werner Ceusters
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
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:Chris Stoeckart
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a 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
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.
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.
proper name
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)
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.
dubbing process
A personal name is a proper name identifying an individual person.
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
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.
family name
A document that denotes some identity and is concretized by the bearer of some credential role.
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.
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).
authentication
A role that inheres in a concretization of an identity document and is realized by an authentication process.
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.
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.
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
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
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.
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
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
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.
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
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
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.
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
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
taxonomic bridge ontology module
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
ontology module subsetted by OWL profile
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.
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.
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.
immunosuppressed organism
A material entity with a pathogenic disposition.
pathogen
A process that attenuates an immune response.
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.
pathologic immunosuppression
A disposition whose realization negatively regulates an immune response.
immunosuppressive disposition
An immunosuppression induced by progesterone and other factors upregulated in pregnant women.
pregnancy-induced immunosuppression
An immunosuppressed organism that is a human experiencing HIV-based immunosuppression.
immunosuppressed human experiencing HIV-based immunosuppression
An immunosuppressed organism that is a human experiencing chronic systemic steroid use-based immunosuppression.
immunosuppressed human experiencing chronic systemic steroid use-based immunosuppression
A pathologically immunosuppressed organism that is a human experiencing drug-based immunosuppression.
immunosuppressed human experiencing drug-based immunosuppression due to organ transplant
post-transfusion hepatitis non A non B virus
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 type 2 HIV-2
human immunodeficiency virus type 2, HIV-2
The method by which conception or impregnation is prevented. This may be achieved through the use of devices, drugs or surgery.
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.
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.
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.
Denotes a person whose ancestry is in the country of South Africa.
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.
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.
Denotes a person whose ancestry is in the country or continent of Australia.
Denotes a person whose ancestry is in the country of New Zealand.
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.
A collection of ethnic geographical categories including Australian and New Zealander.
An indicator that a person previously received radiation treatment for the same condition.
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.
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.
Previous chemotherapy administered as treatment for this cancer.
An indication that an individual has been previously treated with hormonal therapy.
Any intervention for management of a malignant neoplasm.
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
Xp11.2 Translocation-Related Renal Cell Carcinoma
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.
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
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
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.
Clear cell cystic tumor of borderline malignancy
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
Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka.
Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere.
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.
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
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
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
A morphologic variant of lung adenocarcinoma characterized by the presence of mucin pools containing islands of well differentiated adenocarcinoma cells.
Lung Mucinous Cystic Tumor of Borderline Malignancy
Mucinous cystic tumor of borderline malignancy
A morphologic variant of lung adenocarcinoma characterized by the presence of signet ring cells.
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.
Ovarian Serous Neoplasm of Low Malignant Potential
Ovarian Serous Tumor of Low Malignant Potential
Proliferating Serous Neoplasm 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
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.
Pulmonary Solid Adenocarcinoma with Mucin
Solid Adenocarcinoma of the Lung with Mucin
An invasive malignant epithelial tumor that arises from the colon. There is no morphologic, immunophenotypic, or molecular biological evidence of glandular or squamous differentiation.
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
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: The number of cigarettes smoked per day times the number of years smoked divided by 20 (the number of cigarettes in a pack)
Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe.
Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France.
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.
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.
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 the Ovary
Borderline Ovarian Endometrioid Neoplasm
Borderline Ovarian Endometrioid Tumor/Atypical Proliferative Ovarian Endometrioid Tumor
Endometrioid Neoplasm of Low Malignant Potential
Endometrioid Neoplasm with Proliferating Activity, Ovarian
Endometrioid Tumor of Low Malignant Potential
Endometrioid Tumor with Proliferating Activity, Ovarian
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 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
A description of an individual's current and past experience with alcoholic beverage consumption.
A surgery that is a surgical procedure to remove all or part of your colon.
A textual entity providing information about a biobank and that is written in English.
biobank description
biobank description in english
A proper name that refers to a sample collection.
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.
freezer shelf
A planned process that gets rid of a material that is no longer useful or desirable.
discarding
A worker role of recruiting human subjects to partcipate in a clinical investigation in which data about human subject is collected.
human subject recuiter role
A device that is intended to hold cryovials.
cryovial box
A container that is used for discarded material.
trash container
A device that is part of a freezer for keeping material in the freezer in a defined position and prevents movement.
freezer rack
A device that is designed to contain blood spot cards.
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).
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.
form filling
A patient questionnaire which has been filled out by a patient.
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.
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.
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.
blood additive role
A worker role that performs the practical hands-on work in laboratories and is realized during study design execution.
lab technician role
A collection packet which contains a container with a specimen.
collection packet with specimen
A collection packet which contains an empty container that will be used for holding a specimen.
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.
A data confirm questionnaire which has been filled out by a human subject recruiter.
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).
collection packet
A material entity that is bearer of a medication role.
medication material
A device that is designed to collect, ship and store blood specimens in an easy and inexpensive way.
blood spot card
A test tube that designed to store materials at very low temperatures.
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.
vacutainer
A planned process for receiving specimens such as into a laboratory.
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)
adding specimen into a container
An adding specimen into a container process that spots the blood from an organism on the blood spot card.
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.
buffy coat specimen
A blood specimen that is located on a blood spot card.
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.
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)
duration time of smoking regularly
An average value of use of cigarettes per day.
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.
nicotine patch
A processed material which is a small cylinder of finely cut tobacco leaves rolled in thin paper for smoking.
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.
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.
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.
chewing tobacco
A processed material that contains nicotine.
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.
smoking pipe
A processed material that vaporizes a liquid solution containing nicotine and simulates tobacco smoking by producing an aerosol that resembles smoke.
nicotine e-cigarette
A time measurement datum which is the start date of a smoking behavior.
smoking start date
A smoking behavior that uses a smoking pipe to inhale or taste tobacco material.
pipe smoking behavior
A time measurement datum about how long a person has been smoking.
duration time of smoking
A time measurement datum which is the end date of a smoking behavior.
smoking end date
A processed material which is made from tobacco for smoking tobacco using a pipe.
pipe tobacco
A Eukaryota that is within the genus Nicotiana of the Solanaceae (nightshade) family.
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.
tobacco material
An anatomical location that is just below (1 cm) the site of surgery.
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
adjacent to tissue for PAXgene fixation.
An anatomical location that is adjacent to the site where tissue was collected and subjected to fixation.
A time measurement datum that states the duration during which a specimen was submerged in fixative.
A collection from organism that occurs after the organism is dead.
postmortem collecting specimen from organism
A collecting specimen from organism that occurs during the process of organ donation.
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.
internal body temperature measurement assay
An internal body temperature measurement assay where the thermometer is placed in the rectum.
An internal body temperature measurement assay where the thermometer is placed in an organ.
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.
anesthesia probe temperature measurement assay
An identifier that refers to a collection packet used in a specimen collection process.
A role which inheres in a person and is realized in the dissection of a body for anatomical instruction or pathological examination.
A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations.
A standard operating procedure for the transportation of specimens.
A standard operating procedure for collecting specimens from organism.
A standard operating procedure for properly and completely filling out a case report form.
A textual entity that is a short communication to provide advisory or informative matter about a standard operating procedure.
A protocol that provides deviations or changes to part of an existing standard operating procedure.
A date of specimen collection for the first collection of blood from a donor.
A date of specimen collection for the first collection of a tissue from a donor.
A data item that reports the calendar date when the data collected on a form was verified.
A data item that reports the time of day when a blood specimen was collected.
A blood draw time for the first collection of a blood specimen from a donor.
A time of surgical removal of specimen for the first removal of tissue from a donor.
A data item that reports the time of day when a clamp or ligature was applied to an organ for specimen collection.
time of surgical ligature for specimen collection
A planned process to assess the correctness of data entered on a form.
A planned process to stop blood flow for an organ during a surgical procedure using a clamp or ligature.
An organization at which the process of collecting a specimen from an organism occurred.
organization conducting specimen collection from organism
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.
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
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.
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.
A comment from tissue procurement that is an explanation as to why frozen specimens were not collected.
reason for not collecting frozen specimens
A comment from tissue procurement made in regards to the resolution of an issue with the tissue.
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.
specimen donor body refrigerated indicator
A time measurement datum that states the duration during which the specimen donor's body was refrigerated.
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).
A life-death temporal boundary marked by the natural cessation of cardiac activity.
A data item that indicates the amount of a serum analyte is at a level above a threshold considered to be present.
A data item that indicates the amount of a serum analyte is at a level below a threshold considered to be present.
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.
An information content entity that is about the status of an assay and indicates that the assay has not been started or completed.
A date of specimen collection on which the surgery was performed during which the specimen was collected.
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.
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.
preoperative intravenous administration of opioid analgesic
A planned process to administer antiemetic agents intravenously prior to surgery to prevent nausea or vomiting.
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.
preoperative intravenous administration of antacid
A planned process to administer medication intravenously prior to surgery.
preoperative intravenous administration of medication
A planned process to administer anaesthetic to a restricted or localized area in order to produce a loss of feeling.
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.
A planned process to administer anaesthetic within or into a vein or veins in order to produce a loss of feeling.
administration of intravenous anaesthetic
A planned process to administer opioid analgesics intravenously in order to induce total or partial loss of sensation especially tactile sensation and pain.
intravenous administration of opioid analgesic
A planned process to administer muscle relaxant intravenously in order to relax skeletal muscles and reduce muscle contraction.
intravenous administration of muscle relaxant
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.
administration of inhalation anaesthetic
A planned process to administer anaesthetic in order to produce a loss of feeling.
A planned process to administer insulin during a surgical procedure.
administration of insulin during surgery
A planned process to administer steroid during a surgical procedure.
administration of steroid during surgery
A planned process to administer antimicrobial agent(s) during a surgical procedure.
administration of antimicrobial agent during surgery
A planned process to administer medication(s) during a surgical procedure.
administration of medication during surgery
A data item that reports the time of day at which the first incision is made during surgery.
A surgical procedure in which the anus, rectum, and sigmoid colon are removed.
A colectomy that is the surgical removal of the left side of the large intestine.
A colectomy that is the surgical removal of the sigmoid colon.
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.
A colectomy that is complete resection of the colon
A colectomy that is resection of part of the colon or a resection of all of the colon without complete resection of the colon
A colectomy that is resection of the transverse colon along with the middle colic vessels and its mesentery.
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.
A surgical procedure to remove all or part of the rectum. It is often needed to treat rectal cancer.
A colectomy that is the surgical removal of the rectum and all or part of the colon.[
A colectomy that is the surgical removal of the rectum and sigmoid colon.
A data item that reports the time of day when the first clamp was applied to the vasculature of an organ for specimen collection.
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.
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.
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.
BP excursions from time of anesthesia induction to 15 minutes post
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.
BP excursions from 15 minutes post anesthesia induction to organ excision
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.
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.
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.
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.
carbon dioxide level of specimen donor recorded at time closest to organ excision
A measurement datum of the volume of albumin administered during surgery.
albumin volume administered intraoperatively
A count of the number of units of packed red blood cells administered during surgery.
amount of packed red blood cells administered intraoperatively
A measurement datum of the volume of platelets administered during surgery measured.
platelet volume administered intraoperatively
A count of the number of units of fresh frozen plasma administered during surgery.
amount of fresh frozen plasma administered intraoperatively
A measurement datum of the volume of intraoperative blood loss from the specimen donor.
intraoperative blood loss of specimen donor
specimen donor intraoperative blood loss volume measurement datum
A specimen donor intraoperative blood loss volume measurement datum obtained prior to organ excision.
intraoperative blood loss of specimen donor prior to organ excision
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.
intraoperative blood loss of specimen donor at end of surgery
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.
specimen donor intraoperative urine excreted volume measurement datum
A specimen donor intraoperative urine excreted volume measurement datum obtained during prior to organ excision.
intraoperative urine volume excreted of specimen donor prior to organ excision
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.
intraoperative urine volume excreted of specimen donor at end of surgery
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.
indicator of ascites fluid collection during surgery
A measurement datum of the volume of ascites fluid collected from the specimen donor during surgery.
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.
Duration of fasting by specimen donor prior to surgery
A comment from tissue procurement of the pre-operative bowel preparation performed prior to surgery.
comment on donor pre-operative bowel preparation prior to surgery
A comment from tissue procurement of notable events that occurred during surgery.
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.
A surgical procedure with the removal of the uterus, cervix, fallopian tubes, and ovaries. This is the most common surgery done for endometrial cancer.
hysterectomy with bilateral salpingo-oophorectomy
A surgical procedure with the removal of the uterus, cervix, left fallopian tube, and left ovary.
hysterectomy with left salpingo-oophorectomy
A surgical procedure with the removal of the uterus, cervix, right fallopian tube, and right ovary.
hysterectomy with right salpingo-oophorectomy
A surgical procedure with the removal of both ovaries.
A surgical procedure with the removal of the left ovary.
A surgical procedure with the removal of the right ovary.
A surgical procedure that removes all organs from a person's pelvic cavity including the urinary bladder, urethra, rectum, and anus.
A surgical procedure to remove a mass (growth or tumor) on the ovary or in the pelvis.
A surgical procedure to remove both ovaries and both fallopian tubes.
A surgical procedure to remove the left ovary and left fallopian tube.
A surgical procedure to remove the right ovary and right fallopian tube.
A protocol providing the action or system by which the surgical procedure is to be performed.
A surgical method in which operations are performed through the abdomen.
A surgical method in which operations are performed through the vagina.
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.
Laparoscopically Assisted Vaginal Hysterectomy (LAVH)
A surgical method in which operations are performed through the vagina aided by laparoscopic tools and techniques.
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.
A surgical method using very small tools attached to a robotic arm. The surgeon controls the robotic arm with a computer.
An information content entity that is an indication of whether pelvic washings were collected during ovarian surgery.
indicator of pelvic washings collected during ovarian surgery
A surgical procedure to remove a mass (growth or tumor) in the left kidney.
A surgical procedure to remove part of the left kidney.
A surgical procedure to remove the entire left kidney.
A surgical procedure that is minimally invasive to remove a patient's left renal pelvis, kidney, ureter, and bladder cuff.
A surgical procedure to remove a mass (growth or tumor) in the right kidney.
A surgical procedure to remove part of the right kidney.
A surgical procedure to remove the entire right kidney.
A surgical procedure that is minimally invasive to remove a patient's right renal pelvis, kidney, ureter, and bladder cuff.
A surgical method in which an incision is made using a scalpel. Open surgery is the traditional type of surgery.
A surgical procedure to remove one of the lobes of the left lung.
A surgical procedure to remove one of the lobes of the right lung.
A surgical procedure to remove a mass (growth or tumor) in the left lung.
A surgical procedure to remove a mass (growth or tumor) in the right lung.
A surgical procedure performed to remove an entire left lung
A surgical procedure performed to remove an entire right lung
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.
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.
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.
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.
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.
A reason for not banking pre-operative blood specimen which is a minimum amount of required pre-op blood was not drawn.
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.
A reason for not banking pre-operative blood specimen which is the 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.
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.
data and time of biobank receipt of specimen
A personal name that designates the person who received a specimen in the biobank.
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.
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.
A personal name that designates the person who performed the dissection of a surgical specimen to create a specimen family.
A data item indicating the time that the dissection of a specimen for specimen family creation began.
beginning time of parent specimen dissection.
A data item indicating the time that the dissection of a specimen for specimen family creation ended.
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.
A specimen gross appearance of a tumor manifestation.
A biopsy that uses a thin, hollow needle to draw cells from a body.
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.
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.
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.
A protocol specifying the buffer formula of the fixative in which tissue specimens are processed.
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.
A manufacturer that produces fixatives used in specimen collection.
A manufacturer that produces materials to be sold for profit.
A manufacturer that produces materials internally for the internal needs of the organization.
A buffered formalin condition by virtue of the formalin having undergone a recycling process such as fractional distillation by temperature.
A quality that inheres in buffered formalin by virtue of its usage and processing.
A buffered formalin condition by virtue of being newly prepared with formalin that has not been previously used.
A standard operating procedure for collection and processing of blood specimens.
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.
minimum required pre-operative blood tubes collected
An information content entity indicating whether approval was received 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.
A health care provider role borne by a medical practitioner trained in anesthesia and perioperative medicine.
A nurse role borne by a nurse who specializes in the administration of anesthesia.
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.
A data item indicating the date and time when a blood specimen was collected.
A blood specimen collection that occurs pre-operatively or pre-anesthesia relative to surgery.
A collecting specimen from organism that results in a blood specimen.
A personal name that designates the person who performed the collection of a blood specimen.
A specimen container for collecting blood and has ethylenediaminetetraacetic acid (EDTA) as an anticoagulant.
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.
A specimen container developed by PreAnalytiX that contains a proprietary reagent for stabilization of intracellular RNA immediately upon collection.
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
A blood specimen collection that is performed with a fresh needle inserted into a vein.
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��
A data item indicating the date and time at which the specimen was received in the laboratory for processing.
data and time of laboratory receipt of specimen
A personal name that designates the person who received a blood specimen in the laboratory.
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
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.
humidity in lab when blood specimen was received
A specimen barcode that is associated with a vacutainer.
Time DNA PAXgene tube was frozen at -20�_C �� 2�_C
A time of specimen freezing which occurred at approximately -20�_C.
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.
time of specimen freezing at -70 to -80 degrees C
A personal name that designates the person who stored a 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.
specimen was collected and stored in accordance with the specified SOP
A textual entity that states additional information about the blood specimen or donor that is deemed relevant for the specimen storage process.
A data item indicating the time when a blood specimen was processed.
An identifier that specifically identifies a particular conical centrifuge tube.
A blood specimen volume of blood contained in a conical centrifuge tube.
blood specimen volume in conical centrifuge tube
A specimen barcode that is associated with a blood plasma specimen.
A scalar measurement datum that is the output of a volume measurement assay that has a blood plasma specimen as evaluant.
A data item indicating the time when a blood plasma specimen was placed on dry ice.
time of blood plasma specimen placement on dry ice
A specimen barcode that is associated with a cryovial.
A data item indicating the time when a blood plasma specimen was transferred to a freezer.
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.
name of person processing blood plasma specimen aliquots
A personal name that designates the person who transferred blood plasma specimens to freezer.
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.
specimen was processed in accordance with the specified SOP
A textual entity that states additional information about the blood specimen or donor that is deemed relevant for specimen processing.
An information content entity indicating whether the presence of gross hemolysis of plasma was observed.
presence of gross hemolysis of plasma observed
A scalar measurement datum that is the output of a volume measurement assay that has a cell pellet as evaluant.
Whole Cell Pellet Aliquot Specimen Barcode ID
A specimen barcode that is associated with a cell pellet specimen.
A data item indicating the time when processing of a blood cell pellet specimen was completed.
time of completion of blood cell pellet processing
A data item indicating the time when the blood cell pellet specimen was transferred to storage.
time of blood cell pellet transfer to storage
A personal name that designates the person who performed processing of the blood cell pellet specimen.
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.
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.
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.
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.
A data item indicating the time when a specimen was transported to another institution.
A role borne by an organization that is the provider of a specimen that is transported to another organization.
A role borne by an organization that is the recipient of a specimen that is transported from another organization.
A personal name that designates the person who is responsible for the transport of a specimen to another organization.
name of person responsible for specimen shipment
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.
name of IATA-trained person verifying specimen shipment
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.
A data item indicating the time when a specimen was received after transport from another institution.
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.
temperature of interior kit at time of receipt
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.
name of person receiving specimen shipment
An information content entity indicating that the physical condition of a specimen upon receipt after transport was good.
specimen shipment received in good condition
An information content entity indicating that the physical condition of a specimen upon receipt after transport was poor.
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.
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.
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.
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.
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.
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.
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.
An information content entity that indicates whether equipment was maintained following the manufacturers recommendations.
equipment maintained as per manufacturer recommendations
A textual entity that states information about maintenance discrepancies from manufacturer recommendations.
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.
An information content entity that indicates whether duration of the alcohol stage followed that prescribed in the FFPE tissue processing SOP.
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.
An information content entity that indicates whether duration of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
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.
An information content entity that indicates whether temperature of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
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.
An information content entity that indicates whether the number of stages and replicates followed that prescribed in the FFPE tissue processing SOP.
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.
An information content entity that indicates whether the duration in clearing agent followed that prescribed in the FFPE tissue processing SOP.
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.
An information content entity that indicates whether the temperature of clearing agent followed that prescribed in the FFPE tissue processing SOP.
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.
An information content entity that indicates whether the paraffin impregnation method followed that prescribed in the FFPE tissue processing SOP.
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.
An information content entity that indicates whether the paraffin temperature followed that prescribed in the FFPE tissue processing SOP.
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.
A textual entity that states information relevant to tissue processing in a formalin-fixed paraffin-embedded (FFPE) process.
A standard operating procedure for the paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue.
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.
FFPE paraffin processing for embedding temperature
A paraffin that has not been previously used or recycled.
A scalar measurement datum that is the output of an age measurement assay performed on 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.
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.
FFPE tissue block handling, tracking, and storage SOP
An information content entity that indicates whether the FFPE tissue block storage SOP was followed.
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.
A textual entity that states information relevant to paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue.
comment on paraffin embedding of FFPE tissue
A personal name that designates the person who performed a specimen slide preparation.
name of specimen slide preparation technician
A standard operating procedure for the preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
An age that inheres in a microtome blade.
A microtome blade age that indicates that the microtome blade is as new as possible.
A protocol describing the preparation on the faced block prior to sectioning of a formalin-fixed paraffin-embedded (FFPE) tissue.
preparation of FFPE block face for sectioning protocol
A textual entity that describes the carge on a glass slide.
An information content entity that indicates that a glass slide has been positively charged.
An information content entity that indicates that a glass slide has not been positively charged.
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.
An information content entity that indicates the frequency with which microtome maintenance is performed and recorded.
A microtome maintenance frequency that indicates that microtome maintenance is performed and recorded daily.
A textual entity that states information about deviations from a microtome daily maintenance standard operating procedure.
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.
A water bath maintenance frequency that indicates that microtome maintenance is performed and recorded daily.
A textual entity that states information about deviations from a water bath daily maintenance standard operating procedure.
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.
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.
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.
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.
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.
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.
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.
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.
FFPE tissue section H&E cover slip protocol
A planned process involving the manual performance of the FFPE tissue section H&E deparaffinization protocol.
manual FFPE tissue section H&E deparaffinization
A planned process involving the manual performance of the FFPE tissue section H&E staining protocol.
A planned process involving the manual performance of the FFPE tissue section H&E clearing protocol.
A planned process involving the manual performance of the FFPE tissue section H&E cover slip protocol.
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.
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.
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
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.
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.
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.
Consent or Research Analyst/Coordinator role
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.
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.
serology alert associated with specimen donor
A data item indicating the date and time at which the parent specimen ID was recorded.
data and time parent specimen ID was recorded
A textual entity that states additional information deemed relevant for 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.
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.
A laboratory that specializes in acquiring human tissues and analyzing components such as DNA and RNA from them.
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).
A data item indicating the time when a specimen was placed in a container with stabilizing reagent.
An identifier that specifically identifies a particular component of a collection packet.
A data item indicating the date and time at which a specimen was frozen by placement in liguid nitrogen.
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.
A protocol for the fixation step of a formalin-fixed paraffin-embedded (FFPE) process.
A FFPE fixation protocol that specifies the planned delay to fixation time.
A specimen ID that specifically identifies a particular tissue cassete used in a formalin-fixed paraffin-embedded (FFPE) process.
A data item indicating the date and time at which the FFPE tissue cassette ID was recorded.
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.
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.
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.
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.
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.
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.
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.
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.
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.
date and time FFPE tissue cassette was frozen
A protocol for the freezing step of a formalin-fixed paraffin-embedded (FFPE) process.
A FFPE freezing protocol that involves the use of dry ice.
A FFPE freezing protocol that involves the use of liquid nitrogen vapor phase.
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.
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.
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.
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.
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.
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.
An identifier that specifically identifies a particular specimen image.
A textual entity that states information relevant to an image from a formalin-fixed paraffin-embedded (FFPE) slide.
A personal name that designates the person who was the submitter of a pathology case summary report.
name of submitter of pathology case summary report.
A data item that reports the calendar date when a pathology case summary report was submitted.
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.
name of reviewer of pathology case summary report.
A data item that reports the calendar date when a pathology case summary report was reviewed.
date of review of pathology case summary report
A comment from tissue procurement that was submitted as feedback by a pathologist
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.
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.
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).
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.
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%).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
presence of sarcomatoid features on specimen slide
A textual entity that describes sarcomatoid features observed on a formalin-fixed paraffin-embedded (FFPE) slide.
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).
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.
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).
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).
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).
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).
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.
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.
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.
gross appearance of disease in resected tissue
A textual entity that states information relevant to gross evaluation of a resected tissue specimen.
comment on gross evaluation of resected tissue specimen
A diagnosis that is based on the gross evaluation of a resected tissue specimen.
An information content entity that is an indicator of whether a photograph was taken in the pathology gross room of a resected tissue specimen.
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.
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.
pathology ink used on resected tissue specimen
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.
An information content entity that is an indicator of whether a tumor tissue specimen was released to a biobank.
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.
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.
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.
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.
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).
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.
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.
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.
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.
A comment from tissue procurement that was submitted as part of a follow-up documenting donor outcome after initial specimen collection.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
case meets all requirements for an investigation and is released for shipment.
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.
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.
case was stopped because not enough blood collected
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.
case was stopped because not enough tissue
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.
case was stopped because tissue was too necrotic
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.
case was stopped because tissue was benign
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.
case was stopped because tissue was not released to biobank
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.
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.
obtainer of research authorization for post-mortem specimen donation
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.
research authorization documentation for post mortem specimen donation
An information content entity that indicates whether research authorization for post mortem specimen donation was obtained.
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.
agreed to research authorization for post mortem specimen donation
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.
refused research authorization documentation for post mortem specimen donation
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.
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.
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.
refused because legally authorized representative felt pressured
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.
refused because legally authorized representative too distraught
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.
refused because legally authorized representative needed more time to make a decision
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.
refused because legally authorized representative was uncomfortable with the risks
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.
refused because legally authorized representative was afraid the decision would affect surgery plans
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.
refused because legally authorized representative did not agree with the activity of biobanking.
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.
refused because legally authorized representative did not show up to the appointment as scheduled.
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.
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.
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.
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.
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.
research authorization verification date
date of research authorization verification
A personal name that designates who performed the screening of a potential specimen donor for a research study.
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.
Research authorization obtainer for post-mortem specimen donation
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.
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.
identifier for legally authorized representative
A relationship that may be biological or legal, between the specimen donor and the legally authorized representative who signed the research authorization.
relationship between person signing research authorization and specimen donor
A date of birth that signifies the calendar date on which a particular donor of a specimen was born.
Biological sex of the person who bears the role of donor.
A role borne by a person who has died from whom specimens are collected.
An age measurement datum that indicates the age of the specimen donor at the time that authorization from their legally authorized representative was obtained.
age of specimen donor at time that authorization from legally authorized representative was obtained
An Information content entity that indicates whether the specimen donor has reached the age of majority as defined by the appropriate regulation.
indicator of whether specimen donor has reached the age of majority
A textual entity that provides additional information that may be relevant to the research authorization verification process.
comments related to research authorization process
An information content entity that signifies the willingness of an individual to be contacted for a research study.
willingness to be contacted for a research study
An authorization documentation in which a legally authorized individual agrees to a specific research addendum for the person they represent.
agreement to a specified research addendum
An authorization documentation for postmortem specimen donation in which specimens are to be used for a specified purpose (e.g., transplantation, research, education).
authorization documentation for postmortem specimen donation for a specified purpose
An authorization documentation for postmortem specimen donation for a specified purpose which is solely for the purpose of transplantation to another person or persons.
authorization for postmortem specimen donation for transplantation purposes only
An authorization documentation for postmortem specimen donation for a specified purpose which is for transplantation, research, education and the advancement of science.
tissue donation for transplant and research
authorization for postmortem specimen donation for transplantation and research
An authorization documentation for post mortem specimen donation in which authorization is not obtained for whole brain donation.
authorization not obtained for whole brain donation
An authorization documentation for postmortem specimen donation in which authorization includes specific limitations or additional information related to the use of tissue for research.
limitations on research authorization for use of donated specimens
An exclusion criterion that defines whether a metastatic tumor is present, which if met, makes an individual unsuitable for a given task or participation in a given process.
presence of metastatic tumor exclusion criterion
An exclusion criterion that defines whether a tumor is larger than a specified size, which if met, makes an individual unsuitable for a given task or participation in a given process.
presence of a tumor larger than a specified size exclusion criterion
An inclusion criterion that defines whether the specimen donor has provided authorization to allow for the minimum number of organs/tissue types for a specific study to be collected, which when met, makes a specimen donor suitable for a given task or participation in a given process.
authorization to collect of minimum number of organ/tissue types for a specific study inclusion criterion
A challenging inclusion criterion is defined as whether it is likely that tissue collection can be started AND the first tissue can be placed in fixative within eight hours of death.
An inclusion criterion that is defined by whether it is likely that tissue collection can be started AND the first tissue can be placed in fixative within a specified period of time from cardiac cessation or recorded time of death (observed or presumed) for a specimen donor, which if met, makes a specimen donor suitable for a given task or participation in a given process.
tissue collection timing and placed in fixative inclusion criterion
A time measurement datum that is the result of measuring the time elapsed since radiation therapy prior to surgery.
time since radiation therapy was received prior to surgery
A time measurement datum that is the result of measuring the time elapsed since chemotherapy prior to surgery.
time since chemotherapy was received prior to surgery
A time measurement datum that is the result of measuring the time elapsed since immunotherapy prior to surgery.
time since immunotherapy was received prior to surgery
A time measurement datum that is the result of measuring the time elapsed since hormonal therapy prior to surgery.
time since hormonal therapy was received prior to surgery
A data item that reports the calendar date when radiation therapy was received prior to surgery.
date of radiation therapy prior to surgery
A data item that reports the calendar date when chemotherapy was received prior to surgery.
A data item that reports the calendar date when immunotherapy was received prior to surgery.
A data item that reports the calendar date when hormonal therapy was received prior to surgery.
date of hormonal therapy prior to surgery
An Alcohol Use History in which there is no alcohol consumption.
An Alcohol Use History in which there was alcohol consumption in the past but is currently a non-drinker of alcohol.
An Alcohol Use History in which alcohol consumption was equal to or less than 2 drinks per day for men and 1 drink or less per day for women.
An Alcohol Use History in which alcohol consumption was more than 2 drinks per day for men and more than 1 drink per day for women.
greater than moderate alcohol consumption history
A time measurement datum that is the result of measuring the duration of greater than moderate alcohol consumption (more than 2 drinks per day for a man or more than 1 drink per day for a woman) prior to study enrollment.
duration of greater than moderate alcohol consumption prior to enrollment
Less than 100 cigarettes smoked in lifetime
A Smoking History in which there was no or an insignificant level of smoking.
A Smoking History in which there is current smoking either on a daily or non-daily basis.
A Smoking History in which there is no current smoking and has not been smoking for more than 15 years.
current reformed smoker for more than 15 years history
A Smoking History in which there is no current smoking and has not been smoking for less than 15 years.
current reformed smoker for less than 15 years history
A one-dimensional temporal region during which a cancer patient's performance status (general well-being and activities of daily life) was assessed.
A timing of scoring performance status that occurs prior to an operation to treat cancer.
A timing of scoring performance status that occurs prior to adjuvant therapy to treat cancer.
A timing of scoring performance status that occurs after adjuvant therapy to treat cancer.
A textual entity that states additional information relevant to the filling out of a clinical data entry form.
A birth control method that involves the use of an oral hormone-based contraceptive typically taken as a pill.
pill-based hormonal birth control method
A birth control method that involves the injection of hormones.
injection-based hormonal birth control method
A birth control method that involves the use of an intrauterine device (IUD) to deliver hormones.
intrauterine device-based hormonal birth control method
A birth control method that involves the administration of hormones through a transdermal patch delivery system.
patch-based hormonal birth control method
A birth control method that involves the administration of hormones through a vaginal ring.
vaginal ring-based hormonal birth control method
A time measurement datum that is the result of measuring the duration of use of hormonally based birth control prior to enrollment in a study.
duration of hormonal birth control use prior to enrollment
A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally based birth control.
time since last usage of hormonal birth control
A textual entity that states additional information relevant to the use of hormonally based birth control.
comment on the use of hormonally based birth control
A time measurement datum that is the result of measuring the duration of hormone replacement therapy prior to enrollment in a study.
duration of hormone replacement therapy prior to enrollment
A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally replacement therapy.
time since last usage of hormone replacement therapy
A textual entity that states additional information relevant to the use of hormone replacement therapy.
comment on the use of hormone replacement therapy
A textual entity that states additional information relevant to the history of exposure to environmental and workplace carcinogens.
comment on exposure to environmental and workplace carcinogens
A risk factor that is associated with increased likelihood of colorectal cancer.
a diet that is high in beef, lamb, or liver and hot dogs and some luncheon meats.
A colorectal cancer risk factor that is having a diet that is high in red meats and processed meats.
high meat diet colorectal cancer risk factor
A colorectal cancer risk factor that is having been obese.
A colorectal cancer risk factor that is having Type II diabetes mellitus.
Type II diabetes colorectal cancer risk factor
A colorectal cancer risk factor that is having had colorectal polyps.
previous colorectal polyps colorectal cancer risk factor
A colorectal cancer risk factor that is having familial adenomatous polyposis or having a family member with familial adenomatous polyposis.
familial adenomatous polyposis colorectal cancer risk factor
A hormone replacement therapy where the hormone is estrogen.
estrogen alone hormone replacement therapy
A hormone replacement therapy where the hormones are estrogen and progestin.
estrogen with progestin hormone replacement therapy
A hormone replacement therapy where the hormone is progestin.
progestin alone hormone replacement therapy
A hormone replacement therapy where the hormone is testosterone.
testosterone hormone replacement therapy
A clinical history in which there is a history of sepsis.
A clinical history in which there is a history of pneumonia.
A clinical history in which there is a history of open wounds.
A clinical history in which there is a history of a high unexplained fever .
clinical history of high unexplained fever
A clinical history in which there is a history of positive blood cultures.
clinical history of positive blood cultures
A clinical history in which there is a history of abnormal white blood cell levels.
clinical history of abnormal white blood cell levels
A clinical history in which there is a history of fungal infections.
A clinical history in which there is a history of the presence of ascites fluid.
A clinical history in which there is a history of cellulitis.
A clinical history in which there is a history of receiving a blood transfusion while in another country.
clinical history of blood transfusion in foreign country
A clinical history in which there is a history of receiving a human tissue or organ transplant .
clinical history of human tissue transplant
A clinical history in which there is a history of receiving an animal tissue or organ xenotransplant.
clinical history of animal tissue xenotransplant
A clinic history in which there is a history of a recent of smallpox vaccination.
clinical history of smallpox vaccination
A clinical history in which there is a history of contact with someone who recently had smallpox.
a clinical history of contact with someone with smallpox
The patient had a clinical history of dialysis treatment three times a week for longer than one month.
A clinical history in which there is a history of significant regular dialysis treatment.
A clinical history in which there is a current diagnosis of cancer at death.
A clinical history in which there is a history of cancer diagnosis in the preceding five years.
A clinical history in which there is a history of cancer diagnosis within a specified time frame.
clinical history of cancer within a time period before death
A clinical history in which there is a history of tuberculosis .
A clinical history in which there was active meningitis at death.
A clinical history in which there was active encephalitis at death.
A clinical history in which there is a history of long term steroid use.
clinical history of long term steroid use
A clinical history in which there is a history of osteomyelitis.
A clinical history in which there is a history of unexplained seizures.
clinical history of unexplained seizures
A clinical history in which there is a history of unexplained weakness and fatigue described as flu-like symptoms.
clinical history of unexplained weakness and fatigue
A clinical history in which there is a history of exposure to toxic substances that may have led to chronic conditions.
A clinical history in which there is a history of an animal bite in the last 12 months, from an animal suspected to have rabies.
A clinical history in which there is a history of an animal bite in recent past, from an animal suspected to have rabies.
An information content entity that indicates whether an individual ever used heroin in any manner.
The participant's clinical history included cocaine use in the last 5 years.
An information content entity that indicates whether an individual recently used cocaine.
An information content entity in that indicates whether a man has ever had sex with another man.
indication of male homosexual sexual activity
An information content entity in which the individual used illegal injectable drugs in the last 5 years.
An information content entity that indicates whether an individual recently used injectable drugs for non-medical purposes in the recent past.
an indication of illegal injectable drug use
A clinical history in which there is a history of clotting disorders, such as hemophilia, requiring treatment with human-derived clotting factors.
A clinical history in which there is a history of growth hormone use.
A clinical history in which there is a history of the donor not being able to be tested for Human Immunodeficiency Virus (HIV) because of hemodilution.
clinical history of inability to have Human Immunodeficiency Virus testing due to hemodilution
A clinical history in which there is a history of unexplained weight loss.
clinical history of unexplained weight loss
A clinical history in which there is a history of night sweats.
A clinical history in which there is a of blue or purple spots on the skin or mucus membranes (typical of Kaposi's sarcoma).
clinical history of blue or purple spots on skin or mucous membranes
A clinical history in which there is a history of unexplained lymphadenopathy lasting more than one month.
A clinical history in which there is a history of unexplained lymphadenopathy of a specific duration.
clinical history of unexplained lymphadenopathy
A clinical history in which there is a history of fever of at least 38.6 Celsius for more than 10 days.
A clinical history in which there is a history of fever of at least 38.6 Celsius for a specified duration.
A clinical history in which there is are active signs of unexplained persistent cough and/or shortness of breath.
clinical history of an unexplained cough or shortness of breath
A clinical history in which there is a history of opportunistic infections.
clinical history of opportunistic infections
A clinical history in which there is a history of sexually transmitted diseases
clinical history of sexually transmitted disease
A clinical history in which there is a history of drug abuse.
A clinical history in which there is a history of a Severe Acute Respiratory Syndrome (SARS) diagnosis.
clinical history of Severe Acute Respiratory Syndrome
A clinical history in which there is a history of recent contact with someone who has Severe Acute Respiratory Syndrome (SARS).
clinical history of exposure to Severe Acute Respiratory Syndrome
A clinical history in which there is a history of West Nile Virus (WNV) infection.
A clinical history in which there is a history of contact with a human or animal who has West Nile Virus (WNV).
clinical history of West Nile Virus exposure
A clinical history in which there is a history of current gonorrhea infection or treatment for gonorrhea in the last 12 months.
A clinical history in which there is a history of active gonorrhea infection or treatment for gonorrhea in the recent past.
A clinical history in which there is a history of current syphilis infection or treatment for syphilis in the last 12 months.
A clinical history in which there is a history of active syphilis infection or treatment for syphilis in the recent past.
A clinical history in which there is a history of Hepatitis B infection.
A clinical history in which there is a history of Hepatitis C infection.
A clinical history in which there is a history of Human Immunodeficiency Virus (HIV).
clinical history of Human Immunodeficiency Virus
A clinical history in which there is a history of systemic lupus
A clinical history in which there is a history of sarcoidosis.
A clinical history in which there is a history of scleroderma.
A clinical history in which there is a history of Reye's Syndrome.
A clinical history in which there is a history of rheumatoid arthritis.
clinical history of rheumatoid arthritis
A clinical history in which there is a history of idiopathic heart disease.
clinical history of idiopathic heart disease
A clinical history in which there is a history of Alzheimer's Disease.
A clinical history in which there is a history of dementia with unknown cause that is not caused by a previous Cerebrovascular Accident (CVA) infection, head trauma or brain tumor).
clinical history of dementia of unknown cause
A clinical history in which there is a history of Multiple Sclerosis (MS).
A clinical history in which there is a history of Amyotrophic Lateral Sclerosis (ALS)
clinical history of Amyotrophic Lateral Sclerosis
An information content entity in which there is an indication of whether an individual resided on a Northern European military base for 6 months from 1980-1990.
An information content entity in which there is an indication of whether an individual resided on a Northern European military base for a specified duration during a specific time frame.
indication of having resided in a Northern European military base
An information content entity in which there is an indication of whether an individual resided in Europe from 1980-1996.
An information content entity in which there is an indication of whether an individual resided in Europe during a specific time frame
indication of having resided in Europe during a specific time frame
An information content entity in which there is an indication of whether an individual ever performed sexual acts in exchange for money or drugs.
indication of performing sexual acts in exchange for money or drugs
An information content entity in which there is an indication of whether an individual spent more than 72 hours in a correction/detention center in the last year.
An information content entity in which there is an indication of whether an individual spent more than 72 hours in a correction/detention center in the recent past.
An information content entity in which there is an indication of whether an individual had a tattoo done in a state that does not regulate tattoo parlors, in the last year.
An information content entity in which there is an indication of whether an individual had a tattoo done in a state that does not regulate tattoo parlors, in the recent past.
indication of a tattoo from unregulated tattoo parlor
An information content entity in which there is an indication of whether an individual has used prescription pills that were not prescribed to them.
indication of illegal prescription drug use
An information content entity in which there is an indication of whether an individual has used illegal intravenous drugs in the past 5 years.
An information content entity in which there is an indication of whether an individual has used illegal intravenous drugs in a specified time frame.
An information content entity in which there is an indication of whether an individual spent a total of three or more months in the United Kingdom, any time from 1980-1996.
An information content entity in which there is an indication of whether an individual spent a total of three or more months in the United Kingdom, in a specified time frame.
indication of having lived in the United Kingdom during specific time frame
An information content entity in which there is an indication of whether an individual has signs of non-professional body piercing.
indication of body piercing from non-professional
An information content entity in which there is an indication of whether an individual has signs of non-professional tattoos.
indication of tattoo from non-professional
An information content entity in which there is an indication of whether an individual was a resident of a state-run group home at time of death.
indication of residence in state-run group home at time of death
An indication of whether an individual lived in Europe for at least 5 years since 1980.
An information content entity in which there is an indication of whether an individual lived in Europe for at least 5 years during a specific time.
indication of having resided in Europe during specific time frame
A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data.
definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
biobank
A human biobank is a collections of samples of human body substances (e.g. Tissue, blood, DNA) which are linked to personal data and socio deographic information about the donors of the material. They have a dual nature as collections of samples and data."
Deutscher Ethikrat: Human biobanks for research. Opinion. Berlin, 2010. http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
human biobank
The part of a sample collection or study contact's adress denoting a settlement.
Sample Collection/Study contact city
settlement part of address of sample collection or study contact
An identifier in natural language referring to a biobank.
Name of biobank
biobank proper name
An identifier that consists of two letters, is part of the ISO 3166-1, and designates countries, dependent territories, and special areas of geographical interest.
Two-letter country codes defined in ISO 3166-1, part of the ISO 3166 standard published by the International Organization for Standardization (ISO), to designate countries, dependent territories, and special areas of geographical interest.
ISO 3166-1 alpha-2 code
A biobank identifier that has an ISO 3166-1 alpha-2 code as a part.
Biobank ID
Textual string of letters starting with the country code (according to standard ISO1366 alpha2) followed by the underscore “_” and post-fixed by a biobank ID or name specified by its juristic person (nationally specific).
biobank idenfier with ISO 3166-1 alpha-2 code
The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address.
Sample Collection/Study contact country
ISO 3166-1 alpha-2 code for sample collection or study contact
An organization bearing legal personality that owns or adminstrates a biobank.
biobank juristic person
biobank organization
A planned process that involves a human being and is intended to initiate a communication with another human being.
Contacting is the process of one human being starting a communication process with another human being. Contacting can be done using all modes of communication used by humans.
contacting
A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process.
contact role
A human being that is member of a biobank organization and bears the organization contact role.
biobank contact person
A personal name that designates the person acting as contact for a biobank.
Biobank contact person
name of biobank contact person
An email address for the purpose of contacting a biobank contact person.
Biobank contact email
email address of biobank contact person
Postal address used as a directive for deliveries to the biobank contact person.
postal address of biobank contact person
An organization with a specific responsibility that is a part of a larger organization with a specific responsibility.
department
A department that has a contact person for a biobank as an organizational member.
Biobank contact department
department of biobank contact
A CRID that constitutes a reference to an Internet resource.
uri
unique resource locator
A unique resource locator referring to the homepage of a biobank.
Biobank URL
biobank's unique resource locator
A telephone number is a textual entity consisting of a sequence of digits used to call from one telephone line to another in a public switched telephone network.
MB: This class should probably be a subclass to CRID. However, the textual definition of CRID right now states that each instance has the CRID identifier as a part. This is not the case for telephone numbers. Therefore, they cannot be subsumed under CRID now. I am looking into changing IAO accordingly. Once that is done, the class ought to be a subclass of CRID.
telephone number
A telephone number that is contact information about a biobank contact person.
Biobank contact phone
telephone number of biobank contact
An identifier denoting a post-office box.
post-office box number
A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable.
post-office box
A telephone number that is contact information about a sample collection or study contact person.
Sample Collection/Study contact phone
telephone number of sample collection or study contact
The postal code that is part of the postal address of the biobank contact person.
Biobank contact ZIP
postal code of biobank contact
The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address.
ISO 3166-1 alpha-2 code for biobank contact person
A textual entity that is part of a postal address and denotes a human settlement for the purpose of delivering mail.
settlement part of address
The part of a biobank contact's adress denoting a settlement.
Biobank contact city
settlement part of address biobank contact
A textual entity that is part of a postal address and specifies the location inside the settlement (which is specified by another part of the address). This can be a street name and a house number, or just a number or a post-office box number.
intra-settlement specification part of address
An intra-settlement specification part of address that is part of a biobank contact's postal address.
Biobank contact address
intra-settlement specification part of address of biobank contact
A object aggregate that consists of specimens, participates in a study and is part of a biobank.
Hosted studies
hosted study collection
The proper name that designates a hosted study collection.
name of hosted study collection
An email address for the purpose of contacting a sample collection or study contact person.
Sample Collection/Study contact email
email address of sample collection or study contact
A textual entity describing a study aim or a sample collection.
Sample collection or study description
sample collection or study aim description
A proper name that designates a study.
Study name
study proper name
A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study.
Sample Collection Responsible / Principal Investigator
name of sample collection responsible or principal investigator
A personal name that designates the person acting as contact for a sample collection or a study.
Sample Collection/Study contact person
name of sample collection or study contact person
A department that has a contact person for a sample collection or a study as an organizational member.
Sample Collection/Study contact department
department of sample collection or study contact
A street is a thoroughfare in a built environment.
street
An intra-settlement specification part of address that is part of a sample collection or study contact's postal address.
Sample Collection/Study contact address
intra-settlement specification part of address of sample collection or study contact
Postal code that is part of the address of a human being serving as sample collection or study contact.
Sample Collection/Study contact ZIP
postal code for sample collection or study contact
An ISO 3166-1 alpha-2 code that designates the country a biobank is located in.
Biobank country code
biobank location ISO 3166-1 alpha-2 code
An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program.
CTEP organization identifier
A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code.
biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
A processed specimen that is the output of a fixation process.
Alice Nzinga
fixed tissue specimen
A fixed tissue specimen that is in block form.
fixed tissue block specimen
A fixed tissue specimen that is placed in a slide.
fixed tissue slide specimen
A frozen specimen that has been instantly/quickly frozen by subjecting the specimen to cryogenic temperatures, or in direct contact with liquid nitrogen at -320.8F 0r -196C.
flash frozen specimen
A fresh specimen that is in a tissue form.
fresh tissue specimen
A frozen specimen is a tissue sample preserved in a block.
frozen tissue block specimen
A frozen specimen that has been sliced from a tissue block into thin layers that are placed on a glass to be examined under a microscope.
frozen tissue slide specimen
A specimen that has been procured from a histology slide under direct microscopic visualization.
microdissected specimen
A data item that contains the outcome of a survey.
survey data
The process of collecting or selecting an aggregate of specimens into a biobank.
sampling specimens for biobank
A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.
biobank contact role
A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study.
sample collection or study contact role
A human being acting as bearing the contact role for a sample collection or a study.
sample collection or study contact person
A data item that indicates the pathological assessment of a specimen.
specimen disease state datum
A specimen disease state datum item that specifies that the specimen in question consists of a disorder.
diseased state specimen datum
A specimen disease state datum that specifies that the specimen in question consists of partially normal tissue and a disorder.
mixed state specimen datum
A specimen disease state datum that specifies that the specimenin questions consists of normal tissue.
normal state specimen datum
A material processing that uses chemical process by which biological tissues are preserved from decay. Fixation terminates any ongoing biochemical reactions and may increase stability of the treated tissues.
The choice of fixation depends on the type of study.
fixation
An information content entity that is about a data set that has age information and specifies the range of age information in that data set.
Martin Fransson
Example: age interval is 18-65
age interval information
An average value of age for a certain group of individuals.
average age
A data set of collected secondary data related to patients with a specific diagnosis, condition, or procedure and plays an important role in post marketing surveillance of pharmaceuticals.
patient register data
It can be said to be a formal record of an internationally agreed minimum amount of information about clinical trial.
patient registry data
A data item that indicates the time when data about the sample collection was reported into a database.
It is denoted by Date in ISO-standard (8601) time format.
date of data entry
A data item that indicates the time when data about the sample collection was last updated in a database.
It is expressed as a Date in ISO-standard (8601) time format.
date of data update
A data item that indicates the time when the sampling of specimens for a biobank ended.
end date of sampling for biobank
A data item that indicates the time when the sampling of specimens for a biobank started.
start date of sampling for biobank
A diagnosis that is the outcome of a diagnostic process targeting a second or additional health problem.
secondary infection, nosocomial infection
amended from http://en.wikipedia.org/wiki/Comorbidity
It is argued that Comorbidity occurs due to a disposition established by a prior infection with a pathogenic organism of a different kind.
comorbidity
A diagnosis that is the main reason for the inducement of medical care.
main diagnosis
Hint: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
primary diagnosis
A count that is about the aggregate of individuals who have contributed biological specimens in a study.
count of current sampled human study participant
A count that is about the aggregate of individuals who have been recruited to participate in a study.
count of current total human study participant
A measurement datum that contains the assessment information about the functioning of a major organ system, the extent of disease or disability,as well as the provision and/or response to therapeutic interventions.
Examples: Audiology, Cardiac Physiology, GI Physiology, Neurophysiology, Ophthalmic and Vision Science, Respiratory and Sleep Physiology, Urodynamics, Vascular Technology
physiological measurement data
A setting datum that specifies the temperature inside a container participating in a storage process.
Examples: -18 °C to -35 °C, -60 °C to -85 °C, Liquid nitrogen, Room temperature etc
storage temperature setting
An objective specification that aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
A tentative procedure that is aimed at discovering some characteristic of a large familiy of cellular molecules, having named by appending suffix "-omics."
Technologies that measure some characteristic of a large family of cellular molecules, such as genes, proteins, or small metabolites, have been named by appending the suffix "-omics," as in "genomics." Omics refers to the collective technologies used to explore the roles, relationships, and actions of the various types of molecules that make up the cells of an organism.
interrelated experiments.
omics experiment on specimen
An objective specification that specifies the number of individuals to participate in a study and provide biological specimens to the study.
number of sampled human study participants objective
An objective specification that specifies the total number of individuals who are planned to participate in study.
number of total human study participant objective
A study design that compares two groups of subjects; those with the disease or condtion under study and a similar group of subjects who do not have the condition.
case control study design
A study design in which all participants or a representative subset of participants are examined at only a single time for characteristics of a interest (e.g. a specific disease).
cross sectional study design
A study design that involves repeated observations of the same entity over time. In the biobank context, longitudinal studies sample a group of people in a given time period, and study them at intervals by the acquisition and analyses of data and/or samples over time.
longitudinal study design
A longitudinal study that aims to study a case-defined population who presently have a certain condition or recepient of a particular treatment that are followed over time and are compared with a similar group who do not have condition.
cohort study design
A longitudinal study that samples a cross-section and studies it at regular intervals.
panel study design
A study design that is multidisciplinary done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
population based study design
A study design where some aspect of the experiment is quality controlled for the purposes of quality assurance.
quality control study design
A study design usually in behavior genetics which aids the study of individual differences between genetically identical twins by highlighting the role of environmental and genetic causes on behavior.
twin study design
A plan specification that is realized by process of gathering information (e.g. by asking questions).
survey plan specification
A document that contains information representing health-relevant qualities of a patient written in a chronological manner and that is primarily used for patient care in a clinical setting.
It is a chronological written account of examination, treatment, medical history or complaints.
It is used interchangeably with health record and medical chart. https://en.wikipedia.org/wiki/Medical_record
medical record
A medical record of a specimen donor.
sample medical record
A document that outlines the procedures employed to preserve and protect the material collected during specimen collection as an indication of sample quality.
It could be argued as to why this class was not created as an 'objective specification'. However, the emphasis here is to 'a briefing of how the specimen in the sample collection have been handled as an indication of specimen quality.'
It could be freeze chain, freze time, SPREC compliant, etc.
sample handling summary
Age interval information that is age information of specimen donors.
sampled group age interval
age interval information for sampled donors
Registry data for a patient who participates as a donor in a study.
donor patient registry data
A survey data for a specimen donor.
Examples: Individual Disease History, Individual History of Injuries, Medication, Perception of Health, Women's Health, Reproductive History, Familial Disease History, Life Habits/Behaviors, Sociodemographic Characteristics, Socioeconomic Characteristics, Physical Environment, Mental Health, Other.
study subject survey data
A planned process that involves the initial entering of data about sample collection into a database.
sample collection data entry
A planned process which involves editing of specimen collection data into a database after its initial entry.
sample collection data update
A planned process that realizes the concretization of a survey to generate an output(survey data.)
survey execution
A planned process that aims to control or maintain the temperature of a material entity to a given or required measurement datum.
As per placing the term as a planned process, it can be argued that nature does play a role in the final output of the actual temperature.
temperature regulating
A textual entity that states additional information about the specimen or donor that is deemed relevant for the specimen collection process.
comment from tissue procurement
3mm X 3mm X 3mm
A measurement datum that is the result of measurement of the three dimensions of a specimen.
specimen measurement
A data item that indicates the time when the collection of a specimen occurred.
date of specimen preparation
date of specimen collection
All specimens that meet the set parameters to be procured on.
adherance to specification
specimen meeting specification
mastectomy / craniotomy / liver resection e.t.c.
A planned process that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, or to help improve bodily function or appearance.
surgical procedure
A personal name that designates the person who prepared the specimen.
specimen preparation contact
15min
A time measurement datum that states the duration during which a specimen was submerged in formalin.
time in formalin measurement
A collecting specimen from organism process that involves removing the specimen from an individual through a surgical procedure.
specimen surgical removal
A freezing storage for the specimen.
specimen freezing
A proper name that identifies a specimen and is usually in form of a label included in the specimen cassette.
specimen ID
An identifier that refers to a specimen donor who is participating in specimen collection process for tissue procurement purposes and is usually assigned at the time of donor procurement.
case ID
An directive information entity that states the technical standard measurement set and values that determines if a specimen qualifies for procurement or not.
A specification (often abbreviated as spec) may refer to an explicit set of requirements to be satisfied by a material, design, product, or service.
specimen measurement specification
A data item that reports the time when a specimen was frozen.
time of specimen freezing
A data item that reports the time when a specimen was collected by a surgical procedure.
time of surgical removal of specimen
A specimen that is normal.
normal specimen
A biobank that collects and stores specimen during specimen collection primarily for the purposes of some study.
hosting biobank
A Homo sapiens who contributes specimen.
sample donor
specimen donor
A planned process of preparing and submitting specimens to storage.
specimen handling
sample handling
The process boundary marking the beginning of a sampling of specimens into a biobank.
start of sampling specimens for biobank
The process boundary marking the end of a sampling of specimens into a biobank.
end of sampling specimens for biobank
specimen position
specimen integrity
A mass measurement datum that is the result of an assay to measure the weight of a specimen.
specimen weight
An identifier that specifically identifies a particular specimen slide.
specimen slide ID
A cancer therapeutic procedure that involves a surgical procedure as a main part.
surgical cancer treatment
specimen gross appearance of metastatic tumor
A specimen gross appearance of a tumor that has spread from its original site by discontinuous (not direct) spread, e.g. by blood or lymphatics.
specimen gross appearance of tumor center
A specimen gross appearance of the most internal topographic location of the tumor.
A specimen gross appearance of the border of the tumor with non-tumorous tissue.
specimen gross appearance of tumor edge
research authorization for post mortem specimen donation for a specific tissue or fluid
A research authorization documentation for postmortem specimen donation in which the authorization is for a specified tissue or biological fluid.
tissue specimen suitability for molecular analysis
A conclusion textual entity that signifies whether a specimen is acceptable for molecular analysis based on the assessment by a pathologist of a tissue specimen based on qualities such as purity and size.
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
OBI
regulator role
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
OBI, CDISC
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
measuring
scientific observation
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
culture medium
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
GROUP:Role Branch
CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
patient role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
participant under investigation role
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Person: Jennifer Fostel
responsible party role
a responsible party role played by a person responsible for the overall conduct of a study
CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
principal investigator role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker role
A device manufacture with the intent to provide a porous unsized paper used for filtering.
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
PERSON: Philippe Rocca-Serra
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
plan
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
AR, BP, JM, MC, PRS
branch derived
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
analyte role
drug added to a buffer contained in a tube; substance injected into an animal;
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
9 March 09 from discussion with PA branch
material to be added role
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
contain function
A contain function is a function to constrain a material entities location in space
heat function
A heat function is a function that increases the internal kinetic energy of a material
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
mechanical function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
transfer function
A transfer function is a function to displace a material from one location to another.
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
image acquisition function
An image acquisition function is a function to acquire an image of a material
An image creation device is a device which captures a digitized image of an object
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
environment control function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
averaging objective
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
a portion of urine collected from an organism
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
are we happy calling collection of urine a material separation?
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
blood drawn from a human for glucose assay
a material entity derived from a portion of blood collected from an organism
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
average value
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
is an objective to obtain an output material that contains several input materials.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material entity that has the material sample role
An objective specification maintains some or all of the qualities of a material over time.
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
A person or organization that has a manufacturer role
A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
An information content entity created to indicate that information about something is not available to the person recording it.
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
material obtained through a liver biopsy from a human patient
a specimen that was taken from a live organism
MO_705 premortem
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
A storage process in temperature that maintenance the frozen status of the stored entities.
2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen.
Person: Alan Ruttenberg, Mathias Brochhausen
MO_481 frozen_storage
type of sample used in the PCIRN influenza network
A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
A specimen that has been frozen in order to store it.
a storage process with input material entity and output freeze dried material for long time storage
can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
A device with a separation function realized in a planed process
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
A function that is realized when a reagent is automatically added to some research material.
PERSON: Nicole Vasilevsky, Matthew Brush
4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people?
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
a specimen that is output of a specimen creation process used for an investigation without storage.
a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
need to specify paraffin or wax is one of specified input of the process
a specimen that is output of a process that cell culture inoculated into agar for long term storage.
An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation.
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
a storage process with input cell culture and agar and output agar stab for long time storage
need to specify that agar is one of input for this process
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
A planned process that captures an image of an object.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
age since planting measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call
age since hatching measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
age since egg laying measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
age since germination measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
age since eclosion measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
age since sowing measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
age since coitus measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage.
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
discussed on Nov 15, dev call All subtype will be defined by textual definition now.
age since fertilization measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
Definition of fertilization comes from GO.
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony.
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
genetic characteristics information
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
Person: Chris Stoeckert, Jie Zheng
MO_66 IndividualGeneticCharacteristics
MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
specimen with pre- or post-mortem status
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
organizational term, used in description of specimen that is created from known pre- or post-mortem status
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
Services performing DNA sequencing or Cell Analysis
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer.
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
collection date
NIAID GSCID-BRC metadata working group
selection criterion
rats should be aged between 6 and 8 weeks and weight between 180-250grams
A directive information entity which defines and states a principle of standard by which selection process may take place.
Person: Philippe Rocca-Serra
selection rule
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
reagent
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.
(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
A cultured cell population that is derived through one or more passages in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
selection
PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
selection process
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
specimens derived from shared ancestor
Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy.
A collection of specimens derived from one common specimen via one or more material processing process(es).
Chris Stoeckert, Jie Zheng
specimen family
Duke Biobank, OBIB, OBI
containing a specimen function
A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
Chris Stoeckert
Biobank
COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
A container with the function of containing a specimen.
A container with an environmental control function.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
specimen family creation
Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum.
A material processing that has as its input a specimen and as its output a collection of specimens.
For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Mathias Brochhausen, Chris Stoeckert, Jie Zheng
OBI, OBIB
IHC slide staining
A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues.
Chris Stoeckert, Ned Haubein
H&E slide staining
A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink.
H&E-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of H&E slide staining.
OBIB, OBI
IHC-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
immunohistochemistry slide specimen
A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace.
RNA Integrity Number calculation
RNA Integrity Number value specification
A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact).
A value specification that specifies the temperature of some thing.
temperature value specification
A value specification that specifies the volume of some thing.
volume value specification
An assay to determine the temperature of an evaluant.
An assay to determine the volume of an evaluant.
Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens
An analyte assay that measures the presence or amount of antibodies to a specified antigen.
An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens.
HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36)
An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens.
An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens.
An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens.
An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens.
venereal disease research laboratory test
An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood.
An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope.
An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens.
An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids.
An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids.
An organization that delivers messages, packages, and mail.
courier organization
A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item.
courier tracking number
An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories.
A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right.
A device that is the part of a microtome used to slice specimens to a desired thickness.
Sakura Low profile Accu-Edge microtome blade
A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering.
A length measurement datum that is the result of an assay measuring the thickness of a tissue section.
tissue section thickness
molecular analysis facility organization
An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs.
An organization that provides molecular analysis service.
cannot be assessed, not applicable, unknown
An information content entity that provides an explanation why a data item is not provided.
A reason for lack of data item that is the negative output of a determination if assay will provide reliable results.
determination if assay will provide reliable results
A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay.
AJCC 7th edition GX: cannot be assessed.
A cannot be assessed determination for histologic tumor grade.
AJCC 7th edition pTX: cannot be assessed.
A cannot be assessed determination for pathologic primary tumor staging.
AJCC 7th edition pNX: cannot be assessed.
A cannot be assessed determination of pathologic staging of lymph nodes.
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
A clinical history in which there is a diagnosis of cancer.
A clinical history in which there was no diagnosis of cancer.
A clinical history in which it is not known whether there was a diagnosis of cancer.
A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer.
A clinical history in which there is a diagnosis of cancer in a blood relative.
A clinical history in which there is a diagnosis of cancer in the female sibling of a parent.
A clinical history in which there is a diagnosis of cancer in a male sibling.
A clinical history in which there is a diagnosis of cancer in a person's female child.
A clinical history in which there is a diagnosis of cancer in a male parent.
A clinical history in which there is a diagnosis of cancer in a female parent.
A clinical history in which there is a diagnosis of cancer in a female sibling.
A clinical history in which there is a diagnosis of cancer in a person's male child.
A clinical history in which there is a diagnosis of cancer in a male sibling of a parent.
A clinical history in which there is a diagnosis of cancer in a female parent of a parent.
A clinical history in which there is a diagnosis of cancer in a male parent of a parent.
A clinical history in which there is a diagnosis of cancer in a male child of a sibling.
A clinical history in which there is a diagnosis of cancer in a female child of a sibling.
A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease.
A diagnosis of infectious disease caused by the hepatitis B virus.
A diagnosis of infectious disease caused by the hepatitis C virus.
A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2).
A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays.
A clinical history in which there has been second hand exposure to tobacco smoking.
exposure to second hand smoke in household during childhood
An exposure to second hand smoke that occurred in the (patient's) household when the person was a child.
exposure to second hand smoke in current household
An exposure to second hand smoke in person's current household.
A clinical history in which a female has had a pregnancy.
A measurement datum of the total number of pregnancies a woman has had.
A measurement datum of the total number of live births a female has had.
An age measurement datum performed on a female when her first biological child was born.
A clinical history in which a woman has had gynecologic surgery in the past.
A gynecologic surgery history in which a woman has had a hysterectomy.
A gynecologic surgery history in which a woman has had a unilateral oophorectomy.
neither hysterectomy nor oophorectomy history
A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy.
An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy.
hormonal birth control former use history
A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user.
hormonal birth control current use history
A hormonal birth control use history that indicates an individual is currently a hormonal birth control user.
A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user.
A clinical history in which an individual has had hormonal replacement therapy in the past.
delivery form for hormonal replacement therapy
A processed material used for delivery of hormones in hormone replacement therapy.
pill delivery form for hormonal replacement therapy
A delivery form for hormonal replacement therapy that is a pill for oral administration.
patch delivery form for hormonal replacement therapy
A delivery form for hormonal replacement therapy that is a patch for transdermal administration.
cream delivery form for hormonal replacement therapy
A delivery form for hormonal replacement therapy that is a cream for transdermal administration.
An information content entity that indicates the state of a female's cessation of menstruation.
A menopausal status that is neither pre- nor post-menopausal.
A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement.
A menopausal status indicating that it has been 6-12 months since last menstrual period.
A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy.
exposure to environmental and workplace carcinogens history
An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment.
An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic.
An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos.
An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust.
An exposure to environmental and workplace carcinogens history where the carcinogen is chromium.
An exposure to environmental and workplace carcinogens history where the carcinogen is silica.
indicator of whether an inclusion criterion was met
An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process.
indicator of whether all inclusion criteria were met
An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process.
An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process.
chemotherapy treatment exclusion criterion
An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
chemotherapy treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years.
An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
radiation treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years.
An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0
An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process.
history of metastatic cancer exclusion criterion
An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process.
intravenous drug use exclusion criterion
Donor eligibility based on history of intravenous drug abuse in the last 5 years.
An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of blood borne infection exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of intravenous drugs exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process.
exposure to blood borne infectious disease exclusion criterion
Donor eligibility based on whether the donor has been exposed to HIV/AIDS.
An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process.
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
health status inclusion criterion
‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension'
An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
MIABIS2.0
clinically relevant lifestyle inclusion criterion
'smoking behavior’
An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process.
clinically relevant exposure inclusion criterion
'exposure to cigarette smoke’, ‘exposure to lead through drinking water'
An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process.
gravidity inclusion criterion
'pregnant’, ‘not pregnant'
An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process.
inclusion based on age, sex, and living region (rural area or specified city).
An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
defined population inclusion criterion
age since culture seeding measurement datum
An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish).
Stephen A. Fisher, Junhyong Kim, Dan Berrios
A specimen that is derived from amniotic fluid.
A specimen that is derived from cerbrospinal fluid.
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
A specimen that is derived from pericardial fluid.
A specimen that is derived from synovial fluid.
A specimen that is derived from vireous humor.
A specimen that is derived from bone marrow.
A specimen that is derived from placenta.
A specimen that is derived from peritoneal fluid.
A specimen that is derived from pleural fluid.
A specimen that is derived from prostate gland.
A specimen that is derived from skeletal muscle.
A specimen that is derived from renal medulla.
A specimen that is derived from adrenal gland.
A specimen that is derived from urinary bladder.
A specimen that is derived from tibial artery.
A specimen that is derived from pancreas.
A specimen that is derived from stomach.
A specimen that is derived from pituitary gland.
A specimen that is derived from adipose tissue.
A specimen that is derived from cortex of kidney.
A specimen that is derived from esophagus mucosa.
A specimen that is derived from esophagus muscularis mucosa.
A specimen that is derived from cerebral cortex.
A specimen that is derived from thyroid gland.
A specimen that is derived from cerebellum.
A specimen that is derived from tibial nerve.
A specimen that is derived from coronary artery.
A specimen that is derived from the atrium auricular region.
A specimen that is derived from the esophagogastric junction.
A specimen that is derived from minor salivary gland.
A specimen that is derived from omentum.
A specimen that is derived from female gonad.
A specimen that is derived from sigmoid colon.
A specimen that is derived from suprapubic skin.
age group inclusion criterion
"18-33 years old"
An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process.
minimum age value specification
A value specifcation that specifies the youngest age when specifying an age range.
maximum age value specification
A value specifcation that specifies the oldest age when specifying an age range.
use of medication inclusion criterion
"received at least 2 days of vancomycin"
An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process.
hospital patient inclusion criterion
"included hospital patients"
An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process.
family status inclusion criterion
"included married and unmarried patients", "included divorced individuals"
An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process.
sex inclusion criterion
"included males and females", "included male patients"
An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
country of residence inclusion criteria
"include US residents"
An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process.
ethnicity inclusion criterion
"include only Hispanic individuals"
An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
A specimen that is stored on a swab as the output of a collecting specimen with swab process.
A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
A specimen that is collected with a swab from the surface of an areola of a breast.
A specimen that is collected with a swab from the surface of a breast.
A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth.
A specimen that is collected with a swab from the surface of a nasopharynx.
A specimen that is collected with a swab from the inside surface of a mouth.
A specimen that is collected with a swab from the surface of a oropharynx.
A specimen that is collected with a swab from the surface of a rectum.
A specimen that is collected with a swab from the surface of a tongue.
A specimen that is collected with a swab from the surface of a vagina.
A specimen that is collected with a swab from the surface of a feces.
A specimen that is collected with a swab from the surface of an environmenal material.
The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases.
A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up.
A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design.
A study design for which material and information is collected from subjects that have already developed a particular disease.
genealogical record
A family tree is a type of genealogical record.
A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption.
national registry
The Social Security Administration's Death Master File is a national registry in the United States.
An information content entity that contains information about a nationwide group of individuals.
national biomedical registry
The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry.
A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes.
A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.
Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland.
A biopsy which uses an imaging procedure to guide a needle biopsy.
A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle.
A needle biopsy guided by real-time computed tomography (CT) scan images.
Computed Tomography-Guided Needle Biopsy
An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid.
A needle biopsy guided by ultrasound visualization.
A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin.
A biopsy that uses a hollow needle to extract cells.
A fine needle aspiration biopsy is commonly performed in order to test for cancer.
A biopsy that uses a thin needle to extract cells.
Chris Stoeckert, Helena Ellis, Jie Zheng
A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed.
A biopsy that uses a hollow tube to collect a core of tissue.
Surgical biopsy may be required to collect hard-to-reach tissue.
A biopsy involving a surgical incision into an organism to access the biopsy material.
The makeup of fat in the abdominal wall can be investigated by fat biopsy.
A biopsy involving the collection of a small part of the abdominal wall fat pad.
A mouse tail biopsy was performed to collect material for DNA extraction.
A biopsy involving the collection of the tip of a mamallian tail.
A bone marrow biopsy removes bone with the marrow inside to look at under a microscope
A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected.
A three or four millimeter punch is used in s skinpunch biopsy proceedure.
A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool.
Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source.
A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material.
molecular label role
A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743.
Group: OBI
molecular tracer role
molecular label
A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744.
molecular tracer
A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue.
A biopsy performed with a needle augmented with a vacuum device.
A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
platelet-poor plasma specimen
A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter.
PERSON: Matthew Diller
platelet-poor plasma preparation process
A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm.
A person or organization that provides material supplies to other people or organizations.
blood plasma specimen
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
PERSON: Maura Gasparetto
plasma
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood serum specimen
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
bronchial alveolar lavage
solution containing lung derived T cells, eosinophils, and TNFa.
Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
BAL
GROUP: IEDB
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
PERSON: James Malone
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
pool of specimens
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
The OBI manuscript is (much) edited imformation
A document which is the output of a document editing process
edited document
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
OBI-Branch: adapted from wikipedia and wordnet
filtration
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
storage
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
is a planned process with specified input original document and specified output edited document
document editing
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
digital curation
A device with a rapidly rotating container that applies centrifugal force to its contents
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
eligibility criterion
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion criterion
PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
inclusion condition
inclusion rule
exclusion rule
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
exclusion criterion
human subject enrollment
enlisting familiy members of HIV patients into a study
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
As with group assignment, should the specified output here be an organism which bears a role
IEDB
criteria come from plan / clinical trial branch
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
physical combination of several instances of like material
sample pooling
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
pooling specimens
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
aliquoting
apportioning
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
cell culture splitting
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.
addition of molecular label
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
OBI developer call, 3-12-12
lavage
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
This is not washing, in which case the material of interest is not the resulting fluid
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
PERSON:Kevin Clancy
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
requested by Helen Parkinson for MO
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
cell pellet
Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension
PERSON: Helen Parkinson
GROUP: CEBS
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
donor
A cell culture into which a mixture of peptides is being added.
A material entity that receives the addition of another material entity in an “adding a material entity into a target” process.
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/
A specimen that has been fixed in formalin and embedded in paraffin.
formalin-fixed paraffin-embeded specimen
A specimen that is derived from some uterine cervix
Christian Stoeckert ORCID:0000-0002-5714-991X
A specimen that is derived from some urethra
A specimen that is derived from some cervical mucus
A specimen that is derived from some throat
A specimen that is derived from some eye
A specimen that is derived from some respiratory system
A specimen that is derived from some upper respiratory tract
A specimen that is derived from some nasopharynx
A specimen that is derived from some semen
A specimen that is derived from some bodily fluid
A specimen that is derived from some chorionic villus
A specimen that is derived from some meconium
A specimen that is derived from some umbilical cord blood
A specimen that is derived from some arterial blood
A specimen that is derived from some venous blood
A specimen that is derived from some capillary blood
A specimen that is derived from some erythrocytes
A specimen that is derived from some reticulocytes
A specimen that is derived from some leukocytes
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
The representation of a conclusion of a diagnostic process.
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
obsolete settlement part of address of sample collection or study contact
obsolete biobank idenfier with ISO 3166-1 alpha-2 code
obsolete sample collection or study identifier
obsolete ISO 3166-1 alpha-2 code for sample collection or study contact
obsolete email address of biobank contact person
obsolete postal address of biobank contact person
obsolete biobank's unique resource locator
obsolete telephone number of biobank contact
obsolete telephone number of sample collection or study contact
obsolete ISO 3166-1 alpha-2 code for biobank contact person
obsolete settlement part of address biobank contact
obsolete intra-settlement specification part of address
obsolete intra-settlement specification part of address of biobank contact
obsolete name of hosted study collection
obsolete email address of sample collection or study contact
obsolete sample collection or study aim description
obsolete name of sample collection responsible or principal investigator
obsolete name of sample collection or study contact person
obsolete department of sample collection or study contact
obsolete intra-settlement specification part of address of sample collection or study contact
obsolete postal code for sample collection or study contact
obsolete biobank location ISO 3166-1 alpha-2 code
obsolete biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
obsolete sample collection or study contact role
obsolete sample collection or study contact person
obsolete study principle investigator or responsible
obsolete end date of sampling for biobank
obsolete start date of sampling for biobank
obsolete count of current sampled human study participant
obsolete count of current total human study participant
obsolete number of sampled human study participants objective
obsolete number of total human study participant objective
obsolete age interval information for sampled donors
obsolete comment from tissue procurement
obsolete specimen measurement specification
obsolete time of surgical removal of specimen
obsolete start of sampling specimens for biobank
obsolete end of sampling specimens for biobank
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
health care role
human health care role
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
nurse
based on: http://en.wikipedia.org/wiki/Nursing
nurse role
An object aggregate all of whose components are human beings.
collection of humans
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan Amanda Hicks
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
legal person role
material entity role
Homo sapiens role
An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context.
S. Clint Dowland
Matthew Diller
Sarah Bost
We include (i)-(iii) to acknowledge that there are different senses of "identify" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way.
social identity information content entity
A social identity information content entity that is about whether some person identifies as some ethnicity.
Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian.
ethnic identity information content entity
An ethnic identity information content entity that uses OMB terminology for ethnicity or terminology that is strictly mapped onto the OMB ethnicity terms.
OMB dichotomizes ethnicity into Hispanic or Latino and Not Hispanic or Latino, and ignores all other forms of ethnicity.
OMB ethnic identity information content entity
An OMB ethnic identity information content entity that is about some person's identifying as Hispanic or Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
It comprehends people of Portuguese culture or origin in Brazil.
OMB Hispanic or Latino identity information content entity
An OMB ethnic identity information content entity that is about some person's identifying as neither Hispanic nor Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
OMB not Hispanic or Latino identity information content entity
A social identity information content entity that is about whether some person identifies as some gender.
gender identity information content entity
A gender identity information content entity that is about some person's identifying as female in gender.
female gender identity information content entity
A gender identity information content entity that is about some person's identifying as male in gender.
male gender identity information content entity
A gender identity information content entity that is about some person's identifying as non-binary in gender.
non-binary identity information content entity
A social identity information content entity that is about whether some person identifies as some race.
racial identity information content entity
A racial identity information content entity that uses OMB terminology and definitions for race or terminology that is strictly mapped onto the OMB race terms.
OMB racial identity information content entity
An OMB racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
This definition corresponds to that used by OMB. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment.
OMB American Indian or Alaska Native identity information content entity
An OMB racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
OMB Asian identity information content entity
An OMB racial identity information content entity that is about some person's identifying as black or African American which is intended to mean having origins in any of the black racial groups of Africa.
OMB black or African American identity information content entity
An OMB racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
OMB Native Hawaiian or other Pacific Islander identity information content entity
An OMB racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa.
OMB white identity information content entity
A role inhering in an entity realized by social interactions in human society.
Previous definition: A role played by an entity in human social processes.
role in human social processes
A time quality inhering in a bearer by virtue of how long the bearer has existed.
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A physical quality of the thermal energy of a system.
A quality in which events occur in sequence.
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality which inheres in a continuant.
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
A structural quality inhering in a bearer by virtue of whether the bearer includes all its components.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
A quality that inheres in an entire organism or part of an organism.
A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content.
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof.
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
A multicellular structure that is a part of an organ.
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
A fluid that is composed of blood plasma and erythrocytes.
The upper ventral region of the torso of an organism.
A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
The inner portion of the kidney consisting of the renal pyramids.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
A gonad of a male animal. A gonad produces and releases sperm.
Anatomical group that has its parts adjacent to one another.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
Anatomical system that has as its parts the organs concerned with reproduction.
The gonad of a female organism which contains germ cells.
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
Functional system which consists of structures involved in respiration.
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
A filament, mostly protein, that grows from follicles found in the dermis[WP].
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
The terminal portion of the intestinal tube, terminating with the anus.
Transudate contained in the pleural cavity.
Excretion that is the output of a kidney.
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
A lobe of thyroid gland that is in the right side of a thyroid gland.
A lobe of thyroid gland that is in the left side of a thyroid gland.
Muscle tissue that consists primarily of skeletal muscle fibers.
The body of the pancreas is a subsection of the pancreas organ in the human body. It is somewhat prismatic in shape, and has three surfaces: anterior, posterior, and inferior. It is at the same level as the transpyloric plane. [WP,unvetted].
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].
The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
An adrenal gland that is in the right side of the abdomen.
An adrenal gland that is in the left side of the abdomen.
Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
Transudate contained in the peritoneal cavity.
The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg.
The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia].
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.
A muscular organ in the floor of the mouth.
The section of the pharynx that lies above the soft palate.
The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.
A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.
One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP].
Lip that covers the lower portion of the mouth.[TAO].
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
Organism substance that is composed of sperm cells suspended in seminal fluid.
Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
A vessel through which blood circulates in the body.
Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple.
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
Respiration organ that develops as an outpocketing of the esophagus.
A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
Cardiac chamber in which blood enters the heart.
A cardiac ventricle that is in the left side of the heart.
The organ covering the body that consists of the dermis and epidermis.
The organ that functions to filter blood and to store red corpuscles and platelets.
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
A paired organ of the urinary tract which has the production of urine as its primary function.
The portion of the small intestine that extends from the jejunum to the colon.
An ovary that is part of a right side of organism [Automatically generated definition].
An ovary that is part of a left side of organism [Automatically generated definition].
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA].
Lung which consists of the left upper lobe and left lower lobe.[FMA].
A serous membrane that lines the peritoneal cavity[VHOG,modified].
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
The soft tissue that fills the cavities of bones.
Transudate contained in the pericardial cavity.[FMA].
An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail.
A mucosa that is part of a esophagus [Automatically generated definition].
A fold of peritoneum originating at the stomach and supporting the viscera.
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
Initial section of the oviduct through which the ova pass from the ovary to the uterus.
A kidney that is part of a left side of organism [Automatically generated definition].
A kidney that is part of a right side of organism [Automatically generated definition].
A muscularis mucosa that is part of a esophagus.
lamina muscularis of esophageal mucous membrane
The greater omentum (also the great omentum, omentum majus, gastrocolic omentum, epiploön, or, especially in animals, caul) is a large fold of peritoneum that hangs down from the stomach, and extends from the stomach to the posterior abdominal wall after associating with the transverse colon.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A small conical pouch projections located on the upper anterior portion of each atrium of the heart.
One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot.
The junction between the esophagus and the stomach epithelium.
Anterioinferior portion of left upper lung lobe.
The part of the uterus above the isthmus and below the orifices of the uterine tubes.
Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon.
Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
The splenic (or left colic) flexure is a sharp bend between the transverse and the descending colon in the left upper quadrant of humans. The left colic flexure is near the spleen, and hence called the splenic flexure. There are two colic flexures in the transverse colon — the other being the hepatic flexure in the right upper quadrant.
Hepatic (or the right colic) flexure is the sharp bend between the ascending and the transverse colon. The right colic flexure is adjacent to the liver, and is therefore also known as the hepatic flexure. Thus, the left colic flexure is also known as the splenic flexure (as it is close to the spleen). The hepatic flexure lies in the right upper quadrant of the abdomen in humans.
Muscularis mucosa from the lowest portion of the esophagus, just proximal to the stomach.
gastro-esophageal junction muscularis mucosa
esophagogastric junction muscularis mucosa
A life cycle temporal boundary that marks the end of the life cycle of the organism.
Area of skin in the hypoastric region of the abdomen.
An anatomical junction that is between the sigmoid colon and rectum.
An organizational unit (as opposed to the physical facility) that performs research, provides services, or processes materials
An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.
Any aspect of an individual's life, behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a disease, condition or injury.
Therapeutic use of hormones to alleviate the effects of hormone deficiency.
Inhaling and exhaling the smoke of tobacco or something similar to tobacco.
Mastication of tobacco, correlated with an increased risk of oral cancers.
The point in time at which an individual was born.
The point at which a clinical diagnosis is made.
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
obsolete_core
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
An organization which supplies technology, tools and protocols for use in high throughput applications
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Advanced Instruments Inc. (AI Companies)
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues.
0-non autolyis
An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues.
1-slight autolysis
An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues.
2-moderate autolysis
An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues.
3-severe autolysis
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
3: symptomatic in bed more than 50% of the day but not bed ridden
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
2: symptomatic but in bed less than 50% of the day
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
A Karnofsky score vaue specification indicating that a patient is asymptomatic.
A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
60-70: symptomatic but in bed less than 50% of the day
A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
An organization that is developing and selling nanopore sequencing products and is based in the UK.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.