Anna Maria Masci
Chris Stoeckert
Cui Tao
Helena Ellis
Jian Guan
Jihad Obeid
Jonathan Bona
Mathias Brochhausen
William Duncan
Alla Karnovsky
Asiyah Yu Lin
Christoph Brochhausen
Cooper Stansbury
Elizabeth Eisenhauer
Elizabeth Umberfield
Frank Manion
J. Neil Otte
Jie Zheng
Jonathan Vajda
Kathleen Ford
Marcy Harris
Yongqun "Oliver" He
The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.
Informed Consent Ontology (ICO)
Terms were identified from a sample of informed consent templates, and definitions were selected based on concordance between the defintion and the use of the term in the source informed consent template document. We preferentially selected defintioins from the NCI thesuarus.
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
DUO_preferred_label
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
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
A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor
alternative label
alternative term
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.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
retired from use as of
relates a class of CRID to the date after which further instances should not be made, according to the central authority
In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
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
term_mapping_to_UMLS
term_mapping_to_NCIT
term_mapping_to_HL7v3
This annotation property specifies classes that were developed as part of an alignment effort between the Common Rule Ontology and the Informed Consent Ontology in the Summer of 2018. These classes represent entities that are necessary for understanding the regularatory frameworks that influence informed consent, often at a different level of granularity than individual consent processes. These classes were created to be compatible with regulatory frameworks outside the Unitied States, hence they are general.
RUBRIC
All classes and properties with this annotation are members of the PICO grammar.
PICO CLASS
Merriam-Webster Definition
A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus.
A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
A property representing an alternative Preferred Name for use in some NCI systems.
A property representing the word or phrase that NCI uses by preference to refer to the concept.
A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
A property representing the English language definition of a concept from a source other than NCI.
A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
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).
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
An entity responsible for making contributions to the content of the resource.
Contributor
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the content of the resource.
Creator
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the resource.
Date
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
An account of the content of the resource.
Description
Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
The topic of the content of the resource.
Subject and Keywords
A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
An association that connects the concept defining a particular terminology subset with concepts that belong to this subset.
label
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
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
preceded by
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
A is restricted to B iff A is a consent code and B is an investigation and A may only participate in instances of a class C, of which B is an instance.
E.g. A dataset is restricted to an instance of an investigation for a specific disease or at geographical location.
has measurement unit label
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
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.
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
denotes
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
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
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
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
A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
Person:Bjoern Peters
is quality specification of
inverse of the relation of is quality specification of
quality is specified 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
d socio-legally revokes s if s participates in d and at the end of d s no longer exists. It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question.
legally revokes
d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical.
obsolete_legally transfers
An object property that represents a relation between a form and the person or organization who acts as a signer and signs the form.
Yongqun He, Elizabeth Eisenhauer
A relation that links an informed consent form to an associated IRB number.
Elizabeth Eisenhauer, Yongqun He, Asiyah Yu Lin, Alla Karnovsky, Marcy Harris
obsolete is associated with review board approval number
An object property that represents a relation between a unique identifier (ID) and an organization that assigns the ID.
Yongqun He, Elizabeth Eisenhauer, Asiyah Yu Lin, Alla Karnovsky, Marcy Harris
A relation holding between an instance of a deontic role and an instance of an intentional action when the deontic role bearer participates in the intentional action and is allowed to do so.
permits
J. Neil Otte, Jonathan Vajda, Cooper Stansbury
A relation between an instance of Process and an instance of Continuant, where the continuant is a causal participant in the process.
has agent
A relation between a continuant and a process, where the continuant is a causal participant in the process.
agent in
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
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
has specified input
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
is specified input of
is_specified_input_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
The inverse property of is specified output of
has specified output
is_specified_output_of
is specified output 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.
A relation between an information content entity and a value specification that specifies its value.
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.
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
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.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
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 relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
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 or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
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.
A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes 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/
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
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.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
has active participant
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
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
The inverse of designates, which relates an Entity to some Information Content Entity.
Note on modification: Changed relation to hold between an IAO: Information Content Entity instead of a Designative Information Content Entity.
Imported 08.09.2018
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designated by
A relationship between persons by virtue of ancestry or legal union.
Retrieved from Common Core Ontologies 2/06/2019
has familial relationship to
The inverse of presecribes, which relates an Entity to some Directive Information Content Entity.
prescribed by
For all types T1 and T2, if T1 prescribes T2, then there is some instance of T1, t1, that serves as a rule or guide to some instance of T2, t2 (if T2 is a type of bfo:Occurrent) or that serves as a model for some instance of T2, t2 (if T2 is a type of bfo:Continuant).
prescribes
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
my filling in an immigration form, a judge's signing and stamping a court order
A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
obsolete_deontic document act
A planned process that has specified output a software product and that involves the creation of source code.
William R. Hogan
A planned process resulting in a software product involving the creation of source code.
software development
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
software source code version control repository
A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based
source code repository
process of compiling software
A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
compiling software
creating a data set
A planned process that has a data set as its specified output.
data set creation
dataset creation
dataset creating
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])
from BFO
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
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
obsolete dependent 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 relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
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
material entity
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]
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
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.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
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.
polymer
A planned process in which materials are removed permanently from the laboratory or repository.
makes no judgement about whether this is a good way to do it, or a bad way such as tipping down the sink.
A planned process that involves all aspects of dealing with the waste produced in experiments.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
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 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 leukocyte with a single non-segmented nucleus in the mature form.
A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.
A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
data use permission
A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016.
This term was depreacted as it is not used to tag datasets but instead as patterns for DUO codes capture. This is an archive specific requirement, e.g. "one code from a primary category and one or more from a second category' This is better done by Schemablocks and constraining the pattern of usage of DUO terms at each archive level.
A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016.
obsolete consent code secondary category
This data use permission indicates there is no restriction on use.
20180907, Meeting Moran Melanie: This is to be thought about more carefully - what is the intent when using 'no restriction' as usually users still need to be researchers.
Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service
no restriction
This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited.
population origins or ancestry research prohibited
This data use limitation indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.
General Research Use, DUO_0000042 Clinical Care USe, DUO_0000043
This term includes clinical care, which was not defined in the original consent codes paper. This term does not have a usage in our current use cases and we recommend using DUO:0000042, General Research Use, instead
This term was made obsolete as per https://github.com/EBISPOT/DUO/issues/45
obsolete general research use and clinical care
This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
health or medical or biomedical research
This data use permission indicates that use is allowed provided it is related to the specified disease.
This term should be coupled with a term describing a disease from an ontology to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms.
disease specific research
This data use permission indicates that use of the data is limited to the study of population origins or ancestry.
population origins or ancestry research only
This data use modifier indicates that use is limited to studies of a certain research type.
research specific restrictions
This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care).
Deprecated as GRU-CC was split into GRU and CC, so this is not applicable anymore as a qualifier of GRU-CC
obsolete research use only
This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).
no general methods research
This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively)
genetic studies only
Data use modifiers indicate additional conditions for use.
data use modifier
This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
not for profit, non commercial use only
This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
publication required
This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).
This could be coupled with a string describing the primary study investigator(s).
collaboration required
This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.
ethics approval required
This data use modifier indicates that use is limited to within a specific geographic region.
This should be coupled with an ontology term describing the geographical location the restriction applies to.
geographical restriction
This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.
publication embargo
This should be coupled with a date specified as ISO8601
publication moratorium
This data use modifier indicates that use is approved for a specific number of months.
This should be coupled with an integer value indicating the number of months.
time limit on use
This data use modifier indicates that use is limited to use by approved users.
user specific restriction
This data use modifier indicates that use is limited to use within an approved project.
project specific restriction
This data use modifier indicates that use is limited to use within an approved institution.
institution specific restriction
This data use modifier indicates that the requestor must return derived/enriched data to the database/resource.
return to database or resource
An investigation concerning development of methods, algorithms, software or analytical tools.
This definition is a placeholder as a result of meetings at ICBO2018.
An investigation concerning a specific population group.
Should be paired with the an ontology term representing this population (e.g., xxx).
An investigation concerning ancestry or population origins.
An investigation concerning specific age categories.
An investigation concerning specific gender categories.
An investigation concerning use of data as reference or control material.
An investigation concerning health, medical, or biomedical research.
Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity).
Biomedical research concerning drug development.
Biomedical research research concerning specific disease/s
This data use permission indicates that use is allowed for general research use for any research purpose.
This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.
general research use
This data use modifier indicates that use is allowed for clinical use and care.
Clinical Care is defined as Health care or services provided at home, in a healthcare facility or hospital. Data may be used for clinical decision making.
clinical care use
This data use modifier indicates that use of the data is limited to not-for-profit organizations.
not for profit organisation use only
This data use modifier indicates that use of the data is limited to not-for-profit use.
This indicates that data can be used by commercial organisations for research purposes, but not commercial purposes.
non-commercial use only
A material entity which other material entities in an environmental system are primarily or partially composed of.
Data containing moving pictures stored in digital and analog formats.
video
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".
governmental organization
The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
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
narrative object
Examples of narrative objects are reports, journal articles, and patents submission.
A narrative object is an information content entity that is a set of propositions.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
person:Chris Stoeckert
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.
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
obsolete_digital entity
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
obsolete2_digital entity
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
A report that is published in a journal.
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
binary digital entity
MS Word document, ZIP file, DICOM file, JPEG file
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
digital_entity
obsolete2_binary digital entity
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
programming language
R, Perl, Java
A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
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
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.
integer numeral
A numeral that denotes an integer
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
directive information entity
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
time trigger
obsolete_study interpretation
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
2009-03-16: work has been done on this term 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.
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
Lawrence Hunter
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
text based digital entity
XML file, C++ source code file
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
obsolete2_text based digital entity
rule
example to be added
A rule is an executable which guides, defines, restricts actions.
MSI
PRS
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
obsolete2_report figure
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)
software interpreter
R program, Perl interpreter, Java virtual machine
A software interpreter is a software application that executes some specified input software.
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
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)
density plot
Density plot of SSC-H and FSC-H.
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
report element
A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
2009-03-16: needs some more work (clarify relations).
2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
PERSON: Allyson Lister
obsolete_report element
binary executable
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
person:Jennifer Fostel
obsolete2_binary executable
source code module
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
report table
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
obsolete_report table
data format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
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.
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 that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
digital document
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
obsolete2_digital document
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?
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
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
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
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
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Need to rework digital entity. Digital quality was suggested by Barry.
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
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.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
obsolete_survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
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.
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
A textual entity intended to identify a particular publication.
author identification
L. Hunter
A textual entity intended to identify a particular author
institutional identification
University of Colorado Denver School of Medicine
A textual entity intended to identify a particular institution
caption
Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
A textual entity that describes a figure
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
table
| T F --+----- T | T F F | F F
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
table of abbreviations
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
A table where the constituent texts are abbreviations and their expansions
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.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
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
publication
journal article, newspaper story, book, etc.
A document that is the output of a publishing process.
PERSON: Jie Zheng
published document
Revisit the term in Octorber 2020. Improve the defintion.
publication about an investigation
Most scientific journal articles
A publication that is about an investigation
scientific publication
patent
US Patent 6,449,603
A document that has been accepted by a patent authority
document part
An abstract, introduction, method or results section.
An information content entity that is part of a document.
abstract
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
precis
introduction to a publication about an investigation
Section labelled 'introduction' of a typical scientific journal article
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
background
introduction
overview
methods section
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
A part of a publication about an investigation that is about the study design of the investigation
experimental
experimental methods
experimental procedures
experimental section
method
methodology
methods
results section
The section labelled 'results' in a typical scientific journal article
A part of a publication about an investigation that is about a study design execution
results
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
discussion
discussion section
discussions
references section
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
A part of a document that has citations as parts
literature cited
reference
reference list
references
author list
Lawrence Hunter and Kevin Brettonel Cohen
A part of a document that enumerates the authors of the document
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
A part of a document that has parts that are institution identifications associated with the authors of the document
author contributions section
LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
A part of a publication that is about the specific contributions of each author
author contributions
authors' contribution
authors' contributions
authors' roles
contributions by the authors
contributorship
acknowledgements section
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
Part of a publication that is about the contributions of people or institutions other than the authors.
acknowledgement
acknowledgements
acknowledgment
acknowledgments
footnote
The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
endnote
footnotes
supplementary material to a document
A part of a document that is segregated from the rest of the document due to its size
additional file
additional files
additional information
appendix
electronic supplementary material
electronic supplementary materials
supplemental data
supplemental information
supplemental material
supplementary data
supplementary files
supplementary information
supplementary material
supplementary materials
supporting information
table of contents
A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
table of figures
A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
running title
A shorter version of a document title
copyright section
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
A document part that describes legal restrictions on making or distributing copies of the document
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
AR notes: We need to discuss whether it should include site.
cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
three dimensional cartesian spatial coordinate datum
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
hypothesis textual entity
A textual entity that expresses an assertion that is intended to be tested.
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
author role
A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
data item extraction from journal article
A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
Person: Jie Zheng
VEuPathDB
publishing process
A document that is in preparation for submission to be published.
EFO_0001795 in preparation
document in preparation for publication
documenting
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
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Melanie Courtot
assigning a centrally registered identifier
Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
A planned process in which a CRID registry associates an information content entity with a CRID symbol
associating information with a CRID in the CRID registry
associating information with a centrally registered identifier in its registry
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
centrally registered identifier registry
Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
looking up a centrally registered identifier
time stamped measurement datum
pmid:20604925 - time-lapse live cell microscopy
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
time sampled measurement data set
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software method
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software module
A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
software library
A software application is software that can be directly executed by some processing unit.
software application
A software script is software whose instructions can be executed using a software interpreter.
software script
abbreviation textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
A textual entity listing abbreviations and their expansions that are used in a document.
PERSON: Bill Baumgartner
abbreviations section
The section labelled 'abbreviations' in a typical scientific journal article.
A part of a document where abbreviations and their long-forms used within the document are listed.
abbreviation and acronyms
abbreviation list
abbreviations
abbreviations and acronyms
abbreviations list
abbreviations used
definitions for abbreviations
list of abbreviations
list of abbreviations used
non-standard abbreviations
nonstandard abbreviations
nonstandard abbreviations and acronyms
author information section
The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author information
authors’ information
biographies
contributor information
author information textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author summary section
The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
author summary
summary
synopsis
Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
author summary textual entity
From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
availability section
The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
availability
availability of data
data archiving
data availability
data availability statement
data sharing statement
availability textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
case report section
The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
A part of a document about the medical history of a specific patient as it relates to the topic of the document.
case presentation
case report
case report textual entity
Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
conclusion section
The section labelled 'conclusion' in a typical scientific journal article.
A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
concluding remarks
conclusion
conclusions
findings
conflict of interest section
The section labelled 'conflict of interest statement' in a typical scientific journal article.
A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
authors' disclosures of potential conflicts of interest
competing financial interests
competing interests
conflict of interest
conflict of interest statement
conflict of interests
conflicts of interest
declaration of competing interest
declaration of competing interests
declaration of interest
declaration of interests
disclosure of conflict of interest
disclosure of potential conflicts of interest
duality of interest
statement of interest
SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
conflict of interest textual entity
consent section
The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
A part of a document about the consent process that was used to enroll patients in a study.
consent
consent textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
A textual entity that documents the consenting process used to enroll patients in a study.
ethical approval section
The section labelled 'ethical approval' in a typical scientific journal article.
A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
ethical approval
ethical requirements
ethics
ethics statement
ethical approval textual entity
From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
A textual entity that documents the ethical approval of some study design.
figures section
The section labelled 'figures' in a typical scientific journal article.
A part of a document that contains one or more figures.
figures
funding source declaration section
The section labelled 'funding' in a typical scientific journal article.
A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
financial support
funding
funding information
funding sources
funding statement
funding/support
grants
role of the funding source
source of funding
sources of funding
study funding
funding souce declaration textual entity
From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
A textual entity documenting the source of funding that supported some study.
funding source declaration textual entity
future directions section
The section labelled 'future directions' in a typical scientific journal article.
A part of a document detailing extensions of the described work that may be implemented at some future point in time.
future challenges
future considerations
future developments
future directions
future outlook
future perspectives
future plans
future prospects
future research
future research directions
future studies
future work
outlook
future directions textual entity
Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
genome announcement section
The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
A document part announcing the publication of a novel draft genome sequence.
genome announcement
genome announcement textual entity
Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
A textual entity that describes the generation and public release of a novel, draft genome sequence.
keyword textual entity
From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
A textual entity listing keywords indicating the major theme(s) of a document.
keywords section
The section labelled 'keywords' in a typical scientific journal article.
A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
keywords
study limitations section
The section labelled 'limitations' in a typical scientific journal article.
A part of a document about biases or short comings related to the study design and execution.
limitations
study limitations
Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
study limitations textual entity
Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
A textual entity addressing a shortcoming or bias of a study design or execution.
materials section
The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
A part of a document about the materials required to reproduce the content of the document.
materials
notes section
The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
notes
patients section
The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
A part of a document about the patients that participated in a study.
patients textual entity
Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
A textual entity expressing information regarding the patients used in a study.
pre-publication history section
The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
notice of republication
pre-publication history
pre-publication history textual entity
From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
related work section
The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
A part of a document about work in other publications that is relevant to the content of the document.
related literature
related work
related work textual entity
Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
requirements section
A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
requirements
requirements textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
A textual entity that expresses the requirements necessary to use a resource, e.g. software.
statistical analysis textual entity
From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
A textual entity documenting statistical analysis tools and techniques employed.
statistical analysis section
The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
A part of the document used to describe the statistical methodologies employed in the work presented in the document.
statistical analysis
tables section
The section labelled 'tables' in a typical scientific journal article.
A part of a document that contains one or more tables.
tables
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
A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
Postal delivery route
A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
ZIP code
zone improvement plan code
database extract, transform, and load process
A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
ETL
descriptive data section
A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
additional results section
A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
research participants section
A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
measurement methods section
A methods section that describes details of data assessment methods (data measurement).
research settings section
A document part that describes the physical/social/cultural conditions around a research trial.
study bias section
A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
graphical abstract
An abstract that is pictorial summary of the main findings described in the document.
visual abstract
identifier
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
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.
Amanda Hicks
credential role
obsolete_claim
deontic document act
A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document.
obsolete_document act
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that needs to be perceived.
social act
the claim of a piece of land, the obligation to pay rent to the owner of a rental property
Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities.
obsolete_socio-legal generically dependent continuant
deontic declaration
my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract.
A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document.
declaration
status function declaration
obsolete_deontic declaration
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
obligee role
A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification).
document act input document
A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave.
Neil Otte
deontic role
A social act that creates or revokes a deontic role.
obsolete_obligation
The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration.
obsolete_declaration executive role
the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline
The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant.
not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants.
obsolete_document template creator role
The role of a human being or an aggregate of human beings concretizing a claim.
obsolete_claimant role
The role of a human being or an aggregate of human beings concretizing an obligation.
obsolete_obligator role
me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act
The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.
obsolete_declaration target
The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified
A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act.
document act template creator role
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration.
declaration performer role
deontic declaration performer role
obsoleted_document act target
a judge's role of signing a court order
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act.
document act performer role
A social act that postulates a socio-legal fact for a specified group of people or organizations.
enactment
standing declaration
A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
John Judkins
obligor 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.
The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. For instance, whereas the NCIt definition restricted informed consent forms to clinical trials, the present definition does not.
Alla Karnovsky, Frank Manion, Yongqun He, Asiyah Yu Lin, Marcy Harris, Elizabeth Eisenhauer, Jonathan Vajda, Cooper Stansbury, J. Neil Otte
informed consent document
NCIt C16468
See curator note for 'incomplete informed consent form'.
informed consent form
A planned process that involves the design of an informed consent form.
Alla Karnovsky, Frank Manion, Yongqun He
This class is under group discussion as of 03/26/2019.
designing an informed consent form
A planned process that validates an informed consent form.
validating an informed consent form
A planned process that approves an informed consent form.
approving an informed consent form
A social act that is a part of an informed consent process and has output of a signed informed consent form. The signing process leads to a legal obligation.
Alla Karnovsky, Frank Manion, Yongqun He, Jihad Obeid, Chris Stoeckert, and Mathias Brochhausen
Signing here does not mean that we have to sign with a pen. It may happen in terms of signing a piece of a paper or an electronic form.
signing an informed consent form
An organization charged with approving clinical study protocols and ensuring that applicable governing rules and laws are upheld.
informed consent regulatory body
A document that is a part of an informed consent form.
informed consent form element
part of informed consent form
A descriptive information content entity that describes potential harm or estimates the likelihood of harm.
Alla Karnovsky, Frank Manion, Yongqun He, Cooper Stansbury
description of participation risk
A document part that prescribes a method of contact in the future.
recontact method directive
An answer directive that is part of a document and whose filling in or leaving blank is incidental to the completion of the form.
Alla Karnovsky, Frank Manion, Yongqun He, J. Neil Otte
A document part of an informed consent form for which an answer is required in order to complete the form.
required informed consent element
A document part of an informed consent form for which an answer is not required in order to complete the form.
optional informed consent element
An informed consent form that documents a voluntary decision to deposit a human biospecimen.
WEB: http://www.irb.umich.edu/policies/consent/
WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/
informed consent form for human biospecimen collection
An informed consent form that is specifically for human blood sample collection.
informed consent form for human blood sample collection
An informed consent form that has been signed by at least one participant.
Yongqun He
Note from J. Neil Otte (7.24.18): 'signed informed consent form' is not a synonym nor subclass of 'complete informed consent form indicating consent'. A signed informed consent form may bear the signature of a witness or doctor, but not yet be complete. Also, a complete informed consent form may need only have been stamped or witnessed by checking a box in an electronic form, and may not require a signature.
signed informed consent form
A directive information entity that specifies the scope of allowed research and is derived from a research protocol.
allowed research scope in informed consent form
An informed consent form that has been signed by all participants.
obsolete fully signed informed consent form
An informed consent form that has been signed by a human subject
informed consent form signed by human subject
A document part that is specified as a place to receive a signature.
signature section
A signature section in informed consent element that that is specified as a place to receive a signature from a human subject.
human subject signature section in informed consent form
A signature section in an informed consent form that is specified as a place to receive a signature from an investigator.
investigator signature section in informed consent form
A information content entity that designates a temporal region.
temporal region identifier
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 date specification in an informed consent form that specifies an effective date of an investigation.
effective date specification in informed consent form
A date specification in an informed consent form that specifies the expiration date of an investigation.
obsolete expiration date specification in informed consent form
A date specification in an informed consent form that specifies the starting date of an investigation.
starting date specification in informed consent form
A document part that describes and specifies human blood sample collection procedures.
obsolete human blood sample collection section
An informed consent form that is used for a clinical study.
informed consent form for clinical study
An informed consent form that is used for a storage and future use of unused samples.
informed consent form for storage and future use of unused samples
An informed consent form that is used for a qualitative study.
informed consent form for qualitative study
An informed consent form that is adapted to the cognitive abilities and reading abilities child or minor.
Yongqun He, Jonathan Vajda
informed assent form for child or minor
An informed consent form for qualitative study that involves children.
informed consent form for qualitative research involving children
An informed consent form for clinical study that involves children.
informed consent form for clinical research involving children
A data item that indicates a date that specified on an informed consent form.
5/7/2014 Asiyah Yu Lin: It is the date specification that appears on the informed consent form, which is may different with the actual date.
Yongqun He, Asiyah Yu Lin, J. Neil Otte
date specification in informed consent form
A date specification that designates when an informed consent form was signed.
5/7/2014 Asiyah Yu Lin: look at the OBI example of sample collection date http://purl.obolibrary.org/obo/OBI_0001619
Yongqun He, J. Neil Otte
A temporal region identifier that designates a project duration.
A date specification that designates the date when a project begins.
project starting date specification
A date specification that designates the date when a project ends.
project end date specification
A human subject who provides informed consent without a legal guardian.
human subject consenter
A directive information entity that specifies the deontic roles that are produced, revoked, or modified following a process of informed consent, where those deontic roles inhere in the human subject consenter signing an informed consent form, and the investigator or organization leading a research study or providing health care.
informed consent rule specification
An example is that the organization leading a study may be obliged to destroy a patient's biospecimens after 10 years as required in an informed consent form.
An informed consent rule specification that specifies a course of action legally required to be taken.
obligation informed consent rule specification
An informed consent rule specification that specifies an optional course of action that is an option for a participant to take.
An example is that a human subject consenter is given the option to withdraw from a consented study any time as specified in an informed consent form.
permission informed consent rule specification
A data item consisting of a unique identification code designating an informed consent.
informed consent identification code
A role borne by an agent that, if realized, is realized in an investigation.
investigator role
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.
The alternative term of 'permission' has semantic similarity with authorization in the sense of 'approval to do something' and 'the act of giving a formal (usualy written) authorization. The semnatic similarity measuremment of permission and authorization is done using WordNet::Similarity (http://marimba.d.umn.edu/cgi-bin/similarity/)
Asiyah Yu Lin, Yongqun He, Elizabeth Umberfield
permission
NCIt C41192
act of authorizing
A population of human beings.
human population
An organization that is operated without the principal goal of making a financial profit.
nonprofit organization
An organization which has the principle goal of earning financial profit.
profit organization
An investigation that involves animal research.
An investigation that targets cancer research.
cancer research investigation
A cancer research investigation that specifically targets metastatic melanoma research.
obsolete metastatic melanoma research investigation
An investigation that targets drug testing.
drug testing investigation
An investigation that involves human research.
human research investigation
An investigation that has process part some genetic analysis.
An investigation that is conducted with a nonprofit purpose.
nonprofit research investigation
An investigation that is conducted with the purpose of earning a profit.
for-profit research investigation
A one-dimensional temporal region to which an investigation stands in the occupies_temporal_region relation.
investigation period
A directive information entity prescribes an ethical requirement.
Yongqun He, Cooper Stansbury
ethics directive
A planned process that involves placing a specimen in some location in order to maintain possession of it.
act of storing a specimen
An informed consent form that is designed for use in genetic studies.
Asiyah Yu Lin, Marcy Harris, Alla Karnovsky, Yongqun He
informed consent form for genetic study
A human subject who is unable to give informed consent. In this case, another person is generally authorized to give consent on his behalf, e.g., parents or legal guardians of a child, though in this circumstance the child may be required to provide informed assent, and conservators for the mentally ill.
web: http://en.wikipedia.org/wiki/informed_consent
human subject unable to give informed consent
obsolete informed consent form for quantitative study
An investigation that requires an informed consent process.
study requiring informed consent
A study that is a clinical trial that requires an informed consent process.
Elizabeth Eisenhauer, Yongqun He
Based on NCI/PT, a clinical trial is a type of research study that tests how well new medical approaches work in people. These studies test new methods of screening, prevention, diagnosis, or treatment of a disease.
Needs work. Best fit is to rely on SIO_0001000, which has a fine-grained hierarchy. Parent is 'intervention study' (SIO_0000994) which is an investigation (SIO_0000747). However, we have investigation already defined in OBI_0000066.
clinical trial
UMLS: C0008976
An investigation title that designates a clinical trial study, briefly identifying the purpose or design of the investigation.
clinical trial title
obsolete general requirement for informed consent
§46.116 General requirements for informed consent
A person who is the contact for questions about research.
Marcy Harris, Alla Karnovsky, Frank Manion, Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He
contact person for questions about research
A person who is the contact for questions about research subject right.
contact person for questions about research subject rights
A person who is the contact for questions in the event of a research-related injury to the subject
obsolete contact person in the event of a research-related injury to the subject
A person who can be contacted during an informed consent process.
contact person in informed consent process
A role that inheres in human being and is an output of some participation in a research study.
The term definition is adapted from the definition of the NCIt term 'Human Study Subject' with modification.
Yongqun He, Elizabeth Eisenhauer, Asiyah Yu Lin, Asiyah Yu Lin, Marcy Harris
human patient
research subject role
An act of authorizing that is signed by a patient, or his legal representative, or clinical study participant for the use or disclosure of oral, written, or electronic form of confidential health information that identifies the individual and relates to the medical history, diagnosis, treatment, or prognosis of his condition.
Asiyah Yu Lin, Yongqun He
NCIt C70679
authorization for release of confidential health information
A document that is the output of an authorization process.
JV: This probably belongs in D-Acts
An authorization process aims to release the medical record.
obsolete authorization for medical records release
UMLS CUI: C2921556
A benefit is a disposition or the potential positive effects that may arise from participating in a study.
This term definition is adopted from the NCIt definiton of "benefit" (C25387) with modification.
Asiyah Yu Lin, Marcy Harris, Yongqun He, Elizabeth Eisenhauer, Alla Karnovsky, Frank Manion, J. Neil Otte, Cooper Stansbury
Note that a payment is not a benefit of a study.
A risk is a disposition or the potential future harm that may arise from some present action. It is often combined or confused with the probability of an event which is seen as undesirable.
This term definition is adapted from the NCIt definiton of "Risk" (C17102) . The following source is alos referenced: BMEO(Biomedical Ethics Ontology) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725426/
Asiyah Yu Lin, Marcy Harris, Yongqun He, Elizabeth Eisenhauer, Alla Karnovsky, Frank Manion
NCIt: C17102
risk
A specially constituted organization comprised of medical, scientific and non-scientific members established and designated by an entity to ensure the protection of the rights, safety and well-being of human subjects recruited to participate in biomedical or behavioral research according to the requirements outlined in Title 38, part 16 (same as Title 45, part 46 and Title 21, part 56) of the U.S. Code of Federal Regulations. IRB responsibility include but not limited to the reviewing, approving, and providing continuing review of trial protocol and amendments and of the methods and material to be used in obtaining and documenting informed consent of the trial. Other equivalent committees with the same or similar functions are also considered to be IRBs.
IRB
NCIT C16741
institutional review board
a role inhering in a homo sapiens that, if realized, is realized in assisting with a research process.
Asiyah Yu Lin, J. Neil Otte
A role that inheres in an individual who is authorized under applicable State or local law to consent on behalf of a child or incapable person to general medical care including participation in clinical research.
Yongqun He: Based on the definition, may be better to label it as consent legal guardian role
legally authorized representative role
NCTI C51828
legal guardian role
Yongqun He: Based on the definition of 'legal guardian role', it may be better to label the term as 'consent legal guardian' of 'legal guardian of consent'.
legally authorized representative
A protected health information entity which identifies an individual; or with respect to which there is a reasonable basis to believe the information can be used to identify an individual.
Cooper Stansbury, Jonathan Vajda, J. Neil Otte
Individually identifiable health information includes many common identifiers such as name, address, birth date, Social Security Number.
This is adapted from HIPAA.
individually identifiable health information entity
An informed consent process that has an act of communicating assent as a process part, where the person who provides the assent does not bear a competency to consent.
Asiyah Yu Lin, Yongqun He, Frank Manion, Chris Stoeckert, Jihad Obeid, Jonathan Bona, Mathias Brochhausen
J. Neil Otte, Jonathan Vajda
informed consent process with assent
A document that explains relevant information regarding the expectations and requirements of participation in a research study or clinical procedure, is adapted to the cognitive capacities of that individual so as to assist in that individual's understanding, and is designed to record the assent of that individual.
informed assent form
A role that inheres in a patient or the legal guadian when he/she participates the consenting process.
consenter role
A time measurement datum that measures the duration of a study.
study duration measurement
A temporal interval during which a human being participates in a process.
participation duration
Total length of time of subject's participation in a clinical study; from the time of enrollment to the completion of follow-up.
This duration is different with the 'planned duration of study subject participation'
actual duration of study subject participation
A document that certifies that 1) a person may perform some action, or 2) which provides authentication for a claim, or 3) which confirms position or status.
5/8/2014 Asiyah Yu Lin: May not included in the final ontology.
The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done.
Elizabeth: Pay attention to definition "after study procedures and treatments have concluded." Does it fit our purposes?
A risk that is equal or lesser than those ordinarily encountered in daily life or during the performance of routine physical or psychological examinations or tests.
(45 CFR 46.102(i)). Available online from: http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html#46.102 Accessed 7/31/13.
Definition varies slightly for research on prisoners; see (45 CFR 46.303(d)).
minimal risk
A medical record that records the history of a subject's treatment for alcohol abuse.
A medical record that describes a patient's mental health care history.
A planned process that involves explanation to a human subject candidate with relevant study information, including study purpose, protocol, and human subject benefits and risks, that indicated in an informed consent form.
explaining to participant candidate about the study participating information
An informed consent form designed for use in human urine collection.
informed consent form for human urine biospecimen collection
A physical injury or illness that is a direct result of the treatment, or procedures required by the protocol, to which the subject would not have been exposed had they not participated in the study.
1) Citing Resnik, (2006), Mamotte N, Wassenaar D, Singh N (2013) define Research-related injury as “a physical, psychological, social, financial, or other injury, harm, or adverse event that a research participant experiences as a direct result of research participation or from use of the study product.” 2) Resnik, (2006)“A research-related injury is an injury that occurs to a subject as a result of research participation. Injuries may range from relatively minor harms (such as bruises or infected wounds) to major injuries (such as organ damage or temporary disability) to catastrophic injuries (such as permanent disability or death). An injury may require only acute or emergency care, or it may require continuing care. Injuries can be physical or psychological, or emotional.”p. 264
research-related injury
An information content entity which is created or received by a health care provider, health plan, public health authority, employer, life insurer, school or university, or health care clearinghouse; and relates to the past, present, or future physical or mental health or condition of any individual, the provision of health care to an individual, or the past, present, or future payment for the provision of health care to an individual.
health information entity
The process that shares the information under the informed consent context
The definition needs to be improved.
A health information entity which is created, received, stored, or transmitted by covered entities and their business associates in relation to the provision of healthcare, healthcare operations and payment for healthcare services.
Cooper Stansbury, J. Niel Otte, Jonathan Vadja
protected health information entity
An informed consent form that contains a questionnaire section.
informed consent form containing questionnaire
As a partial process of inform the candidate about the study participating information, the purpose of the study will be explained to make sure that the candidate is informed adequately from his/her perspective.
explaining study purpose to participant candidate
Legal name is the person name that identifies a person for legal, administrative and other official purposes. A person's first legal name generally is the name of the person that was given for the purpose of registration of the birth and which then appears on a birth certificate (see birth name), but may change subsequently.
A process that terminates a study.
Note from J. Neil Otte (7.24.18): This class is not to be confused with the terminal process boundary of a study process.
study termination
A planned process in which an agent decides to discontinue further participation in a study.
withdrawing participation in study
A planned process that revokes a permission role inhering in some agent.
act of canceling a permission
A treatment currently in wide use and approved by a regulatory body or health authority, considered to be effective in the treatment of a specific disease or condition.
CDISC
standard medical treatment
A character string that is assigned by a review board upon approval of a regulatory document.
For the review board approval, different countries or continents may have different responsible entities for approving the study. For example, in USA, the board is called "Institutional Review Board" (IRB). In many countries in Europe, it is called Ethics committee.
This term definition is adapted from the definition of the NCIt term 'Review Board Approval Number Text'.
Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He, Alla Karnovsky, Marcy Harris
review board approval number
An organizational function that involves the areas of information systems and computer science; and that may be realized in planning, organizing, describing, and controlling data resources.
data administration function
An information content entity that has been processed to prevent the identification of the person with whom the data are associated, thereby enduring in a stasis of anonymization.
Jonathan Vajda, Asiyah Yu Lin
Anonymized data is applicable particularly for secondary use of health data.
anonymized information content entity
An anonymized data item that is about a genomic sample.
Anonymized data and samples are initially single or double coded but the link between the subjects identifiers and the unique code(s) are subsequently deleted. Once the link has been deleted it is no longer possible to trace the data and samples back to the individual through the coding key(s). Anonymisation is intended to prevent subject re-identification. As anonymised samples and associated data are not traceable back to the subject it is not possible to undertake actions such as sample withdrawal, or the return of individual results. The use of anonymised data and samples does not allow for clinical monitoring, subject follow-up or the addition of new data. The deletion of the coding key(s) linking the data and samples to the subjects identifiers provides additional confidentiality and privacy protection over coded data and samples, as it prevents subject re-identification through the use of the coding key(s) (ICH).
Asiyah Yu Lin, Yongqun He, J. Neil Otte
An anonymized information content entity about a genomic sample.
Anonymized data and samples are initially single or double coded but the link between the subjects identifiers and the unique code is subsequently deleted. Once the link has been deleted it is no longer possible to trace the data and samples back to the individual through the coding key. Anonymisation is intended to prevent subject re-identification. As anonymised samples and associated data are not traceable back to the subject it is not possible to undertake actions such as sample withdrawal, or the return of individual results. The use of anonymised data and samples does not allow for clinical monitoring, subject follow-up or the addition of new data. The deletion of the coding key linking the data and samples to the subjects identifiers provides additional confidentiality and privacy protection over coded data and samples, as it prevents subject re-identification through the use of the coding key (ICH).
A planned process that involves using data which was an output of a human being's participation in a study and which is about that human being.
J. Neil Otte, Elizabeth Umberfield
act of using study participant data
In order to make sure that the candidate is informed adequately from his or her perspective, the protocol of the study including the protocol of participating, for example, what kind of procedure the participant will be involved, how many scheduled visits will be explained.
explaining study protocol to participant candidate
A site where documents are preserved.
This term is extracted from Nick's comment on the ICBO paper draft version0.11_Yongqun He.
repository of documents
UMLS: C0003738
obsolete storage duration of signed informed consent form
A planned process that collect a signed informed consent form. During this process, the information is systematically kept in a repository.
We can put this axiom: inform... 's located in' some 'archive reposigtory of signed informed consent'
Marcy Harris, Alla Karnovsky, Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He
storage of signed informed consent form
archiving signed informed consent form
The potential benefit to the study subject that may arise from participating the study research is to be explained to candidate
explaining benefits of participation to participant candidate
A directive information entity that specifies US federal policy for the protection of human subjects.
Elizabeth Eisenhauer, Marcy Harris, Alla Karnovsky, Yongqun He, Asiyah Yu Lin
Common Rule
WEB: http://www.hhs.gov/ohrp/humansubjects/commonrule/
obsolete US federal policy for the protection of human subjects
An act of storing a complete informed consent form.
Yongqun He, Elizabeth Eisenhauer, Alla Karnovsky, Marcy Harris, J. Neil Otte
Note: there were previously some related classes that distinguished the format of the informed consent form (e.g. electronic vs. paper). These distinctions are collapsed here. If making this distinction is necessary, the outputs of an instance of this class may be distinguished in their formatting. For instance, storing in an electronic format would entail an instance of an act of storing signed informed consent form bearing an 'has output' relation to an instance of an informed consent form that is in an electronic format.
act of storing signed informed consent form
A planned process of storage of signed informed consent form when the form is in digital format.
Marcy Harris, Alla Karnovsky, Elizabeth Eisenhauer, Yongqun He
storage of signed electronic informed consent form
archiving signed electronic informed consent form
A process of storage of signed informed consent form when the form is in digital format.
storage of signed scanned paper informed consent form
archiving signed scanned paper informed consent form
A temporal interval that represents a period of time during which a signed informed consent form is stored.
WEB: http://answers.hhs.gov/ohrp/questions/7223
storage duration of signed informed consent form
A participation time that is the total length of time of subject's participation in a research study; from the time of enrollment to the completion of follow-up.
The term definition is adapted from NCIt definition of "Planned Duration of Study Subject Participation" (C70707) with modification. Compared to the NCIt definition, the ICO definition specifies research research study instead of a clinical study.
planned duration of study subject participation
The potential future harm that may arise from participating the study research is to be explained to candidate
explaining risks of participation to participant candidate
An informed consent form for human sample collection that is specifically for human saliva sample collection.
Alla Karnovsky, Frank Manion, Yongqun He, Elizabeth Eisenhauer, Marcy Harris, Asiyah Yu Lin
WEB: http://www.irb.umich.edu/policies/consent/samples/Sample_SalivaCollection.pdf
informed consent form for human saliva sample collection
A review board approval number that is assigned by an institutional review board.
institutional review board approval number
In order to make sure that the candidate is informed adequately from his or her perspective, the process of collecting, storing or destroying the sample collected from the study subject is to be explained.
In the case of biobanking,collected tissue will be frozen and stored in a biorepository system. Other researchers will search and use the tissue for different purpose. The researchers may come from different organization and may need to access some of the personal information or may need to contact the study subject.
explaining sample process and usage to participant candidate
In the case of promoting future data sharing, the usage of the data derived from a study is to be explained to the candidate.
For example, in the genomic data projects, the study subject's sequence data maybe used outside of the original organization. In this case, the study subject's privacy need to be protected.
explaining study derived data usage to participant candidate
In order to enable the candidate to make voluntary decision, the options for enhancing the protection of confidentiality for participants who have contributed personal information to a study is to be explained.
explaining record confidentiality to participant candidate
A process in which a candidate makes a voluntary decision to join a study, following their consideration of adequate information presented to them regarding the study and their participation in it.
participant candidate making voluntary decision of acceptance
In order for the consent valid, the candidate should be competent to understand what has been explained.
Asiyah Yu Lin.
obsolete assessment of participant candidate understanding
An informed consent form that contains sections specific to procedures in vaccination.
Yongqun He, Asiyah Yu Lin
immunization consent form
informed consent form for vaccination
An informed consent form that is used for vaccination by Walgreens
Walgreens Vaccine Administration Record Informed Concsent Form
obsolete Walgreens vaccine informed consent form'
A questionnaire whose purpose is to aid in identifying whether an agent is eligible to participate in a process.
eligibility questionnaire
A textual entity that is a sentence in the interrogative mood.
question textual entity
A planned process that results in a legally effective consent status.
Frank Manion, Yongqun He
legally effective consenting
A planned process of acknowledgement, or agreement, to participate in a procedure or study, where the participant is incapable of informed consent.
Asiyah Yu Lin, Yongqun He, Frank Manion, Chris Stoeckert, Jihad Obeid, Jonathan Bona, Mathias Brochhausen, 2018 Informed Consent Workshop
assent process
According to the Common Rule, the IRB shall determine that adequate provisions are made for soliciting the assent of the children, when in the judgment of the IRB the children are capable of providing assent.
Specifically, "assent" is a term used to express willingness to participate in research by persons who are by definition too young to give informed consent but who are old enough to understand the proposed research in general, its expected risks and possible benefits, and the activities expected of them as subjects.
A role that inheres in a human being who participates in a consenting process and eventually becomes legally effectively consented.
Frank Manion, Yongqun He, Mathias Bronchhausen, Chris Stoeckert, Jie Zheng, Jihad Obeid, Helena Ellis
legally effective consented participant role
A planned process in which an agent's designated biological specimen is collected after the death of the agent.
postmortem donation of biological specimen
A role that represents the eligibility of a candidate according to a study protocol.
Frank Manion, Yongqun He, Mathias Brochhausen, William Duncan
eligibility of candidate participation
A role inhering in a participant who meets all eligibility criteria defined within a study protocol.
NCI BBRB: Biorepositories and Biospecimen Research Branch
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 planned process in which an agent contacts a participant of an informed consent process regarding opportunities related to future research.
Jonathan Vajda with ICO Workgroup in Ann Arbor (2018)
Yongqun He, Mathias Brochhausen, Jihad Obeid, Frank Manion
act of contact for future research
A planned process to screen the eligibility of a candidate for a study or procedure, verifying whether certain sufficient or necessary conditions for eligibility obtain.
eligibility screening process
A role that inheres in a person that, if realized, is realized in an eligibility screening process.
Frank Manion, Yongqun He, J. Neil Otte
obsolete consenting to be contacted for tissue research
A planned process of communicating information about an informed consent process.
explaining to participant candidate in informed consent process
A planned process that a person agrees to participate in a research project, which is a part of an informed consent process.
YH, 2018 Little Rock CTSOG ontology workshop
An informed consent process where the person who is being asked to consent is an adult.
adult consent process
An informed consent process in which a parent reaches a decision concerning whether or not to grant consent on a minor's behalf, when the minor is incapable of providing consent for themselves.
parental permission
parental permission consent
parental informed consent process
A planned process in which a person decides not to provide consent.
act of declining to provide consent
An informed consent process in which the participant communicates consent orally rather than by filling out and signing a written form.
Yongqun He, 2018 Little Rock CTSOG ontology workshop
informed verbal consent
An informed consent process in which the participant is not able to read and write in the language of the informed consent form, but is aided in understanding the informed consent process by a translation into the agent's native language.
consenting in short form
A planned process in which a biological sample from a subject is collected for testing.
biological sample collecting
A biological sample collecting in which a tissue sample from a subject is collected for testing.
tissue sample collecting
A biological sample collecting in which a blood sample from a subject is collected for testing.
blood sample collecting
A planned process that represents a study participant withdrawing from the study and agreeing to have the participant sample stored for unlimited time.
2018 CTSOG informed consent ontology workshop in Little Rock (http://ncorwiki.buffalo.edu/index.php/Ontology_of_Informed_Consent:_An_Approach_to_Specimen_and_Data_Sharing)
subject withdrawal with sample stored for unlimited time
A planned process that represents a study participant withdrawing from the study and agreeing to have the participant sample stored for a limited time period.
subject withdrawal with sample stored for limited time
Moved to d-acts
A deontic role that if realized is realized by its bearer conducting or overseeing genetic research on the genome of a human donor.
Note: this term wll be transferred to d-acts. - CTSOG ontology workshop 2018 Little Rock
obsolete permittee deontic role in genetic research
A deontic declaration that has output a permittee role that permits genetic research on a human donor as a specified outcome.
will add an equivalent class axiom 'has specified output' some 'permittee deontic role in genetic research'
obsolete genetic research permission deontic declaration
a role that inheres in a human subject who participates in an assending process.
assenter role
A questionnaire that is filled up with answers.
filled questionnaire
A textual entity that is the recorded response to a multiple choice question.
filled multiple choice text entity
A filled multiple choice text entity that records a response indicating 'yes' to a multiple choice question.
yes answer text entity
A filled multiple choice text entity that records a response indicating 'no' to a multiple choice question.
no answer text entity
A planned process that involves the filling of an informed consent form.
filling informed consent form
A planned process that involves the filling of a questionnaire form that includes a list of questions.
filling questionnaire
An informed consent for a subject agrees not to have financial benefit in the future.
Christoph Brochhausen, Yongqun He
consenting not to have financial benefit
A planned process for a subject agrees not to be informed about any incidental finding.
consenting to not to be informed about incidental finding
A planned process for an unspecified range of future research subject to a few content or process restrictions.
Frank Manion, Yongqun He, 2018 Little Rock CTSOG ontology workshop
broad consent process
A broad consent that is for an unspecified range of future research subject to a few content or process restrictions with biological sample.
obsolete process of providing broad consent for research with biological sample
A planned process that involves a human biological specimen originally collected for the purpose of treatment or a different investigation.
Note: not sure if the parent class should be 'investigation' or 'planned process.'
This definition is provisional, as 'secondary use' may apply to non-specimen entities. Adapted from the defintion found here: https://sunnybrook.ca/research/content/?page=sri-crs-reo-faq-secondaryusedata
secondary use
obsolete consenting to the secondary use of EHR
Note that some of these are defined classes.
An informed consent form that is adapted to the cognitive capacities of someone with significant mental impairment.
informed assent form for cognitively impaired
A temporal region during which some act is permitted.
permission temporal region
A deontic role, which may be realized in an Act of Consent, where the bearer of the legal representative role consents on behalf of a person who lacks the capability to provide consent.
It is a requirement of bearing a legal representative role in some jurisdiction(J) that one also bears a competency to consent in (J).
Mathias says this shouldn't mention 'act of consent'. I think the idea is that our definition is narrower than the class label indicates.
Note: Consent roles are created by Acts of Consent. It follows that one can’t be a consenter and bear a consenter role just because one participated in an informed consent process. Here, one would be a mere research candidate or human subject or...etc, who participated in an informed consent process. Assenter Role, likewise, is the output of an Act of Communicating Assent. Both these roles are backward looking--i.e. They are created by the processes of assent and consent and do not pre-date them. By contrast, ‘Legal Representative Role’ and ‘Permission Role’ are not, by definition, tied to Acts of Consenting and Acts of Assenting. Such roles are the output of other processes, including ‘Act of Permitting’ in the latter case, and perhaps ‘Act of Legal Representative Authorization’ in the former.
legal representative role
A role borne by a human being who is part of a group of individuals and acts as a contact person for the group.
organization-specified contact role
A directive information entity that prescribes a human being who is to bear a contact role.
Jonathan Vajda, Cooper Stansbury
contact directive
A descriptive information content entity that describes potential benefit or estimates the likelihood of benefit.
This is circulular. 'Benefit' and 'risk' definitions forthcoming.
description of participation benefit
A document part that describes the action types to be permitted.
obsolete description of allowed action types
A description of allowed action types that has in view a wide, unspecified range of action types, and is restricted only by a regulator body.
description of broad consent
A planned process of providing information according to prompts on a form.
act of filling out form
A process that is carried out by a conscious being or an aggregate of conscious beings, and is spontaneous, directed towards another conscious being or another aggregate of conscious beings, and that needs to be perceived.
This is a D-Act Term, included here as a placeholder untill D-acts is imported.
A social act in which an agent bearing a deontic power role and realizes that role in the creation of a permission role.
Axiom: Every ‘Act of permitting’ has process part some (‘Speech Act’ or ‘Document Act’). Note: This class is very general, and doesn’t only apply to consent and healthcare contexts.
In contrast to the 'authentication' (see OMRSE), an act of permitting always involves a flow of power, in which one who grants permission has a power, and the agent to whom permission is granted gains access to a power that flows from that of the granter. By contrast, although it may be the case that a person who authenticates has power, this power is only the power to authenticate or verify, and this power does not flow to the authenticated document or identity.
Note: ‘Act of permitting’, ‘act of consenting’, and ‘act of communicating assent’ are all success terms, which is to say that no ‘act of permitting’ does not issue a permission, no ‘act of consenting’ does not issue a consent, and no ‘act of communicating assent’ does not issue an assent.
act of permitting
An act of permitting that is a process part of some informed consent process.
Note: This class is very general, and doesn’t only apply to consent and healthcare contexts. There may be further subclasses of consenting for which there are also required process parts, such as a process of informing a patient of the risks associated with a medical procedure or research investigation. Also, 6/28: Mathias writes: This definition is probably incorrect. I assume we don't want to affirm that only within informed consent we do find acts of consenting.
act of informed consenting
An act of communicating one’s agreement.
act of communicating assent
A deontic role that inheres in an agent and which permits certain actions.
Important Note: When we use ‘consent’ to talk about the thing provided to an investigator then what we are referring to is a permission role, that was the output of an Act of Consent. This is all consent is, per this representation.
Note: This may become ‘permittee role’ in order to better distinguish it from the corresponding ‘permittor role’ (the person with the deontic power to grant permissions to others).
Note: Typically, in the context of consent, a permission role will inhere in a clinician or investigator as a result of an act of permitting, but possibly an act of authorizing. Authorizing is different from permitting, but this needs to be worked out. Perhaps one has provided permission, but the process and the documentation need to be authorized by some authority prior to a clinician acquiring a permission role. There is also the case Chris Stockert raised, where an organization authorizes some data or specimens to be used, despite no consent or assent having been provided.
permission role
A deontic power role that, if realized, may permit an Act of Consent and thereby create a permission role, or revoke or modify a previously provided permission role created by permitting an Act of Consent.
Note: A Consent Power Role inheres in all those who bear a legal right to consent. Such a role represents a de jure right that holds within some socio-legal jurisdiction. It follows that one may bear an instance of a consent power role within one jurisdiction but one may lack an instance of a consent power role within a second jurisdiction, given that one’s capability to consent may satisfy legal conditions in the former jurisdiction but not in the latter.
A cognitive capability inhering in some agent, which may be realized in an Act of Consent.
Note: Capability-talk is fraught and so attention to this particular, somewhat stipulative notion is necessary. First: Capabilities are BFO:Dispositions. Hence, we’re not talking about institutional power, which will be represented separately using deontic roles. This is compatible with institutional rules requiring a particular capability. Second: Like roles, capabilities can have other capabilities as parts. Thus, the capability to consent requires, as part, the capability to understand information, the capability to appreciate the consequences of one’s actions, and other capabilities related to a basic, agential capacity to be reasons-responsive. These capacities may be realized in other sub-parts of the informed consent process, and they may be identified in processes of cognitive assessment. Third: Capabilities may be assessed along a scale, with some having a greater capability to consent and some having a lesser ability to consent. The same capability at the same degree may pass muster in some jurisdictions but fail to pass in others. When it does succeed in passing some legal requirement, then the bearer of the capability has a Consent Power Role and their capability to consent now counts as a competency. Fourth: Capabilities are cognitive dispositions. As such, the class ‘capability to consent’ is not intended to be a catch-all for all the necessary conditions for legal consent. For instance, being under the age of 18 is not part of an instance of a capability to consent, but the capability to understand risks and benefits may be. Fifth: A capability that is so low on the scale as to not pass any tests is no longer a capability but a liability. The distinction between capabilities and liabilities may not be vague ontologically, but may be quite difficult to suss out epistemologically. More to the point: This is perhaps the most revisionist aspect of this reading of capabilities, for it requires that in some particular legal context, we might need to say that someone has a capability to consent that is sufficiently low as to not qualify as a competency within that legal context. Since ‘capability’ is often also used in a bi-valent, non-scalable manner (i.e. one either is capable or one is not capable) the notion here involves some stipulation. For this bi-valent notion, we use ‘competent’ (i.e. one either is competent or incompetent). In addition as of this writing (July 2018): There is work on capabilities occurring presently within the National Center for Ontological Research (NCOR), so this reading of capabilities may need revising as that work moves forward.
capability to consent
A capability to consent that is sufficiently robust as to pass the legal requirements of some jurisdiction.
Axiom: all l all c all t all m (competencytoconsent(m) & inheresin(m,x,t) -> (exists l exists c (legalpowerrole(l) & capabilitytoconsent(c) & (exists r exists o (hasorganizationalcontext(l,r,t) & hasorganizationalcontext(l,o,t) & r=o)) & inheresin(l,x,t) & inheresin(c,x,t)) -> (m=c))). %If one bears a competency to consent, then one bears a legal power role and a capability to consent in the same legal context at the same time and the competency to consent is identical to the capability to consent.
One may have the same capability to consent, but whether that capability to consent amounts to a competency might vary between jurisdictions that impose different requirements upon the bearer.
competency to consent
A role that is the output of an act of assent and which inheres in a human being, who, because they fail to satisfy certain criteria for consent, is thereby allowed the aid of a legal representative who aids them in an Act of Consent, and, in some contexts, may be realized in revoking or modifying the permission role that was output of the informed consent process of which the the Act of Assent was a process part.
An agent who has communicated their assent.
assenter
An agent who, at some time, was the bearer of a consent power role, which was, in fact, realized in an act of informed consenting, and who, as a result of this act of informed consenting, now bears a consenter role.
A consenter role may be realized, for example, in the withdraw of consent.
consenter
A deontic role that is output of some Act of Consent and, in some contexts, may be realized in revoking or modifying the permission role that was output of the same Act of Consent.
May be deleted. Consenter role just seems like permission role issued by an act of consenting.
A document act input document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and whose purpose is to assist in obtaining consent.
Note: instances of 'incomplete informed consent form' include both blank informed consent forms that are waiting to be used in a process of informed consent, as well as those that have been left blank by a patient, whether on purpose or in error. Those that have been left blank on purpose have been used in a process of informed consent, where the patient must have reached a decision.
incomplete informed consent form
A document act input document that has, as part, an incomplete informed consent form, along with some additional parts, such as a signature, stamp, or initials, which serve as a record to an act of consent that had the incomplete informed consent form as a specified input.
complete informed consent form indicating consent
A deontic role that, if realized, is realized in the creation, modification, or revoking of other deontic roles.
deontic power role
A planned process that involves altering an information content entity that is associated with an individual, such that such association is lost or inaccessible.
act of anonymizing
An act of anonymization that alters an information content entity by removing information content which identifies that individual.
act of removing identifiable information
A material entity (either a human being or an aggregate of humans such as an organization) which is active in a process or has the relevant capabilities of intentionality.
agent
A social act in which information that is thought to be true, salient, or which is held to have a high degree of certainty is communicated to an agent that previously lacked that information.
If I communicate falsehoods, I do not inform--I mis-inform.
act of informing
An information content entity that is a handwritten depiction of a name.
Jonathan Vajda, Cooper Stansbury, J. Neil Otte.
signature
A deontic power role that may be realized in an act of consent that is a process part of an informed consent process.
a consent power role is a legal right that holds within a jurisdiction and is a necessary requirement to bear a competency to consent.
consent power role
A stasis of generically dependent continuant that has participant some information content entity which, during the stasis, is unable to be used to identify some agent which the information is about.
An information content entity that has previously undergone the process 'act of anonymization' participates in this stasis.
We expect to add a subclass axiom: 'preceded by' some 'Act of Anonymizing'
stasis of anonymization
A planned process that involves placing a material entity in some location in order to maintain possession of it.
act of storing
A planned process in which data possessed by one person or organization is shared with one or more other persons or organizations.
act of data sharing
A contact person role that is the output of either a human subject or patient assigning that person as their point of contact.
emergency contact role
human subject-specified contact person role
A role inhering in a person who is a designated contact for some other agent.
The subclasses of 'contact person role' distinguish two types: a contact person who has been designated by an organization for others (primarily patients and human research subjects in clinical settings) to contact, and a contact person whom an agent has specified for an organization to contact in the event that the organization needs to contact the patient. Examples of the latter include 'emergency contact' persons, who are frequently specified in a form.
contact person role
A site within which a deontic power may be realized, where that deontic power inheres in a formally created regulatory body.
'Jurisdiction' is often defined in two senses: (1) a geopolitical context (BFO site), or (2) a power. We define jurisdiction as a BFO site, identifiable through shared context of other entities, like a country or state border, or the grounds of an institution. The term ‘deontic power role’ reflects the sense of ‘power’ sometimes used to describe jurisdiction.
jurisdiction
An organization that has a deontic power role prescribed by some regulatory document that occurs in a stasis of regulation.
A document that either prescribes actions or prescribes the permissions, obligations, restrictions, or protections relating to public or legal policy.
Rules, legal specifications, guidelines (both categorical and hypothetical), that exist together in one regulatory document. Regulations may contain a single, or multiple rules.
The clause ‘permissions, obligations, restrictions, or protections’ will be replaced with more general superclass, likely from d-acts, when that infrastructure becomes available. IOU Code.
regulatory document
‘HIPAA documents,’ ‘The Common Rule,’ an ‘Informed Consent Regulatory Document.’
A regulatory document designed to prescribe research involving human subjects.
human subject research regulatory document
A regulatory document designed to prescribe an informed consent process or inputs in an informed consent process.
‘Informed Consent Waivers,’ ‘Informed Consent Exemptions.’
informed consent regulatory document
Do action (x).
A rule in an informed consent regulatory document that prescribes either an informed consent process or deontic roles inhering in agents that participate in an informed consent process.
informed consent rule
A rule in an informed consent regulatory document that prescribes an informed consent process and has part trigger condition description.
Those conditions that have important implications are enumerated in a specification of condition.
The logical form of a conditional rule is as follows: if condition (y) obtains, then perform action (x).
conditional informed consent rule
A rule in an informed consent regulatory document that prescribes deontic roles that may be realized in an unspecified range of activities, or which is subject to few restrictions.
broad consent rule
A directive information entity that prescribes information that must be revealed and prescribes to whom that information must be revealed.
disclosure directive
A description of who can consent (but not the conditions required to be realizable).
A directive information entity that prescribes a deontic power role or the process that realizes it.
deontic power role directive
A directive information entity that prescribes the limits of disclosure regarding an agent’s identity.
May need ‘Conditional Confidentiality Directive' in the future.
A ‘signature section,’ an ‘I understand’ clause, or a ‘checkbox.’
A directive information entity that, when signed, stamped, or initialed realizes a deontic role as described by the document specifications, or specifications in another related document.
user input directive
A directive information entity that enumerates the results if a trigger condition describing failure to comply with a rule is met.
Cooper Stansbury, J. Neil Otte, Jonathan Vajda
consequent directive
A 'directive information entity' that prescribes an allowable action, where that action is otherwise impermissible.
Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
(1) There is some ambiguity regarding process repition. This distinction may point to the central question of whether or not we permit 'universals' or . Take the following example: In the case of 'permission to destroy excess tissue' the instance of a 'process of destruction' is permitted only once. However, in the case of 'pemission to share data' this process may be performed multiple times.
permission directive
A conditional specification that prescirbes a permission, should some trigger condition obtain.
Permission to do (x), if condition (y).
obsolete conditional permission directive
A directive information entity that prescribes actions that are impermissible.
When particpating in an informed consent process (a), do not do action (y).
restriction directive
A conditional specification that prescirbes an impermissibility, should some trigger condition obtain.
Cooper Stansbury and J. Neil Otte
When particpating in an informed consent process (a), if conditon (x) do not do action (y).
conditional restriction directive
A directive information entity that prescribes an obligation that is realized a deontic role that is the output of a document act.
obligation directive
A conditional specification that prescirbes an obligation, should some trigger condition obtain.
conditional obligation directive
A directive information entity that prescribes the agent that is liable if a trigger condition is met.
liability directive
The section of an informed consent document that describes a clinical procedure that the agent is consenting to.
A descriptive information content entity that describes a medical procedure.
description of medical procedure
A directive information entity that describes some state of affairs such that, if that state of affairs holds, some other prescription follows.
An antecedent.
trigger condition directive
A descriptive information content entity that reports that participation in the procedures described elsewhere in the document are voluntary.
description of voluntary participation
A role inhering in an agent as a result of that agent having observed some process.
J. Neil Otte and Cooper Stansbury
Typically, someone who bears a witness role has observed some history, such that one may attest to what has occurred.
witness role
A directive information entity that prescribes some process for withdraw from another planned process.
withdrawal from participation directive
A temporal region identifier that designates the temporal region during which a living person is alive, and where the temporal region is such that the living person is qualified to exercise a deontic power within a legal jurisdiction.
legal age
A social act in which formal or official endorsement of some entity is communicated.
This 'act of approving' is distinct from the mental act of approving.
act of approving
A directive information entity that prescribes the language that must be used in an informed consent process.
consent language directive
A descriptive information content entity that describes some process that may be elected.
J. Neil Otte, Cooper Stansbury, Jonathan Vajda
description of alternative
A descriptive information content entity that describes expressions or implications of threat that may compel an agent to act out of fear against the agent's will.
It may be necessary to define processes of coercion in addition to descriptions of the process.
An international review board (IRB) may require a research proposal to identify ways in which a participant may be under undue influence. For example, a prisoner may feel compelled, given their vulnerability, to provide more information or cooperation in a study than they would normally consent to, because of the benefits they might receive.
description of coercion
"§46.102(f) Human subject means a living individual about whom an investigator (whether professional or student) conducting research obtains (1) Data through intervention or interaction with the individual, or 2) Identifiable private information. Intervention includes both physical procedures by which data are gathered (for example, venipuncture) and manipulations of the subject or the subject's environment that are performed for research purposes. Interaction includes communication or interpersonal contact between investigator and subject. Private information includes information about behavior that occurs in a context in which an individual can reasonably expect that no observation or recording is taking place, and information which has been provided for specific purposes by an individual and which the individual can reasonably expect will not be made public (for example, a medical record). Private information must be individually identifiable (i.e., the identity of the subject is or may readily be ascertained by the investigator or associated with the information) in order for obtaining the information to constitute research involving human subjects."
A disposition to abnormality realized in cognitive processes that are qualitatively below those of individuals belonging to some type, to which the bearer of the disposition also belongs.
Adapted from http://purl.obolibrary.org/obo/HP_0100543
Imported and adapted 8.22.2018
cognitive impairment
A vulnerability due to exposure to a depressed or impoverished economic environment.
Cooper Stansbury, Jonathan Vajda
economic vulnerability
A vulnerability due to exposure to a harsh learning environment.
educational vulnerability
A planned process of storing the document output of an 'act of consent' for future use.
act of archiving informed consent
A descriptive information content entity that describes a method of some act of communicating.
contact method description
A directive information entity that prescribes some process in which vulnerable individuals participate.
vulnerable population directive
A directive information entity that prescribes the nondisclosure of information.
confidentiality directive
A planned process in which some entity provides information to another entity.
adapted from "communicate." Merriam-Webster.com. 2011. https://www.merriam-webster.com (30 August 2018).
See ICO: 'act of informing.' This class is perhaps not needed.
A note: 'entity' rather than 'agent' is used in this definition in order to allow that software can communicate with other software. However, it should be noted that this definition of communication excludes broader meanings, such as unintentional sharing of information.
act of communicating
A descriptive information content entity that describes the expected duration of participation of some agent in an investigation.
description of expected study participation duration
A directive information entity that prescribes some research process.
research method directive
A descriptive information content entity that describes the conditions under which compensation is due to some agent.
description of conditional compensation
A descriptive information content entity that describes an emotional state of mental or physical uneasiness.
description of discomfort
A descriptive information content entity that describes biospecimens that have been collected.
description of collected biospecimens
A descriptive information content entity that describes information that may be collected or the processes of information collection.
description of collected information
A descriptive information content entity that describes how biospecimens will be used.
description of future biospecimen use
A descriptive information content entity that describes some procedure for obtaining information only available at some future time.
description of procedure for obtaining further information
For instance, a patient may assert a preferred mode of communication for contact in the future. This may be given in terms of permitting a communication via email, phone call, etc. and it may mention the address or number to be used.
A directive information entity that prescribes methods for contacting an agent.
contact method directive
A descriptive information content entity that describes some conditions that constitute unauthorized disclosure of information.
It is possible that classes like this will be useful in conjuction with descriptions of risk as in: 'description of risk of breach of confidentiality.'
description of breach of confidentiality
A descriptive information content entity that describes legal responsibility that an entity has due to some risk.
description of liability
description of legal responsibility
A description of risk that describes the magnitude of potential financial loss.
description of financial risk
A description of risk that describes the magnitude or probability of damage to the reputation of an agent in a social context.
description of reputational risk
E.g., "There are several definitions available for the term 'vulnerable population', the words simply imply the disadvantaged sub-segment of the community requiring utmost care, specific ancillary considerations and augmented protections in research. The vulnerable individuals’ freedom and capability to protect one-self from intended or inherent risks is variably abbreviated, from decreased freewill to inability to make informed choices." Preethi Shivayogi (2013). Vulnerable population and methods for their safeguard. Perspectives in clinical research, 4(1), 53-7.
A role that inheres in an agent or group of agents that is the output of a process during which the agent or group of agents is designated as belonging to a vulnerable group.
Note: It is possible to belong to a vulnerable population and yet not bear a disposition of vulnerability. Typically, when a person is held to be a vulnerable individual, this is a designation that applies by fiat in virtue of their membership to some legally designated group, and not based on a clear investigation of their individual case. Hence, it seems prudent here to use roles for this purpose.
vulnerable individual role
A role that inheres in a regulatory body that, if realized, is realized in some act of regulatory supervision.
regulatory oversight role
A role inhering in a Homo sapiens that, if realized, is realized within the organizational context of a legal jurisdiction, when the bearer fails to meet the legal threshold for adulthood.
It is possible to create further defined classes here, such as 'abused minor role' that is a minor that participated in a process of abuse.
minor role
A woman who is pregnant.
Could reuse: http://purl.obolibrary.org/obo/ontoneo/ONTONEO_00000197
pregnant woman
A role inhering in a Homo sapiens that is realized in a process of incarceration.
Note from Jonathan Vajda: Depending on the level of granluarity, we could have prisoner role, incarcerated role, etc. and these roles would differentiated by what kind of stasis of incarceration necessary.
prisoner role
A document designed for the purpose of assisting in an act of waiving, and which contains both some description of waiver and some waiver directive.
waiver document
A descriptive information content entity that describes an entity that provides positive motivation for some material entity.
From NCI Thesaurus OBO Edition: Incentive: A benefit, consideration, or positive motivational influence, financial or otherwise, given to induce a specific action. [def-source: NCI]
description of incentive
A protocol that is formal plan of a research activity, including the objective, rationale, design, materials, and methods for the conduct of the activity.
This term was adapted from: http://purl.obolibrary.org/obo/NCIT_C70817
study protocol
A directive information entity that prescribes the information that is permitted to be shared or the processes for sharing that information.
data sharing directive
A directive information entity that prescribes the process of transferring a permission role from one bearer to another.
Note: Strictly speaking, of course, roles are not transferred; rather, the transfer of a permission involves the role of one agent ceasing to exist, and the role of a second agent coming into existence.
permission transfer directive
A directive information entity that prescribes the processes that involve some entity as a participant.
future use directive
A descriptive information content entity that describes the negative impact or harm that may befall an agent who withdraws from an investigation.
description of consequences of voluntarily withdrawal
A stasis of generically dependent continuant that has participant some information content entity and during which that information content entity is recognized within that jurisdiction and directs governance within that jurisdiction.
stasis of regulation
A stasis of regulation that has participant some information content entity and during which that information content entity is recognized as a law within the jurisdiction in which the stasis of regulation is occurring.
Cooper Stansbury, J. Neil Otte
The ‘stasis of law’ designates the spatial and temporal conditions that need to be met in order for a regulatory document to be a ‘law’ or a ‘policy.’ This is necessary because laws, or other regulations are overturned, made obsolete, ect..., but material entities concretizing them persist.
There are many definitions and conceptions of law, which can be elaborated in further work. There is a concern not to define law in such a way that we narrow the scope beyond an international context.
stasis of law
A trigger condition directive that prescribes conditions for which a individual bears a vulnerability role or disposition of vulnerability, or a population of such individuals.
See http://purl.unep.org/sdg/SDGIO_00000024 (Vulnerability): A disposition of an entity to undergo undesirable change in response to some exposure.
protection directive
A planned process in which a regulatory body directs or monitors another planned process.
act of regulatory supervision
A process of mistreating an entity such that the mistreated entity is harmed.
Cooper Stansbury, J. Neil Otte, and Jonathan Vajda
adapted from "abuse." Merriam-Webster.com. 2011. https://www.merriam-webster.com (30 August 2018).
act of abuse
An act of communicating in which information is shared, overriding or violating a judgment that the information should not be shared.
It is possible that there are meaningful defined classes here like: 'act of authorized disclosure' and 'act of unauthorized disclosure.'
act of disclosure
A descriptive information content entity that describes a research procedure.
description of research procedure
A descriptive information content entity that describes how data will be used.
description of future data use
A descriptive information content entity that describes future use of material or information.
description of future use
A social act of relinquishing a right, claim, or privilege.
"waiver." Merriam-Webster.com. 2011. https://www.merriam-webster.com (30 August 2018).
act of waiving
A directive information entity that prescribes an act of waiving.
waiver directive
A descriptive information content entity that describes a directive information content entity that can be ignored.
adapted from: http://purl.obolibrary.org/obo/NCIT_C113777
description of waiver
A role inhering in a Homo sapiens that, if realized, is realized in being a passive participant in some act of abuse process.
A passive participant in such a process would mean that the act of abuse has this entity as its target; i.e., the bearer of this role is entity that is mistreated.
abused person role
A directive information entity that prescribes some investigation of biospecimens.
directive about research of biospecimens
A planned process that involves the investigation of some sequence of DNA.
act of genetic testing
A directive information entity that prescribes some act of genetic testing.
genetic testing directive
A role inhering in some material entity that is realized in an act of artifact modification where the material entity is separated from another portion of material.
excess material role
An objective specification whose intended process endpoint is an investigation.
investigation objective specification
An objective specification that prescribes the participation of an information content entity or a material entity in a process prescirbed by a future invesitgation objective specification.
"The use in research of information or human biological materials originally collected for a purpose other than the current research purpose."
Adapted from: “Secondary Use of Data - FAQs - Research Ethics Office - Sunnybrook Research Institute.” [Online]. Available: https://sunnybrook.ca/research/content/?page=sri-crs-reo-faq-secondaryusedata. [Accessed: 07-Nov-2018].
secondary use objective specification
A directive information entity that prescribes some role.
role directive
A role directive that prescribes the bearer of a patient role in a process.
patient role directive
A role directive that prescirbes the bearer of a regulatory oversight role in a process.
regulatory oversight role directive
A role directive that prescribes the bearer of an investigator role in a process.
investigator role directive
A role directive that prescribes the bearer of a legally authorized representative role in process.
legally authorized representative role directive
A 'permission directive' that prescribes some action that is made allowable by a consenting entity.
(1) We indend instances of 'consent directive' to be stated positively with repect to the act of permitting. A 'consent directive' may only allow for different actions, not forbid them. However, since 'consent directives' may simultaneously create new duties or obligations, we define 'designated consent condition' in order to help manage these nested deontic statements. (2) Another, less formal definition: 'A statement that guides action that is made allowable by a consenting entity, where that action is otherwise impermissible.' (3) The definition from HL7: "The legal record of a healthcare consumer's agreement with a party responsible for enforcing the consumer’s choices, which permits or denies identified actors or roles to perform actions affecting the consumer within a given context for specific purposes and periods of time." https://www.hl7.org/fhir/consent.html
consent directive
A 'permission directive' that prescribes some action that is made allowable by an assenting entity.
(1) We indend instances of 'assent directive' to be stated positively with repect to the act of permitting. A 'assent directive' may only allow for different actions, not forbid them. However, since 'assent directives' may simultaneously create new duties or obligations, we define 'designated consent condition' in order to help manage these nested deontic statements.
assent directive
A 'Directive Information Content Entity' that designates a process as permissable.
(1) It is critical that these classes not be mistaken for processes themselves. If you intend to build logical axioms within the BFO framework it will be necessary to create realtions between instances of 'designated actions' and 'processes.' We leave this mapping undone in order to accomodate various non-BFO process value sets. (2) We believe it is important to separate 'processes' from their inputs, outputs, or participants in action designatation. For example: instead of a 'designated process of blood extraction' we would advocate for creation of a designated action such as 'designated process of extraction' so that this class may also be used with different objects, like teeth. This is of course, application dependent. This is only a guide. (3) It is our intent that all instances of 'designated actions' that are related to instances of 'permission directive' be processes or events in which deontic roles of some kind may be realized. Stated another way, a 'designated action' should be an action that is not allowable unless a process makes it so: for example, a 'process of informed consent' with a subprocess 'act of permitting.'
designated action
A 'Designative Information Content Entity' that designates an entity which can bear deontic roles.
(1) In the general sense, 'designated actors' should designate entities which perform, or participate in an action. While the notion of 'agency' is important for some entiites, at some times, involved in processes of informed consent, we do not define actors in terms of their agency. (2) Within the greater BFO, D-acts, and ICO frameworks, we believe that a 'designated actor' has some capability to bear deontic roles.
designated actor
A 'Designative Information Content Entity' that designates the object of a 'designated action'.
(1) In English, this is typically the 'object' of the clause where the 'designated action' is the verb. We may also refer to this as the 'designated target' of the action. However, we choose 'object' to more clearly separate the objects of the actions from the ends.
designated object
A 'directive information entity' that directs the conditions of 'allowability' for a 'consent directive'.
(1) A 'designated consent condition' defines or delimits the scope, boundaries, requirements, attributes, antecendents, or limitations the 'designated action' which may be permitted. As such, it is specifically tied to permissions to avoid complex nested impertives as much as possible. The central question to ask is: 'what does permission to undertake this action depend on?' (2) Our intent is to focus on conditionals related to 'obtaining permission' rather than all possible conditionals.
permission condition directive
A 'permission condition directive' that directs the purpose for a 'permission directive'.
purpose: https://www.merriam-webster.com/dictionary/purpose (1) to propose as an aim to oneself 'means to an end': https://www.merriam-webster.com/dictionary/a%20means%20to%20an%20end (1) something done only to produce a desired result
(1) We refer to 'designated purpose' as the specific end, outcome, or target of some designated action. We note that this necessarily involves the notion of 'intentionality.' Because this may be regarded as problematic in a realist ontology, please tread with caution.
permission purpose directive
A 'designated action' that designates a process of access as permissable.
access: https://www.merriam-webster.com/dictionary/access (1) to get at (2) to gain access to (3) to be able to use, enter, or get near (something) (4) to open or load (a computer file, an Internet site, etc.) (5) permission, liberty, or ability to enter, approach, or pass to and from a place or to approach or communicate with a person or thing (6) freedom or ability to obtain or make use of something
(1) Access is a complex issue. We intend this class to cover instances whereby an entity may gain the ability to act upon an object whereby they previously were not able to do so. Examples may include: accessing PHI in a database, linking sensitive information to a biospecimen repository, ect.
designated process of access
A 'designated action' that designates a process of analysis as permissable.
analyze: https://www.merriam-webster.com/dictionary/collect (1) to study or determine the nature and relationship of the parts of (something) by analysis
designated process of analysis
A 'designated action' that designates a procedure as permissable.
(1) It is our intent for this term to serve as a blanket class for all types of clinical procedures. If an application demands specificity of procedures, for example administration of anesthetic, this would be a good parent class for such a list or subtree of procedures.
designated procedure
A 'designated action' that designates a process of collection as permissable.
collect: https://www.merriam-webster.com/dictionary/collect (1) to bring together into one body or place (2) to gather or exact from a number of persons or sources (3) to gain or regain control of
(1) It is our intent that this class includes instances of collection of material and of information. We note that the actual processes of 'retention' (read: 'storage') and 'collection' may be ambigously differentiated. (2) We intend this class to primarily cover de novo collection.
designated process of collection
A 'designated action' that designates a process of destruction as permissable.
destroy: https://www.merriam-webster.com/dictionary/destroy (1) to put out of existence
designated process of destruction
A 'designated action' that designates a process of disclosure as permissable.
disclose: https://www.merriam-webster.com/dictionary/disclose (1) to make known or public (2) to expose to view
designated process of disclosure
A 'designated action' that designates a process of duplication as permissable.
duplicate: https://www.merriam-webster.com/dictionary/duplicate (1) to make double or twofold (2) to make a copy of
(1) We intend this designation to include processes of 'copying.'
designated process of duplication
A 'designated action' that designates a process unspecified use as permissable.
'use' (1) to put into action or service (2) to carry out a purpose or action by means of
unspecified: https://www.merriam-webster.com/dictionary/unspecified (1) not named or stated explicitly
(1) this is a 'catch-all' bucket to define those 'designated action'(s) that are not explicit. (2) does this require a 'designated purpose' specification? (this is boarderline rule enforcement that may be appropriate at implmentation, but not here).
designated process of unspecified use
A 'designated action' that designates a process of modifcation as permissable.
modify: https://www.merriam-webster.com/dictionary/modify (1) to make basic or fundamental changes in often to give a new orientation to or to serve a new end
designated process of modification
A 'designated action' that designates a process of contact permissable.
(1) This includes instances of recontact.
designated process of contact
A 'designated action' that designates a process of retention as permissable.
retain: https://www.merriam-webster.com/dictionary/retain (1) to keep in possession or use (2) to keep in one's pay or service (3) to hold secure or intact
(1) these may often be accompanied by a 'designated temporal conditon'. (2) if these are do not follow (1), they may be more approproately labeled 'stases' instead of 'process.' (3) we believe this includes storage, should it be re-labeled 'storage?'
designated process of retention
A 'designated action' that designates a process of sharing permissable.
share: https://www.merriam-webster.com/dictionary/share (1) to partake of, use, experience, occupy, or enjoy with others
(1) this, along with 'transfer' need to be properly fleshed out. Perhaps the difference is 'ownership.' When you share, you may retain the right to ownership, but when you transfer, you yield this right.... (2) does sharing including publishing PHI? De-anonymizing? (3) what about 'release?'
designated process of sharing
A 'designated action' that designates a process of study as permissable.
(1) require link to a 'Descriptive Information Content Entity' like: 'STUDY DETAILS?' (2) STUDY PRTICIPATION
designated process of study
A 'designated action' that designates a process of surveillance.
surveil: https://www.merriam-webster.com/dictionary/surveil (1) to subject to surveillance
(1) our usage more closely resembles the use in NCIT.
A 'designated action' that designates a process of transferral of ownership permissable.
transfer: https://www.merriam-webster.com/dictionary/transfer (1) to convey from one person, place, or situation to another (2) to make over the possession or control of (3) to move to a different place, region, or situation
(1) is collection a tranfer of ownership?
designated process of transfer
A 'permission purpose directive' that designates a research process as its end.
(1) This is a pointer to ADAM Matrix. (2) covers future
designated research purpose
A 'designated research purpose' that designates a biomedical research process as its end.
designated biomedical research purpose
A 'designated research purpose' that designates a process of genetic research as its end.
designated genetic research purpose
A 'permission purpose directive' that designates a process relating to the management of an organization as its end.
administrative: https://www.merriam-webster.com/dictionary/administrative (1) relating to the management of a company, school, or other organization administrative tasks/duties/responsibilities
(1) actions undertaken support system processing
designated administrative purpose
A 'permission purpose directive' that designates a process of diagnosis as its end.
(1) related to, but perhaps not limited to the following classes in OGMS: (2) diagnosis (http://purl.obolibrary.org/obo/OGMS_0000073) (3) diagnostic process (http://purl.obolibrary.org/obo/OGMS_0000104)
designated diagnostic purpose
A 'permission purpose directive' that designates an educational process as its end.
designated educational purpose
A 'permission purpose directive' that designates a process of evaluation as its end.
designated evaluation purpose
A 'permission purpose directive' that designates a for-profit activity as its end.
designated commercial purpose
A 'permission purpose directive' that designates a healthcare operation process as its end.
(1) quality and safety purposes
designated healthcare operation purpose
A 'permission purpose directive' that designates a nonprofit activity as its end.
designated non-commercial purpose
A 'permission purpose directive' that designates a process related to healing a disease as its end.
designated therapeutic purpose
A 'permission purpose directive' that designates an unspecified process as its end.
designated unspecified purpose
A 'permission condition directive' which states a preceding event or condition.
(1) 'antecedent' (2) may need to specific 'post-cendents' also.
permission precondition
A 'permission requirement directive' that directs a 'permissable' limit of a 'consent directive'.
(1) Restrictions narrow the scope of the 'designated action'. They operate on the 'allowability' conditionally. (2) "Allowable IF NOT <'designated restriction'>" (3) Alternatively: 'A LIMIT ON THE SCOPE OF THE ACTION' (4) up until the point of. (5) RESTRAINNING
permission restriction directive
A 'permission restriction directive' that designates an actor.
permitted actor restriction directive
A 'permission restriction directive' that defines the spatial boundaries of a 'designated action'.
(1) 'Jurisdiction' is often defined in two senses: (1) a geopolitical context (BFO site), or (2) a power. We define jurisdiction as a BFO site, identifiable through shared context of other entities, like a country or state border. The term ‘deontic power role’ reflects the sense of ‘power’ sometimes used to describe jurisdiction.
jurisdiction restriction directive
A 'permission restriction directive' that designates the temporal boundaries of the 'designated action'.
temporal restriction directive
A 'permission condition directive' that states an additional requirement.
(1) NOTE: this is an imperitive - it is not strictly part of a permission but is inextricably tied to it. (2) these are obligations that are dependent on a permission (conditioned on a permission) (3) MUST BE FULLFILLED (4) allowability is necessarily dependent on this being fulfilled
permission requirement directive
A 'permission condition directive' that directs another 'consent directive' as a requirement of a primary 'consent directive'.
(1) This permission is dependent on another permission (2) a good example of this are data use agreements that must be signed in addition to an informed consent form to allow for PHI data sharingor disclosure.
permission sub-directive
A 'permission requirement directive' that directs the possibility of withdraw.
(1) typically from 'study participation.'
possibility of withdraw directive
A 'designated object' that designates data or information.
(1) This is really saying that this is information that designates other information content entities (in BFO-speak).
See: http://purl.obolibrary.org/obo/IAO_0000030
designated data
A 'designated data' that designates waveform data.
designated waveform data
A 'designated data' that designates genetic data.
designated genetic data
A 'designated data' that designates data about health.
designated health information
A 'designated data' that designates information that may identify an entity.
(1) How broad is this notion of 'entity' here? (2) NOTE: this not nested under 'designated health information' because information does not need to be health information to be identifiable. (3) HIPAA Identifiers (4) Includes fully and partially identifiable information.
designated identifiable information
A 'designated data' that designates image data.
designated image data
A 'designated data' that designates video data.
designated video data
A 'designated object' that designates a person, or part of a person, as the target of a 'designated action.'
(1) for when the permitting party is the target of the 'designated action' (2) you may operate on my leg (3) this includes 'study participant' as the target of an action. May also include patient.
designated human object
A 'designated object' that designates a biospecimen.
(1) this should be mapped to robust specimen heirarchies such as: http://purl.obolibrary.org/obo/OBI_0100051
A 'designated object' that designates a specimen.
designated biospecimen
A 'designated biospecimen' that designates a portion of excess tissue.
designated residual tissue
A 'designated object' that designates an unspecified object.
designated unspecified object
A 'designated actor' that designates an actor that may bear a permission role that may be realized in the process prescribed by the process designated by the 'designated action.'
(1) This designation points towards deontic roles and social processes. (2) This can be read as: 'the actor TO BE permitted.' It is not intended to create a permission the same way the creation of an ICO:permission role might. However, we leave this somewhat open to implementation interpretation.
designated permitted actor
A 'designated actor' that designates an actor with an affilitation to an organization or institution.
(1) actor with a designated affiliation to an organization/institution. (2) intended for single individuals rather than groups, but as a way to relate groups and actors performing on the group's behalf.
designated affiliated actor
A 'designated actor' that designates a corporation.
designated corporation
A 'designated actor' that designates an institution.
(1) established organization (2) an entity that has independent financial, legal, interests or identity.
designated institution
A 'designated actor' that designates a principal investigator.
designated principal investigator
A 'designated actor' that designates an information system.
designated information system actor
A 'designated actor' that designates an organization.
(1) where does surgical team fit in? (2) how do we define aggregates of people? (3) possible mapping to (OBI: organization) http://purl.obolibrary.org/obo/OBI_0000245
designated organization
A 'designated organization' that desginates an educational organization.
designated educational organization
A 'designated organization' that designates a biobank organization.
designated biobank organization
A 'designated organization' that designates a for-profit organization.
designated for-profit organization
A 'designated organization' that designates a funding organization.
designated funding organization
A 'designated organization' that designates a government organization.
designated government organization
A 'designated organization' that designates a healthcare organization.
designated healthcare organization
A 'designated organization' that designates a regulatory organization.
designated regulatory organization
A 'designated organization' that designates a media organization.
designated media organization
A 'designated organization' that designated a non-profit organization.
designated non-profit organization
A 'designated organization' that designates a public health organization.
(1) groups that may have the ability to override specific norms?
designated public health organization
A 'designated organization' that desginates a research organization.
designated research organization
A 'designated actor' that designates a team.
(1) this is useful in defining things like 'research team' or 'clinical team.'
designated team
A 'designated organization' that designates an unspecified organization.
designated unspecified organization
A 'designated actor' that designates an actor that may permit some 'designated action'.
(1) This designation points towards deontic roles and social processes.
designated permitting actor
A 'designated actor' that designates the entity that is permitting some 'designated action'.
(1) not to be confused with 'designated consenting actor'. (2) this definition is currently the same as the definition for 'designated consenting actor'. We need to remedy this without appealing to U.S. specific legislative definitions.
designated assenting actor
A 'designated actor' that designates the actor that is permitting some 'designated action'.
(1) Not to be confused with 'designed assenting actor' (2) By 'permitting' we mean 'making the otherwise impermissable action permissable' or 'making allowable.'
designated consenting actor
A 'designated actor' that designates an authorized representative.
(1) legally authorized representative (LAR): has the ability to act on behalf of another person (under the rule of law). (2) not sure if this should be under the 'designated permitting actor'. (3) surrogates are included here.
designated authorized representative
A 'designated actor' that designates an unspecified actor.
designated unspecified actor
A 'designated research purpose' that designates a health services research process as its end.
designated health services research purpose
A 'designated research purpose' that designates a process of methods development research as it's end.
designated methods development purpose
A 'designated research purpose' that designates reference control material research processes as its end.
designated control material research purpose
A 'designated research purpose' that designates a process of population research as its end.
designated populations research purpose
A 'designated research purpose' that designates ancestry research as its end.
designated ancestry research purpose
A 'designated biomedical research purpose' that designates a process of drug research as its end.
designated drug research purpose
A 'designated biomedical research purpose' that designates a process of disease specific research as its end.
designated disease research purpose
A 'designated biomedical research purpose' that designates a process of age category research as its end.
designated age category research purpose
A 'designated biomedical research purpose' that designates a process of gender category research as its end.
designated gender research purpose
A 'designated action' that designates a process of administration as permissable.
(1) This class is intended for actions such as 'drug administration.'
designated process of administration
A 'designated object' that designates a pharmaceutical object
designated pharmaceutical object
A 'permission purpose directive' that designates a process of recruitment.
designated recruitment purpose
A 'permission purpose directive' that designates a return of results.
(1) This is intended to cover communication from a healthcare organization to a patient or study participant regarding their health.
designated return of results purpose
A 'permission requirement directive' that directs sensitive infotmation proctection.
(1) This definition is left purposefully broad to cover a wide range of use cases including processes or methods.
sensitive information protection directive
A 'designated action' that designates a process fo treament.
(1) consent to treat
designated process of treatment
A planned process in which data is put to some use by an entity.
Cooper Stansbury, Elizabeth Umberfield
act of data use
An agent who bears a patient role.
patient
A planned process in which goods or services are exachanged for money.
Elizabeth Umberfield, Cooper Stansbury
From definition of 'sell' from Merriam-Webster: To give up (property) to another for something of value (such as money).'
act of selling
A role based on the Health Insurance Portability and Accountability Act that inheres in individuals, organizations, and agencies that are also health care providers, health plans, or health care clearinghouse.
Adapted from HIPAA.
covered entity role
A role which is realized in processes of data disclosure.
Definition from adapted from GDPR Article 4(9): A natural or legal person, public authority, agency or another body, to which the data are disclosed.
data recipient role
Protected health information that excludes HIPAA-specified identifiers of the individual or of relatives, employers, or household members of the individual.
Definition adapted from HIPAA.
limited data set
A directive information entity that prescribes the owner role.
owner role directive
A stasis in which an entity bears an ownership role.
ownership statis
A material entity, collected during some health care process, that bears both a specimen role and an excess material role following some act of artifact modification.
residual clinical biospecimen
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
Homo sapiens
A document containing the determination of the Institutional Review Board (IRB) that the clinical study with human subject participation has been reviewed and may be conducted at a particular study site within the constraints set forth by the IRB and other institutional and federal requirements. The regulations require that an IRB conduct continuing review of research at intervals appropriate to the degree of risk, but not less than once a year.
Study Site specific document containing the determination of the Institutional Review Board (IRB) or Independent Ethics Committee (IEC) that the clinical study with human subject participation has been reviewed and may be conducted at a particular study site within the constraints set forth by the IRB and other institutional and federal requirements. [NCI]
The affirmative decision of the IRB that the clinical trial has been reviewed and may be conducted at the institution site within the constraints set forth by the IRB, the institution, good clinical practice (GCP), and the applicable regulatory requirements. [ICH E6]
Institutional Review Board Independent Ethics Committee Approval
approval (in relation to Institutional Review Boards)
The state of being confined to jail or prison.
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
WEB: http://en.wikipedia.org/wiki/Adverse_event
WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
The OAE official website is: http://www.oae-ontology.org/.
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
An organization bearing legal personality that owns or adminstrates a biobank.
biobank juristic person
biobank organization
An organization with a specific responsibility that is a part of a larger organization with a specific responsibility.
department
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
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
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
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 obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
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
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)
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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.
An organization is a continuant entity which can play 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.
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
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
histological sample preparation
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
contain function
A contain function is a function to constrain a material entities location in space
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).
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
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
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.
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, collecting a stone from a site
A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
Definition updated following discussion on 2024-10-07 OBI dev call.
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.
putting a mouse in the blender. Not: putting a mouse on a scale
A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
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 that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process.
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 with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in 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.
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
A planned process with the objective to maintain some or all of the characteristics of an input material over time.
A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
A RNA extraction process in which the desired output material is RNA in the organelle(s).
A RNA extraction process in which total cellular and organelle RNA are extracted.
A RNA extraction process in which the desired output material is RNA in the cytoplasm.
Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
material obtained through a liver biopsy from a human patient
a specimen that was taken from a live organism
Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
A RNA extraction process in which the desired output material is RNA in the nucleus.
Extraction of total RNA from cells with Qiagen mini RNeasy kit
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
Extraction of organellar RNA from plant cells using organellar RNA binding protein.
A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
a specimen that was taken from a dead organism
a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
type of sample used in the PCIRN influenza network
A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium.
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
A specimen which derives from nasopharyngeal mucosa after aspiration.
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
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.
a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
A specimen that has been frozen in order to store it.
A specimen that has been modified in order to be able to detect it in future experiments
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 specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
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.
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
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
genetic alteration information
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
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)
A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828
PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
A specimen for which it is known whether it has been subjected to storage of a specified type.
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).
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
investigation title
A textual entity that denotes an investigation.
Person:Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
project title
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).
comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting
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
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
grant agency
An organization that provides funding support for projects such as investigations.
'funding organization' http://vivoweb.org/ontology/core#FundingOrganization
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.
A fixed tissue slide specimen that is the output of H&E slide staining.
A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
A cell specimen that contains only one cell.
Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
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.
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
A specimen that is derived from amniotic fluid.
A specimen that is derived from bile.
A specimen that is derived from cerbrospinal fluid.
A specimen that is derived from feces.
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
A specimen that is derived from milk.
A specimen that is derived from pericardial fluid.
A specimen that is derived from saliva.
A specimen that is derived from sputum.
A specimen that is derived from sweat.
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 brain.
A specimen that is derived from hair.
A specimen that is derived from prostate gland.
A specimen that is derived from skeletal muscle.
A specimen that is derived from heart.
A specimen that is derived from renal medulla.
A specimen that is derived from adrenal gland.
A specimen that is derived from breast.
A specimen that is derived from urinary bladder.
A specimen that is derived from tibial artery.
A specimen that is derived from skin.
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 colon.
A specimen that is derived from lung.
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 spleen.
A specimen that is derived from aorta.
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 ileum.
A specimen that is derived from liver.
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.
A specimen that is derived from testis.
A specimen that is derived from uterus.
A specimen that is derived from vagina.
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 RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified.
Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869
A RNA extraction process in which only RNAs lacking a polyA tail are retained
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.
Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation.
An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
A specimen composed of an individual organism to be studied in an investigation.
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.
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 specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito.
A specimen of the blood ingested by an arthropod.
The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human.
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 sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
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.
A specimen that is collected with a suctioning tube from the trachea.
A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity.
A specimen that is collected with a suctioning tube from the nasal cavity.
lower respiratory tract aspirate specimen
A specimen that is collected with a suctioning tube from the lower respiratory tract.
A specimen that is derived from the lower respiratory tract.
A specimen that is derived from the anterior nasal wall
aspiration specimen collection
Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue.
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea.
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube.
A blood specimen that is located in a vacutainer.
A blood specimen that is located on a filter paper.
A specimen that is derived from placental blood.
peripheral blood mononuclear cell specimen
A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system.
A specimen that is derived from a portion of lymph collected from an organism.
A specimen that is derived from part of a digestive tract.
A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.
reactant role
A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction.
A blood serum specimen that contains no albumin.
The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present.
A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions.
A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space.
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.
WEB: http://en.wikipedia.org/wiki/Blood_plasma
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; collecting a stone from a site.
A material entity that is collected for potential use as an input upon which measurements or observations are performed.
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.
organ section
A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
PERSON: Helen Parkinson
GROUP: CEBS
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.
data transformation
A planned process that produces output data from input data.
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
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 planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.
storage
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.
Person: Philippe Rocca-Serra
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
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
IEDB
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
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 planned process with the objective to keep cells alive in a defined environment outside of an organism.
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.
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
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
A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
The process of removing an organ from its source organism
organ harvesting
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.
A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
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 representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen.
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 planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
A disorder that involves some structural damage that is immediately caused by a catastrophic external force.
At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.
http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit
creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015
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).
fixed tissue specimen
A processed specimen that is the output of a fixation process.
fixed tissue slide specimen
A fixed tissue specimen that is placed in a slide.
A role that inheres in an organization and that is realized by the providing of services in a health care encounter.
health care provider organization role
An object aggregate of organisms.
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
collection of organisms
An object aggregate all of whose components are human beings.
collection of humans
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.
obsolete role in human social processes
A role in human social processes that inheres in an organization.
Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
organization social role
An organization social role that, if realized, is realized by either a health care process or an ancillary health care process
Previous definition: An organization social role played by an organization in health care processes.
organization health care role
An aggregate of organizations that have some feature in common, but is not itself an organization.
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
A healthcare provider role that inheres in an organization and is realized by providing inpatient care.
hospital role
An organization that is the bearer of a hospital role.
hospital organization
a role in human social processes that is realized when the bearer provides a wage or salary in exchange for some labour or services as specified by some declaration
employer role
A process in which some participant shares some information content entity about some state of that participant with some other participant.
S. Clint Dowland
Matthew Diller
The term 'participant' in the definition need not refer to a human agent.
obsolete communication
a communication in which some participant requests of some other participant an information content entity about some portion of reality
As with the parent class, 'participant' in the definition need not refer to a human agent.
The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be.
information content entity-request process
educating
A planned process with an active participant who acquires mental representations of information content entities (ICEs), which had no previous mental representation in the cognitive system, and through repeated use or application of these ICEs either (1) becomes the bearer of a new instance of some type of capability, and the participant was not previously the bearer of that instance of that type of capability, (2) "improves" an existing capability as demonstrated through realization(s) of that capability, and/or (3) loses a capability whose realization is considered negative.
learning process
An act of acquiring new information and repeatedly applying that information to develop a new skill, improve an existing skill, and/or losing a skill at doing something "bad".
An interesting question is whether there must be another participant who is the "educator". Some might object that many people are "self taught". A real case of being self taught is the first person who learned to play a stringed instrument, or to spin a ball on the tip of a finger. There was no previous information about that type of skill. The ICEs acquired are via one's sensory systems (vision, proprioception, auditory, etc.). On the other hand, in the case of those who are self-taught by reading books or watching videos, or acquiring some other form of ICEs concretized outside their brain, one argument might be that the author of those ICEs somehow "plays a role" in the education, although they cannot participate in the education process itself (If I read Aristotle, and through repeated application of the information I acquire through doing so, develop the ability to write better ontology definitions, surely Aristotle did not actively participate in my particular education process, although he did influence it in a very real way).
The loss of a "bad" capability is something like losing a bad golf swing and replacing it with a good one. Also a capability to disrupt the classroom might be something an educating process diminishes possibly to the point of "removal" in a student. This addition to the definition notwithstanding, we do not intend to incorporate the receipt of punishment into the definition of educating.
education process
A role that inheres in an organization and that, if realized, is realized by its bearer overseeing the overall operation of a hospital.
Imported 8.30.2018
hospital governing body role
A role that, if realized, is realized in the organizational context of a committee.
Imported 8.30.2018.
committee member role
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A physical quality of the thermal energy of a system.
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 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 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.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
A protein that is a translation product of the human ALB 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.
primary structure of sequence macromolecule
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.
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
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 whose component anatomical structures lie in close proximity to each other.
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.
The gonad of a female organism which contains germ cells.
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].
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.
Muscle tissue that consists primarily of skeletal muscle fibers.
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.
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.
Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
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.
A tube extending from the mouth to the anus.
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
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.
The mucous membrane that lines the nasal cavity[MP].
One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP].
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.
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.
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].
The portion of the small intestine that extends from the jejunum to the colon.
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.
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.
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
Transudate contained in the pericardial cavity.[FMA].
A mucosa that is part of a esophagus [Automatically generated definition].
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
A fold of peritoneum originating at the stomach and supporting the viscera.
A muscularis mucosa that is part of a esophagus.
The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.
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 portion of organism substance that secreted_by a respiratory system.
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.
Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
Area of skin in the hypoastric region of the abdomen.
Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule.
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the dimension in which events occur in sequence.
A category denoting a rather broad domain or field of interest, study, application, work, data, or technology. Topics have no clearly defined borders between each other.
This is a dummy class to be deprecated after it has fulfilled its organization purposes
Editors Note: E.g., "There are several definitions available for the term 'vulnerable population', the words simply imply the disadvantaged sub-segment of the community requiring utmost care, specific ancillary considerations and augmented protections in research. The vulnerable individuals’ freedom and capability to protect one-self from intended or inherent risks is variably abbreviated, from decreased freewill to inability to make informed choices." Preethi Shivayogi (2013). Vulnerable population and methods for their safeguard. Perspectives in clinical research, 4(1), 53-7.
A disposition of an entity to undergo undesirable change in response to some exposure.
Imported 08.22.2018
vulnerability
A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate.
from http://semanticscience.org/resource/SIO_000184
legal name
An information content entity that consists of a set of propositions that describe some entity.
Retrieved from Common Core Ontologies 7/17/2018
descriptive information content entity
An Information Content Entity that consists of a set of symbols that denote some Entity.
[Merriam-Webster] (1) Definition of 'designate as' : to choose (someone or something) for (a particular role or purpose) (2) Definition of 'designate': (Entry 2 of 2) <transitive verb> 1: to indicate and set apart for a specific purpose, office, or duty (3) Definition of 'denote': <transitive verb> 1: to serve as an indication of : BETOKEN 2: to serve as an arbitrary mark for red flares denoting danger, 3: to make known : ANNOUNCE (4) Also 'demarcate' or 'delimit'
Designative Information Content Entity
An Organization that exercises executive, legislative, or judicial authority over a Geopolitical Entity.
is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
government
A process in which some independent continuant endures and one or more of the dependent entities it bears does not change in kind or intensity.
stasis
A stasis in which some independent continuant bears some generically dependent continuant that remains unchanged during a temporal interval.
At this time only stasis of genetically dependent continuant will be represented, leaving open the possibility of modeling other types of stasis as represented in the Common Core Ontologies. An example use case would be the transition of law enumerated by one document to a new iteration of the document for the same law. In this case, the old document would no longer be ‘legally effective’ and the corresponding stasis would cease.
stasis of generically dependent continuant
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.
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
obsolete_other
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.
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Allyson Lister
Barry Smith
Bill Bug
Carlo Torniai
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Holger Stenzhorn
James A. Overton
James Malone
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jessica Turner
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Phillip Lord
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.
OWL-DL
An ontology for the annotation of biomedical and functional genomics experiments.
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
A reference to a place on the Earth, by its name or by its geographical location.
BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation.
BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science.
BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms.
Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif.
The BSD license on the BFO project site refers to code used to build BFO.
This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version.