2017-06-27
Martin N. Fransson
Jie Zheng
Alice Nzinga
Roxana Merino-Martinez
Maria Anderberg
Chris Stoeckert
Jan-Eric Litton
Loreana Norlin
MIABIS_v2_accepted and UPenn Biobank ontology
Mathias Brochhausen
Ontology for BIoBanking (OBIB)
Sanela Kjellqvist
Mikael Eriksson
William R. Hogan
The ontology for biobanking is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigation (OBI) using Basic Formal Ontology (BFO) and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology.
Description
Description
An account of the content of the resource.
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.
term replaced by
Add as annotation triples in the granting ontology
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Use on obsolete terms, relating the term to another term that can be used as a substitute
term replaced by
Contributor
Contributor
An entity responsible for making contributions to the
content of the resource.
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.
curator note
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
has obsolescence reason
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
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.
has obsolescence reason
BFO OWL specification label
BFO OWL specification label
Really of interest to developers only
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.
Creator
Creator
An entity primarily responsible for making the content
of the resource.
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.
Subject and Keywords
Subject and Keywords
The topic of the content of the resource.
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.
IEDB alternative term
An alternative term used by the IEDB.
IEDB
IEDB alternative term
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has axiom label
has associated axiom(nl)
An axiom associated with a term expressed using natural language
Person:Alan Ruttenberg
Person:Alan Ruttenberg
has associated axiom(nl)
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
Person:Alan Ruttenberg
Person:Alan Ruttenberg
has associated axiom(fol)
temporal interpretation
https://code.google.com/p/obo-relations/wiki/ROAndTime
https://github.com/oborel/obo-relations/wiki/ROAndTime
temporal interpretation
elucidation
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
elucidation
person:Alan Ruttenberg
Date
Date
A date associated with an event in the life cycle of the
resource.
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.
Title
Title
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.
BFO CLIF specification label
BFO CLIF specification label
Person:Alan Ruttenberg
Really of interest to developers only
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
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).
NIAID GSCID-BRC alternative term
NIAID GSCID-BRC metadata working group
PERSON: Chris Stoeckert, Jie Zheng
shorthand
expand expression to
Chris Mungall
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
ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
expand expression to
definition
definition
definition
definition
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
definition
editor note
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.
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
editor note
has curation status
OBI_0000281
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition source
definition source
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
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
first order logic expression
definition editor
definition editor
term editor
definition editor
term editor
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.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
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
PERSON:Daniel Schober
term editor
expand assertion to
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
alternative term
Source
Source
A reference to a resource from which the present resource
is derived.
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.
editor preferred term~editor preferred label
editor preferred term
editor preferred label
editor preferred label
editor preferred term
editor preferred term
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred label
editor preferred term
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
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.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
example
example of usage
ISA alternative term
Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA alternative term
Person: Philippe Rocca-Serra
Person: Alejandra Gonzalez-Beltran
ISA tools project (http://isa-tools.org)
An alternative term used by the ISA tools project (http://isa-tools.org).
label
imported from
For external terms/classes, the ontology from which the term was imported
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
imported from
Format
Format
The physical or digital manifestation of the resource.
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).
part of
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 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'.
a core relation that holds between a part and its whole
http://www.obofoundry.org/ro/#OBO_REL:part_of
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)
part of
part_of
this day is part of this year (occurrent parthood)
has part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
a core relation that holds between a whole and its part
has part
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)
realized in
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
[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])
is realized by
realized in
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
realizes
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
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])
preceded by
is preceded by
preceded_by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
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
occurs_in
unfolds in
unfolds_in
contains process
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
[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
site of
has temporal occupant
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
spanOf
span-of
history of
[copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001
b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001
historyOf
history-of
has history
[copied from inverse property 'history of'] b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001
hasHistory
has-history
b has_history c iff c history_of b [XXX-001
member of
has measurement unit label
has measurement unit label
is about
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
is about
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
mentions
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
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
denotes
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
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.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
denotes is 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
person:Alan Ruttenberg
is quality measurement of
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
Alan Ruttenberg
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
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
is duration of
Person:Alan Ruttenberg
is duration of
relates a process to a time-measurement-datum that represents the duration of the process
is quality measured as
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
inverse of the relation of is quality measurement of
is quality measured as
has time stamp
Alan Ruttenberg
has time stamp
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has measurement datum
Alan Ruttenberg
has measurement datum
relates a time stamped measurement datum to the measurement datum that was measured
designates
Mathias Brochhausen
x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context..
is designated by
Mathias Brochhausen
p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
has maximum capacity
A relation that relates a container to a measurement datum that specifies the maximum capacity of the container.
Person: Jie Zheng, Chris Stoeckert
Penn Group
has actual load
A relation that relates a container to a measurement datum that specifies the actual amount of material in the container.
Penn Group
Person: Jie Zheng, Chris Stoeckert
is_supported_by_data
Philly 2011 workshop
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
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.
is_supported_by_data
OBI
OBI
has_specified_input
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: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
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.
PERSON: Alan Ruttenberg
has_specified_input
see is_input_of example_of_usage
is_specified_input_of
PERSON:Bjoern Peters
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
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.
PERSON: Alan Ruttenberg
has_specified_output
is_specified_output_of
is_specified_output_of
PERSON:Bjoern Peters
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
BP, AR, PPPB branch
PPPB branch derived
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.
achieves_planned_objective
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
has grain
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has grain
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PERSON: Alan Ruttenberg
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
objective_achieved_by
OBI
OBI
is member of organization
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Person:Helen Parkinson
Person:Helen Parkinson
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
is member of organization
has organization member
Person: Jie Zheng
Relating an organization to a legal person or organization.
See tracker:
https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
has organization member
has value specification
has value specification
PERSON: James A. Overton
OBI
A relation between an information content entity and a value specification that specifies its value.
owns
Mathias Brochhausen
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
administrates
A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl
Mathias Brochhausen
Mathias Brochhausen
a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
is contact information about
Mathias Brochhausen
a is contact information for b, if a is a information content entity, b is a human being or an organization and a identifies a physical location or electronic resource that allows to initiate communication with a.
is owned by
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
is-aggregate-of
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
true
inheres in
'inheres in at all times'
A dependent inheres in its bearer at all times for which the dependent exists.
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
inheres in
inheres_in
this fragility inheres in this vase
this red color inheres in this apple
bearer of
bearer_of
is bearer of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
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
bearer of
bearer of
bearer_of
is bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
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
has_participant
has participant
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.
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
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)
is concretized as
http://purl.obolibrary.org/obo/obi.owl
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).
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.
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).
concretized by at some time
is concretized as
concretizes
http://purl.obolibrary.org/obo/obi.owl
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.
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).
It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.
concretizes
function of
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.
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
function of
function_of
is function of
this catalysis function is a function of this enzyme
quality of
A quality inheres in its bearer at all times for which the quality exists.
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
is quality of
quality_of
this red color is a quality of this apple
role of
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.
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
is role of
role_of
this investigator role is a role of this person
has function
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.
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has function
has_function
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
has quality
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.
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
has quality
has_quality
this apple has quality this red color
has role
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.
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
has_role
this person has role this investigator role (more colloquially: this person has this role of investigator)
has disposition
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
disposition of
derives from
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
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
derives from
derives_from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
derives into
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'.
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
derives into
derives_into
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
location of
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
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
is location of
location_of
my head is the location of my brain
this cage is the location of this rat
located in
http://www.obofoundry.org/ro/#OBO_REL:located_in
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
located in
located_in
my brain is located in my head
this rat is located in this cage
2D boundary of
2D_boundary_of
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.
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
boundary of
is 2D boundary of
is boundary of
the surface of my skin is a 2D boundary of my body
has 2D boundary
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.
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
my body has 2D boundary the surface of my skin
has component
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.
temporal relation
move to BFO?
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
Allen
temporal relation
starts
inverse of starts with
Chris Mungall
Allen
starts
has input
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
consumes
Chris Mungall
has output
Chris Mungall
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
produces
member of
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
SIO
member part of
is member of
has member
has member is a mereological relation between a collection and an item.
SIO
has member
input of
Chris Mungall
inverse of has input
output of
inverse of has output
Chris Mungall
lacks_part
RO
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
has measurement value
has measurement value
has specified value
OBI
A relation between a value specification and a number that quantifies it.
PERSON: James A. Overton
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
count
An information content entity that is a representation of counting.
It can be denoted as an arithmetic value or in form of a word, and is usually as a result of a process.
counting
A planned process that computes the totality of some material entity.
age data by age brackets
1
A data set consisting of measurements of age organized in age brackets.
entity
entity
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
Entity
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
Julius Caesar
Verdi’s Requiem
entity
the Second World War
your body mass index
per discussion with Barry Smith
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])
continuant
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
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])
Continuant
continuant
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
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
continuant
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) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
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])
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
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [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 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])
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])
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
occurrent
Occurrent
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
An entity that has temporal parts and that happens, unfolds or develops through time.
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])
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.
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
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.
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
occurrent
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
per discussion with Barry Smith
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]
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])
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
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.
independent continuant
(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]
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
independent continuant
the bottom right portion of a human torso
the interior of your mouth
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])
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])
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])
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
(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]
obsolete dependent continuant
true
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
spatial region
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
SpatialRegion
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
s-region
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])
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.
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
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])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
per discussion with Barry Smith
temporal region
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
t-region
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
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])
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
TemporalRegion
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
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])
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
per discussion with Barry Smith
(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]
two-dimensional spatial region
2d-s-region
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
TwoDimensionalSpatialRegion
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
spatiotemporal region
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
SpatiotemporalRegion
st-region
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
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
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [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]
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
process
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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)
process
Process
(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]
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
process
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
disposition
disposition
(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]
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
Disposition
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [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])
an atom of element X has the disposition to decay to an atom of element Y
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])
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
disposition
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
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])
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])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable entity
(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]
RealizableEntity
realizable
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.
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
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])
realizable entity
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
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [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]
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])
(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]
zero-dimensional spatial region
ZeroDimensionalSpatialRegion
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
0d-s-region
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
quality
(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
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
quality
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])
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])
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
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 (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]
specifically dependent continuant
(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]
sdc
(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]
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.
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
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.
SpecificallyDependentContinuant
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])
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.
specifically dependent continuant
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
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])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
(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]
role
role
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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.
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.
Role
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
role
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
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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])
fiat object
(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]
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
FiatObjectPart
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])
fiat-object
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
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]
one-dimensional spatial region
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
OneDimensionalSpatialRegion
1d-s-region
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
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]
object aggregate
object-aggregate
ObjectAggregate
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.
(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]
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).
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)
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])
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.
(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]
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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])
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.
three-dimensional spatial region
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
3d-s-region
ThreeDimensionalSpatialRegion
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
a cube-shaped region of space
a sphere-shaped region of space,
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
site
Site
site
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
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
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])
site
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)
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
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])
object
Object
object
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
atom
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])
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
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])
generically dependent continuant
gdc
GenericallyDependentContinuant
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
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.
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.
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])
generically dependent continuant
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.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
function
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
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])
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
Function
function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
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])
process boundary
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
ProcessBoundary
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])
p-boundary
process boundary
the boundary between the 2nd and 3rd year of your life.
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [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]
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])
one-dimensional temporal region
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
1d-t-region
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
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).
OneDimensionalTemporalRegion
the temporal region during which a process occurs.
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
material entity
material
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
MaterialEntity
(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]
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])
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.
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
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
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
material entity
the undetached arm of a human being
(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 (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
(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]
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])
continuant fiat boundary
ContinuantFiatBoundary
cf-boundary
(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]
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
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])
(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]
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
immaterial entity
ImmaterialEntity
immaterial
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
one-dimensional continuant fiat boundary
OneDimensionalContinuantFiatBoundary
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
1d-cf-boundary
The Equator
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])
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
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
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])
process profile
(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]
ProcessProfile
process-profile
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
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])
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])
(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]
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])
relational quality
(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]
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.
RelationalQuality
a marriage bond, an instance of love, an obligation between one person and another.
r-quality
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
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]
two-dimensional continuant fiat boundary
2d-cf-boundary
TwoDimensionalContinuantFiatBoundary
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
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]
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])
zero-dimensional continuant fiat boundary
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
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])
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])
requested by Melanie Courtot
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.
(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 temporal region
0d-t-region
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
ZeroDimensionalTemporalRegion
a temporal region that is occupied by a process boundary
right now
temporal instant.
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
history
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
history
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
fentanyl
FENTANYL
N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
The carboxamide resulting from the formal condensation of the aryl amino group of N-phenyl-1-(2-phenylethyl)piperidin-4-amine with propanoic acid.
ethanol
A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.
ETHANOL
Ethanol
ethanol
formaldehyde
FORMALDEHYDE
Formaldehyde
The simplest aldehyde.
formaldehyde
dinitrogen oxide
A nitrogen oxide consisting of linear unsymmetrical molecules with formula N2O. While it is the most used gaseous anaesthetic in the world, its major commercial use, due to its solubility under pressure in vegetable fats combined with its non-toxicity in low concentrations, is as an aerosol spray propellant and aerating agent for canisters of 'whipped' cream.
Dinitrogen oxide
dinitrogen oxide
oxidodinitrogen(N--N)
morphine
17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol
A morphinane alkaloid that is a highly potent opiate analgesic psychoactive drug. Morphine acts directly on the central nervous system (CNS) to relieve pain but has a high potential for addiction, with tolerance and both physical and psychological dependence developing rapidly. Morphine is the most abundant opiate found in Papaver somniferum (the opium poppy).
Morphine
nicotine
3-(1-methylpyrrolidin-2-yl)pyridine
An N-alkylpyrrolidine that consists of N-methylpyrrolidine bearing a pyridin-3-yl substituent at position 2. It has been isolated from Nicotiana tabacum.
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
molecular entity
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
xylene
xylene
alcohol
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
Alcohol
alcohols
bupivacaine
A racemate composed of equimolar amounts of dextrobupivacaine and levobupivacaine. Used (in the form of its hydrochloride hydrate) as a local anaesthetic.
Bupivacaine
rac-1-butyl-N-(2,6-dimethylphenyl)piperidine-2-carboxamide
antimicrobial agent
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
macromolecule
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
macromolecule
polymer
steroid
Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene, so may be considered as triterpenoids.
Steroid
steroids
opioid analgesic
A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood.
sedative
A central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety.
local anaesthetic
Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block.
local anaesthetic
anaesthetic
Substance which produces loss of feeling or sensation.
anaesthetic
inhalation anaesthetic
intravenous anaesthetic
ethylenediaminetetraacetic acid
(ethane-1,2-diyldinitrilo)tetraacetate
(ethane-1,2-diyldinitrilo)tetraacetic acid
Ethylenediaminetetraacetic acid
ethylenediaminetetraacetic acid
propofol
2,6-bis(propan-2-yl)phenol
A phenol resulting from the formal substitution of the hydrogen at the 2 position of 1,3-diisopropylbenzene by a hydroxy group.
Propofol
droperidol
1-{1-[4-(4-fluorophenyl)-4-oxobutyl]-1,2,3,6-tetrahydropyridin-4-yl}-1,3-dihydro-2H-benzimidazol-2-one
An organofluorine compound that is haloperidol in which the hydroxy group has been eliminated with the introduction of a double bond in the piperidine ring, and the 4-chlorophenyl group has been replaced by a benzimidazol-2-on-1-yl group. It is used in the management of chemotherapy-induced nausea and vomiting, and in conjunction with an opioid analgesic such as fentanyl to maintain the patient in a calm state of neuroleptanalgesia with indifference to surroundings but still able to cooperate with the surgeon.
etomidate
Etomidate
The ethyl ester of 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylic acid. It is an intravenous general anaesthetic with no analgesic activity.
ethyl 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylate
diazepam
A 1,4-benzodiazepinone that is 1,3-dihydro-2H-1,4-benzodiazepin-2-one substituted by a chloro group at position 7, a methyl group at position 1 and a phenyl group at position 5.
Diazepam
fixative
Any compound used for the purpose of preserving biological tissues from decay in such a way as to allow for the preparation of thin, stained sections for subsequent histological study.
antiemetic
A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors.
muscle relaxant
A drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis.
lormetazepam
7-chloro-5-(2-chlorophenyl)-3-hydroxy-1-methyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one
A 1,4-benzodiazepinone compound having a methyl substituent at the 1-position, a hydroxy substituent at the 3-position, a 2-chlorophenyl group at the 5-position and a chloro substituent at the 7-position.
Lormetazepam
sodium citrate
The trisodium salt of citric acid.
trisodium 2-hydroxypropane-1,2,3-tricarboxylate
hydromorphone
3-hydroxy-17-methyl-4,5alpha-epoxymorphinan-6-one
A morphinane alkaloid that is a hydrogenated ketone derivative of morphine. A semi-synthetic drug, it is a centrally acting pain medication of the opioid class.
Hydromorphone
isoflurane
2-chloro-2-difluoromethoxy-1,1,1-trifluoroethane
Isoflurane
ketamine
2-(2-chlorophenyl)-2-(methylamino)cyclohexanone
A member of the class of cyclohexanones in which one of the hydrogens at position 2 is substituted by a 2-chlorophenyl group, while the other is substituted by a methylamino group.
KETAMINE
Ketamine
succinylcholine chloride (anhydrous)
2,2'-[(1,4-dioxobutane-1,4-diyl)bis(oxy)]bis(N,N,N-trimethylethanaminium) dichloride
A chloride salt in which the negative charge of the chloride ions is balanced by succinylcholine dications.
lidocaine
Lidocaine
N-(2,6-dimethylphenyl)-N(2),N(2)-diethylglycinamide
The monocarboxylic acid amide resulting from the formal condensation of N,N-diethylglycine with 2,6-dimethylaniline.
antacid
Any substance which is used to neutralise stomach acidity.
Meperidine
Meperidine
meperidine
methohexital sodium
The sodium salt of methohexital.
sodium 5-(hex-3-yn-2-yl)-1-methyl-4,6-dioxo-5-(prop-2-en-1-yl)-1,4,5,6-tetrahydropyrimidin-2-olate
Ondansetron
Ondansetron
pancuronium
3alpha,17beta-diacetoxy-2beta,16beta-bis(1-methylpiperidinium-1-yl)-5alpha-androstane
A steroid ester in which a 5alpha-androstane skeleton is C-3alpha- and C-17beta-disubstituted with acetoxy groups and 2beta- and 16beta-disubstituted with 1-methylpiperidinium-1-yl groups. It is a non-depolarizing curare-mimetic muscle relaxant.
Pancuronium
procaine
2-(diethylamino)ethyl 4-aminobenzoate
A benzoate ester, formally the result of esterification of 4-aminobenzoic acid with 2-diethylaminoethanol but formed experimentally by reaction of ethyl 4-aminobenzoate with 2-diethylaminoethanol.
Procaine
ranitidine
(E)-N-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)sulfanyl]ethyl}-N'-methyl-2-nitroethene-1,1-diamine
A member of the class of furans used to treat peptic ulcer disease (PUD) and gastroesophageal reflux disease.
thiopental sodium
An organic sodium salt having thiopental(1-) as the counter-ion.
sodium 5-ethyl-4,6-dioxo-5-(pentan-2-yl)-1,4,5,6-tetrahydropyrimidine-2-thiolate
vecuronium
(2beta,3alpha,5alpha,16beta,17beta)-3,17-diacetoxy-16-(1-methylpiperidinium-1-yl)-2-(piperidin-1-yl)androstane
A 5alpha-androstane compound having 3alpha-acetoxy-, 17beta-acetoxy-, 2beta-piperidino- and 16beta-N-methylpiperidinium substituents.
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
cell
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
cultured cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
cultured cell
experimentally modified cell in vitro
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
experimentally modified cell in vitro
lung combined type small cell adenocarcinoma
A lung combined type small cell carcinoma that has_material_basis_in epithelial tissue of glandular origin.
ovarian serous carcinoma
An ovarian carcinoma that has_material_basis_in the lining of the ovary and produces a serum-like fluid.
ovarian clear cell carcinoma
An ovarian carcinoma that has_material_basis_in cells with clear cytoplasm and glycogen secreting hob nail cells.
clear-cell ovarian carcinoma
colon carcinoma
A colon cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
Colonic carcinoma
carcinoma OF colon
carcinoma of colon
carcinoma of colon (disorder)
cancer
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
malignant neoplasm
malignant tumor
primary cancer
sex cord-gonadal stromal tumor
A reproductive organ cancer that is located_in the sex cord-derived tissues of the ovary and testis.
Sex Cord-Stromal neoplasm
Sex Cord-Stromal tumor
Sex cord stromal tumour
Sex cord-stromal tumor, no ICD-O subtype (morphologic abnormality)
Specialized gonadal neoplasm (morphologic abnormality)
Specialized gonadal neoplasm NOS (morphologic abnormality)
Specialized gonadal tumor (qualifier value)
malignant testicular sex cord-stromal tumor
ovary epithelial cancer
An ovarian cancer that is derives_from ovarian surface epithelium.
Ovarian Surface epithelial-Stromal tumor
epithelial tumor of ovary (disorder)
malignant ovarian germ cell neoplasm
malignant Ovarian germ cell tumor
malignant germ cell tumor of ovary (disorder)
colon adenocarcinoma
A colon carcinoma that derives_from epithelial cells of glandular origin.
Colonic adenocarcinoma
adenocarcinoma of colon
ovarian cancer
A female reproductive organ cancer that is located_in the ovary.
malignant Ovarian tumor
malignant tumour of ovary
ovarian neoplasm
ovary neoplasm
primary ovarian cancer
tumor of the Ovary
granulosa cell tumor
Granulosa cell neoplasm
Granulosa cell tumor, adult type (morphologic abnormality)
Granulosa cell tumour, sarcomatoid
malignant granulosa cell neoplasm
colon mucinous adenocarcinoma
Colonic mucinous adenocarcinoma
colon signet ring adenocarcinoma
Colonic Signet Ring adenocarcinoma
ovarian mucinous cystadenocarcinoma
Ovarian mucinous cystadenocarcinoma
mucinous cystadenocarcinoma of ovary (disorder)
lung carcinoma
A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis.
cancer of lung
lung squamous cell carcinoma
A non-small cell lung carcinoma that has_material_basis_in the squamous cell.
Epidermoid cell carcinoma of the lung
ovary transitional cell carcinoma
malignant ovarian transitional cell neoplasm
ovarian transitional cell cancer
transitional cell carcinoma of Ovary
malignant ovarian Brenner tumor
A malignant ovarian surface epithelial-stromal neoplasm that has_material_basis_in the surface epithelium of the ovary.
renal cell carcinoma
A renal carcinoma that has_material_basis_in the lining of the proximal convoluted renal tubule of the kidney.
RCC
adenocarcinoma of kidney
hypernephroma
renal carcinoma
A kidney cancer that derives_from the lining of the proximal convoluted tubule (the very small tubes in the kidney that filter the blood and remove waste products).
carcinoma of kidney
kidney carcinoma
multilocular clear cell renal cell carcinoma
cystadenocarcinoma of kidney (disorder)
renal cystadenocarcinoma
collecting duct carcinoma
Collecting duct carcinoma is a renal cell carcinoma described as a rare and aggressive type of renal cell carcinoma. The cancerous cells form irregular tubes inside the tumor. Collecting duct carcinoma is more common among young people and unfortunately is diagnosed in most cases when the cancer has metastasized (spread inside the body).
carcinoma of renal Collecting duct
renal Medullary carcinoma
renal carcinoma, collecting duct type
papillary renal cell carcinoma
A renal cell carcinoma that is characterized by the development of multiple, bilateral papillary renal tumors.
Chromophil carcinoma of kidney
Papillary renal cell carcinoma
papillary kidney carcinoma
sporadic papillary renal cell carcinoma
renal clear cell carcinoma
A renal cell carcinoma that has_material_basis_in cells that appear very pale or clear when examined under microscope.
Clear cell carcinoma of kidney (disorder)
clear cell kidney carcinoma
conventional (Clear cell) renal cell carcinoma
conventional renal cell carcinoma
chromophobe renal cell carcinoma
A renal cell carcinoma that has_material_basis_in chromophobe cell that appear pale when viewed under microscope, but that are larger and display different features than clear cells.
Chromophobe carcinoma of kidney
chromophobe adenocarcinoma
kidney chromophobe
renal cell carcinoma, chromophobe cell
mucinous tubular and spindle renal cell carcinoma
bronchiolo-alveolar adenocarcinoma
Alveolar adenocarcinoma (morphologic abnormality)
Bronchioalveolar lung carcinoma
Bronchiolo-alveolar adenocarcinoma (morphologic abnormality)
Bronchioloalveolar adenocarcinoma
Bronchioloalveolar carcinoma (disorder)
colon squamous cell carcinoma
Colonic Epidermoid carcinoma
ovarian squamous cell carcinoma
lung papillary adenocarcinoma
Papillary adenocarcinoma of the lung
adenosquamous colon carcinoma
A colon carcinoma that derives_from squamous cells and gland-like cells.
Colonic Adenosquamous carcinoma
ovarian serous cystadenocarcinoma
An ovary serous adenocarcinoma that has_material_basis_in glandular epithelium, in which cystic accumulations of retained secretions are formed.
serous cystadenoma
endometrioid ovary carcinoma
Ovarian endometrioid carcinoma
endometrioid carcinoma ovary (disorder)
ovarian mucinous neoplasm
Ovarian mucinous tumor
malignant ovarian mucinous neoplasm
mucinous tumor of Ovary
ovarian carcinosarcoma
Ovarian MMMT
ovarian malignant mesodermal (mullerian) mixed tumor
ovarian malignant mixed Mullerian tumor
lung acinar adenocarcinoma
acinar adenocarcinoma of the lung
colon small cell carcinoma
Colonic small cell carcinoma
basaloid lung carcinoma
lung clear cell carcinoma
neuroblastoma
An autonomic nervous system neoplasm that derives_from immature nerve cells.
neuroblastoma (Schwannian Stroma-Poor)
Paraffin
Midazolam
in vitro transcription
Biomolecule synthesis of RNA in vitro used for applications such as can be used in blot hybridizations and nuclease protection assays.
PERSON: Nicole Vasilevsky
http://www.ambion.com/techlib/basics/transcription/index.html
freezer
An instrument that consists of a thermally insulated compartment, cabinet, or room in which a subfreezing temperature is maintained for the rapid freezing and storing of perishable items.
freezer
medical device
A blood pressure monitor is a medical device.
An instrument used in the diagnosis of disease or other conditions or for use in the care, treatment, or prevention of disease that does not achieve any of its primary intended purposes by chemical action or by being metabolized.
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/medical+device
Ashkenazi Jew
A Jewish ethnic group comprised of persons who are descendants of Jews from Germany, Poland, Austria and Eastern Europe.
NCIt:C17950
PERSON:Matthew Brush
Sephardic Jew
A Jewish ethnic group comprised of persons whose ancestors lived in North Africa, the Middle East, Portugal or Spain.
NCIt:C103283
PERSON:Matthew Brush
African
An ethnic group comprised of persons with African ancestral origins who self identify, or are identified, as African.
NCIt:C42331
mixed ethnicity
An ethnic group that includes persons with significant ethnic contributions from more than one group.
PERSON:Matthew Brush
PERSON:Matthew Brush
family relationship
A relationship between persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption
Adapted from PCO_0000020 (family).
PERSON:Matthew Brush
biological family relationship
A family relationship between persons linked through descent from a common ancestor.
PERSON:Matthew Brush
child relationship
A lineal family relationship from a person to their biological parent.
PERSON:Matthew Brush
relationship by marriage
Nordic, Icelandic
PERSON:Matthew Brush
Latino, Carribean
PERSON:Matthew Brush
Latino, South American
PERSON:Matthew Brush
Cortex of left kidney
Left renal cortex
Wall of distal part of ileum
Wall of distal ileum
Anterior wall of vagina
Paries anterior (vagina)
Posterior wall of vagina
Paries posterior (vagina)
Right tibial nerve
Left tibial nerve
Cortex of right frontal lobe
Right frontal lobe cortex
Right leg
Left leg
Skin of right leg
Right leg skin
Skin of left leg
Left leg skin
Left posterior tibial artery
Anatomical location
Spatial association relationship which describes the containment, adjacency and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate.
Right mammary gland
Mucosa of abdominal part of esophagus
Muscularis mucosae of abdominal part of esophagus
Right hemisphere of cerebellum
geographic location
A reference to a place on the Earth, by its name or by its geographical location.
geographic location
subnational entity
1
Amanda Hicks
William R. Hogan
a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority
geopolitical dependency
A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region.
Amanda Hicks
Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. But otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom).
William R. Hogan
geographical entity
http://purl.obolibrary.org/obo/geo.owl
geographical region
http://purl.obolibrary.org/obo/geo.owl
sovereign state
A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states.
Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".
William R. Hogan
http://en.wikipedia.org/wiki/Sovereign_state
nation
nation state
governmental organization
Amanda Hicks
An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii).
Note: this definition was taken over from "geopolitical organization".
IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
biological_process
conditional specification
OBI branch derived
OBI_0000349
PlanAndPlannedProcess Branch
a directive information entity that specifies what should happen if the trigger condition is fulfilled
conditional specification
measurement unit label
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.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Examples of measurement unit labels are liters, inches, weight per volume.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
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?
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
OBI Plan and Planned Process/Roles Branch
OBI_0000217
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
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.
goal specification
objective specification
action specification
Alan Ruttenberg
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
action specification
datum label
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.
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
datum label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
data item
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.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
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.
Data items include counts of things, analyte concentrations, and statistical summaries.
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
a data item is 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.
data
data item
symbol
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://code.google.com/p/information-artifact-ontology/issues/detail?id=154).
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
PERSON: James A. Overton
PERSON: Jonathan Rees
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
based on Oxford English Dictionary
symbol
numeral
A symbol that denotes a number.
PERSON: Jonathan Rees
numeral
information content entity
information content entity
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).
A generically dependent continuant that is about some thing.
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
OBI_0000142
PERSON: Chris Stoeckert
information content entity
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.
scalar measurement datum
1
1
10 feet. 3 ml.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
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.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
scalar measurement datum
directive information entity
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
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
algorithm
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.
OBI_0000270
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
PERSON:Bill Bug
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.
curation status specification
data set
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.
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.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
OBI_0000042
data set
group:OBI
person:Allyson Lister
person:Chris Stoeckert
data about an ontology part
Person:Alan Ruttenberg
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
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
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.
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.
Alan Ruttenberg
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI Plan and Planned Process branch
OBI_0000344
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
plan specification
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
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,}.
OBI_0000305
group:OBI
measurement datum
person:Chris Stoeckert
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.
GROUP: IAO
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
version number
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
GROUP: IAO
batch number
lot number
setting datum
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.
A settings datum is a datum that denotes some configuration of an instrument.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
setting datum
material information bearer
A material entity in which a concretization of an information content entity inheres.
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.
GROUP: IAO
a brain
a hard drive
material information bearer
obsolescence reason specification
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
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.
obsolescence reason specification
textual entity
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
textual entity
document title
A textual entity that names a document
PERSON: Lawrence Hunter
Textual characteristics of traditional and Open Access scientific journals are similar
document title
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
PERSON: Lawrence Hunter
document
running title
A shorter version of a document title
PERSON: Lawrence Hunter
running title
length measurement datum
A scalar measurement datum that is the result of measurement of length quality
Alan Ruttenberg
length measurement datum
denotator type
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
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.
denotator type
mass measurement datum
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A scalar measurement datum that is the result of measurement of mass quality
Person:Alan Ruttenberg
mass measurement datum
time measurement datum
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A scalar measurement datum that is the result of measuring a temporal interval
Person:Alan Ruttenberg
time measurement datum
postal address
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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=59
postal address
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
Person:Alan Ruttenberg
Person:Chris Stoeckart
email address
documenting
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
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.
documenting
wikipedia http://en.wikipedia.org/wiki/Documenting
centrally registered identifier symbol
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
CRID symbol
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
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.
centrally registered identifier symbol
centrally registered identifier
CRID
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.
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
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.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
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.
centrally registered identifier
centrally registered identifier registry
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.
CRID registry
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
centrally registered identifier registry
time stamped measurement datum
time stamped measurement datum
identifier
proper name
A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
Mathias Brochhausen
dubbing process
Mathias Brochhausen
A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
Mathias Brochhausen
personal name
A personal name is a proper name identifying an individual person.
Mathias Brochhausen
Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
http://en.wikipedia.org/wiki/Personal_name
identity document
Amanda Hicks
a document that denotes some identity and is concretized by the bearer of some credential role
documented identity
Amanda Hicks
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?
authentication
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.
Amanda Hicks
Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
credential role
a role that inheres in a concretization of an identity document and is realized by an authentication process
Amanda Hicks
social act
Mathias Brochhausen
A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived.
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
MB: Regarding the use of the term 'sponteneous' in the definition:
The term is used in the following meaning of being self generated. It does not stand in contrast to being planned.
informed consent form
A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject.
NCIt C16468
AK, FM, YH, YL, MH, EE
completely filled informed consent form
an informed consent form that has been filled with all required contents.
YH
partially filled informed consent form
an informed consent form that has been partically filled with required contents.
YH
eligibility of candidate participation
A realizable entity that represents the eligibility of a candidate according to a study protocol.
Frank Manion, Oliver He
candidate eligible for study
the participant meets all eligibility criteria defined within the study protocol
NCI BBRB: Biorepositories and Biospecimen Research Branch
candidate ineligible for study
NCI BBRB: Biorepositories and Biospecimen Research Branch
the participant does not meet all eligibility criteria defined within the study protocol
immunosuppressive disposition
Lindsay Cowell
Alexander Diehl
Albert Goldfain
A disposition whose realization negatively regulates an immune response.
Viruses
Viruses
Euteleostomi
Euteleostomi
bony vertebrates
Bacteria
Bacteria
eubacteria
Archaea
Archaea
Eukaryota
Eukaryota
eucaryotes
eukaryotes
Euarchontoglires
Euarchontoglires
Tetrapoda
Tetrapoda
tetrapods
Amniota
Amniota
amniotes
Opisthokonta
Opisthokonta
Bilateria
Bilateria
Mammalia
Mammalia
mammals
Vertebrata <Metazoa>
Vertebrata
Vertebrata <Metazoa>
vertebrates
Homo sapiens
Homo sapiens
Homo sapiens
human
human being
man
Homo sapiens
colectomy
YH, SS
A surgery that is a surgical procedure to remove all or part of your colon.
WEB: http://www.mayoclinic.com/health/colectomy/MY00141/METHOD=print
biobank description in english
A textual entity providing information about a biobank and that is written in English.
Mathias Brochhausen
biobank description
sample collection identifier
A proper name that refers to a sample collection.
Mathias Brochhausen
freezer shelf
A device that is part of a freezer and consists of a solid horizontal surface to keep material in the freezer on a flat surface.
Person: Jie Zheng, Chris Stoeckert
Penn Group
discarding
A planned process that gets rid of a material that is no longer useful or desirable.
Penn Group
Person: Jie Zheng, Chris Stoeckert
human subject recuiter role
A worker role of recruiting human subjects to partcipate in a clinical investigation in which data about human subject is collected.
Person: Jie Zheng, Chris Stoeckert
Penn Group
cryovial box
A device that is intended to hold cryovials.
Person: Jie Zheng, Chris Stoeckert
Penn Group
trash container
A container that is used for discarded material.
Person: Jie Zheng, Chris Stoeckert
Penn Group
freezer rack
A device that is part of a freezer for keeping material in the freezer in a defined position and prevents movement.
Person: Jie Zheng, Chris Stoeckert
Penn Group
blood spot card box
A device that is designed to contain blood spot cards.
Person: Jie Zheng, Chris Stoeckert
Penn Group
data confirm questionnaire
A questionnaire that comprises a set of questions about patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by a recruiter based on an Electronic Medical Record (EMR).
Person: Jie Zheng, Chris Stoeckert
Penn Group
form filling
A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare.
Penn Group
Person: Jie Zheng, Chris Stoeckert
filled patient questionnaire
A patient questionnaire which has been filled out by a patient.
Person: Jie Zheng, Chris Stoeckert
Penn Group
patient questionnaire
A questionnaire that comprises a set of questions about a patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by the human subject.
Person: Jie Zheng, Chris Stoeckert
Penn Group
collection packet with specimen and information material
A collection packet which contains a container with a specimen and a form filled with information about the collected specimen and specimen source.
Person: Jie Zheng, Chris Stoeckert
Penn Group
blood additive role
A material to be added role that is born by a chemical entity which is added into a blood collection containter to optimize specific blood component(s) preservation and/or separation.
Penn Group
Person: Jie Zheng, Chris Stoeckert
lab technician role
A worker role that performs the practical hands-on work in laboratories and is realized during study design execution.
Penn Group
Person: Jie Zheng, Chris Stoeckert
collection packet with specimen
A collection packet which contains a container with a specimen.
Penn Group
Person: Jie Zheng, Chris Stoeckert
collection packet with empty container
A collection packet which contains an empty container that will be used for holding a specimen.
Person: Jie Zheng, Chris Stoeckert
Penn Group
medication role
Person: Chris Stoeckert, Jie Zheng
Penn Group
A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
filled data confirm questionnaire
A data confirm questionnaire which has been filled out by a human subject recruiter.
Person: Jie Zheng, Chris Stoeckert
Penn Group
collection packet
A material entity used for specimen collection. It can contain a container to hold a specimen and material (e.g. paper) carrying information about the specimen and the specimen source (e.g. patient).
Penn Group
Person: Jie Zheng, Chris Stoeckert
medication material
Penn Group
Person: Chris Stoeckert, Jie Zheng
A material entity that is bearer of a medication role.
blood spot card
A device that is designed to collect, ship and store blood specimens in an easy and inexpensive way.
Penn Group
Person: Jie Zheng, Chris Stoeckert
cryovial
A test tube that designed to store materials at very low temperatures.
Person: Jie Zheng, Chris Stoeckert
Penn Group
vacutainer
A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Vacutainer
specimen receiving
A planned process for receiving specimens such as into a laboratory.
Person: Jie Zheng, Chris Stoeckert
Penn Group
adding specimen into a container
An adding a material entity into a target process where a collected specimen is added to a specimen container. (note, not used for other specimen process that produce new specimens)
Person: Jie Zheng, Chris Stoeckert
Penn Group
blood spotting
An adding specimen into a container process that spots the blood from an organism on the blood spot card.
Person: Jie Zheng, Chris Stoeckert
Penn Group
buffy coat specimen
A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets.
http://en.wikipedia.org/wiki/Buffy_coat
Person: Jie Zheng, Chris Stoeckert
blood specimen on blood spot card
A blood specimen that is located on a blood spot card.
Person: Jie Zheng, Chris Stoeckert
Penn Group
A specimen that located in a blood spot card via blood spotting process.
collection packet with empty container and unfilled information material
A collection packet which contains a container without a specimen and an unfilled form that will be used to fill in information about specimen to be collected.
Person: Jie Zheng, Chris Stoeckert
Penn Group
duration time of smoking regularly
A duration time of smoking about how long a person has been smoking regularly. (better to have criteria of regularly mean, such as smoke everyday)
Person: Jie Zheng, Chris Stoeckert
Penn Group
average daily use of cigarette datum
An average value of use of cigarettes per day.
Person: Jie Zheng, Chris Stoeckert
Penn Group
nicotine patch
A processed material that contains nicotine in the form of a transdermal patch which releases nicotine into the body through the skin. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Nicotine_patch
cigarette
A processed material which is a small cylinder of finely cut tobacco leaves rolled in thin paper for smoking.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Cigarette
nicotine gum or lozenge
A processed material contains nicotine in a form of a chewing gum or a candy-like tablet. It delivers nicotine to the body via absorption by the tissues of the mouth. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Nicotine_gum
cigar
A processed material which is a tightly-rolled bundle of dried and fermented tobacco that is ignited so that its smoke may be drawn into the mouth.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Cigar
chewing tobacco
A processed material which is a kind of smokeless tobacco product consumed by placing a portion of the tobacco between the cheek and gum or upper lip teeth and chewing.
http://en.wikipedia.org/wiki/Chewing_tobacco
Person: Jie Zheng, Chris Stoeckert
nicotine material
A processed material that contains nicotine.
Person: Jie Zheng, Chris Stoeckert
Penn Group
nicotine product
smoking pipe
A device made to allow the user to inhale or taste smoke or vapor derived from the burning or vaporization of some substance.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Smoking_pipe
nicotine e-cigarette
A processed material that vaporizes a liquid solution containing nicotine and simulates tobacco smoking by producing an aerosol that resembles smoke.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Electronic_cigarette
smoking start date
A time measurement datum which is the start date of a smoking behavior.
Penn Group
Person: Jie Zheng, Chris Stoeckert
pipe smoking behavior
A smoking behavior that uses a smoking pipe to inhale or taste tobacco material.
Penn Group
Person: Jie Zheng, Chris Stoeckert
duration time of smoking
A time measurement datum about how long a person has been smoking.
Person: Jie Zheng, Chris Stoeckert
Penn Group
smoking end date
A time measurement datum which is the end date of a smoking behavior.
Penn Group
Person: Jie Zheng, Chris Stoeckert
pipe tobacco
A processed material which is made from tobacco for smoking tobacco using a pipe.
Person: Jie Zheng, Chris Stoeckert
Penn Group
tobacco
A Eukaryota that is within the genus Nicotiana of the Solanaceae (nightshade) family.
Penn Group
Person: Jie Zheng, Chris Stoeckert
tobacco material
A processed material that is made from tobacco. Typically, tobacco material is meant to be used as a source of nicotine as tobacco contains a higher concentration of nicotine than most other plants.
Person: Jie Zheng, Chris Stoeckert
Penn Group
tobacco product
planned process
planned process
'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.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Bjoern Peters
Injecting mice with a vaccine in order to test its efficacy
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.
branch derived
A processual entity that realizes a plan which is the concretization of a plan specification.
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)
planned process
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.
PERSON: Alan Ruttenberg
processed material
investigation
Could add specific objective specification
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
study
Bjoern Peters
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
OBI branch derived
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
evaluant role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
GROUP: Role Branch
OBI
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
evaluant role
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
any method
study assay
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
OBI branch derived
PlanAndPlannedProcess Branch
assay
measuring
scientific observation
culture medium
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.
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
OBI
Person: Jennifer Fostel, Jie Zheng
culture medium
reagent role
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.
PERSON:Matthew Brush
reagent
(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).
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.
Buffer, dye, a catalyst, a solvating agent.
PERSON:Matthew Brush
reagent role
patient role
patient
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
GROUP:Role Branch
OBI, CDISC
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
patient role
material processing
A cell lysis, production of a cloning vector, creating a buffer.
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
A planned process which results in physical changes in a specified input material
OBI branch derived
PERSON: Bjoern Peters
material processing
material transformation
participant under investigation role
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.
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.
OBI
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.
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
GROUP: Role Branch
participant under investigation role
responsible party role
responsible party
OBI
Person: Jennifer Fostel
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
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
responsible party role
principal investigator role
principal investigator
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)
Person: Jennifer Fostel
a responsible party role played by a person responsible for the overall conduct of a study
principal investigator role
specimen role
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.
GROUP: Role Branch
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.
OBI
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
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
worker role
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker
OBI
Person:Jennifer Fostel
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
worker role
filter paper
Frank Gibson
a device manufacture with the intent to provide a porous unsized paper used for filtering.
filter paper
sep:00107
population
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
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
adapted from Oxford English Dictionnary
population
rem1: collection somehow always involve a selection process
investigation agent role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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.
investigation agent role
investigator
study person role
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.
GROUP: Role Branch
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
OBI
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
organization
GROUP: OBI
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
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.
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.
organization
plan
The plan of researcher X to perform an experiment according to a protocol.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
AR, BP, JM, MC, PRS
branch derived
plan
protocol
study protocol
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)
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.
PlanAndPlannedProcess Branch
protocol
adding a material entity into a target
BP
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
branch derived
adding a material entity into a target
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'.
material to be added role
9 March 09 from discussion with PA branch
OBI
Role Branch
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
drawing a conclusion based on data
Bjoern Peters
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.
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
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
planning
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'.
Bjoern Peters
Bjoern Peters
Plans and Planned Processes Branch
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
planning
contain function
A syringe, a beaker
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A contain function is a function to constrain a material entities location in space
contain function
heat function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A heat function is a function that increases the internal kinetic energy of a material
heat function
material separation function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
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.
material separation function
filter function
Frank Gibson
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
filter function
mechanical function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
http://en.wikipedia.org/wiki/Mechanical_work
mechanical function
cool function
Daniel Schober
Frank Gibson
Melanie Courtot
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
cool function
solid support function
Daniel Schober
Frank Gibson
Melanie Courtot
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
environment control function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
environment control function
averaging objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
averaging objective
adding material objective
BP
creating a mouse infected with LCM virus
adding material objective
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
assay objective
PPPB branch
PPPB branch
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
target of material addition role
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.
GROUP: Role Branch
OBI
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
target of material addition role
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
PERSON: Daniel Schober
PERSON: Helen Parkinson
PERSON: Melanie Courtot
PERSON:Frank Gibson
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.
measure function
material transformation objective
GROUP: OBI PlanAndPlannedProcess Branch
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
manufacturing
GROUP: OBI PlanAndPlannedProcess Branch
Manufacturing implies reproducibility and responsibility AR
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
This includes a single scientist making a processed material for personal use.
manufacturing
manufacturing objective
GROUP: OBI PlanAndPlannedProcess Branch
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
is the objective to manufacture a material of a certain function (device)
manufacturing objective
study design execution
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.
a planned process that carries out a study design
a planned process that realizes the concretization of a study design
branch derived
injecting a mouse with PBS solution, weighing it, and recording the weight according to 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.
study design execution
manufacturer role
GROUP: Role Branch
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
OBI
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
manufacturer role
material separation objective
PPPB branch
PPPB branch
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.
material separation objective
material combination
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
bp
bp
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
material combination
blood specimen
Bjoern Peters
Bjoern Peters
a material entity derived from a portion of blood collected from an organism
blood drawn from a human for glucose assay
blood specimen
specimen collection process
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
A planned process with the objective of collecting a specimen.
Bjoern Peters
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.
specimen collection process
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
specimen collection
label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
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.
portioning objective
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
The objective to obtain multiple aliquots of an enzyme preparation.
portioning objective
average value
PERSON: James Malone
PERSON: Monnie McGee
arithmetic mean
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
average value
separation into different composition objective
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).
The objective to obtain cells contained in a sample of blood.
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
separation into different composition objective
specimen collection objective
A objective specification to obtain a material entity for potential use as an input during an investigation.
Bjoern Peters
Bjoern Peters
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
specimen collection objective
material combination objective
PPPB branch
bp
is an objective to obtain an output material that contains several input materials.
material combination objective
material maintenance objective
An objective specification maintains some or all of the qualities of a material over time.
PERSON: Bjoern Peters
material maintenance objective
PERSON: Bjoern Peters
informed consent process
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.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
Person:Alan Ruttenberg
http://clinicaltrials.gov/ct2/info/glossary#informed
informed consent process
measurement device
A device in which a measure function inheres.
A ruler, a microarray scanner, a Geiger counter.
GROUP:OBI Philly workshop
OBI
measurement device
manufacturer
A person or organization that has a manufacturer role
manufacturer
test tube
A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
Bjoern Peters
collection tube
http://en.wikipedia.org/wiki/Test_tube
sample tube
test tube
material maintenance
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance
record of missing knowledge
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
Bjoern Peters
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
a information content entity created to indicate that information about something is not available to the person recording it.
record of missing knowledge
freezing storage
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.
A storage process in temperature that maintenance the frozen status of the stored entities.
OBI
Person: Alan Ruttenberg, Mathias Brochhausen
a fozen pellet used for later assay
freezing storage
MO_481 frozen_storage
frozen specimen
A specimen that has been frozen in order to store it.
Frozen blood plasma
MO_610 frozen_sample
Person:Alan Ruttenberg
frozen specimen
lyophilization storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
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
lyophilization storage
material separation device
A device with a separation function realized in a planed process
flow cytometer
material separation device
paraffin specimen
MO_990 paraffin_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
liver tissue embedded in paraffin
paraffin specimen
processed specimen
A specimen that has been intentionally physically modified.
Bjoern Peters
Bjoern Peters
processed specimen
A tissue sample that has been sliced and stained for a histology study.
A tissue sample that has been sliced and stained for a histology study.
A blood specimen that has been centrifuged to obtain the white blood cells.
reagent application function
4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people?
A function that is realized when a reagent is automatically added to some research material.
An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
PERSON: Nicole Vasilevsky, Matthew Brush
PERSON: Nicole Vasilevsky, Matthew Brush
reagent application function
lyophilized specimen
MO_589 freeze_dried_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
freezing dried DNA
lyophilized specimen
container
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A device that can be used to restrict the location of material entities over time
PERSON: Bjoern Peters
container
device
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 material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
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.
OBI development call 2012-12-17.
PERSON: Helen Parkinson
device
instrument
fresh specimen
MO_730 fresh_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a liver freshly removed from a rat
a specimen that is output of a specimen creation process used for an investigation without storage.
fresh specimen
paraffin storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
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
paraffin storage
agar stab specimen
MO_971 agar_stab
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a process that cell culture inoculated into agar for long term storage.
agar stab specimen
questionnaire
Need to clarify if this is a document or a directive information entity (or what their connection is))
questionnaire
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.
Merriam-Webster
PERSON: Jessica Turner
agar stab storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
a storage process with input cell culture and agar and output agar stab for long time storage
agar stab storage
need to specify that agar is one of input for this process
environmental control device
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
Helen Parkinson
OBI
environmental control device
automatic tissue processor
A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
PERSON: Erik Segerdell
United States Patent 3762362
automatic tissue processor
age since planting measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call.
Term proposed by Bjoern on Nov 8, 2010 dev call
Supported by Alan on Nov 15, 2010 dev call
MO_495 planting
PERSON:Chris Stoeckert, Jie Zheng
age since planting measurement datum
age since hatching measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
MO_745 hatching
PERSON:Chris Stoeckert, Jie Zheng
age since hatching measurement datum
age measurement assay
An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
OBI group
PERSON: Alan Ruttenberg
This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
age measurement assay
age since egg laying measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
MO_767 egg laying
PERSON:Chris Stoeckert, Jie Zheng
age since egg laying measurement datum
age since germination measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
MO_590 germination
PERSON:Chris Stoeckert, Jie Zheng
age since germination measurement datum
age since eclosion measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
MO_876 eclosion
PERSON:Chris Stoeckert, Jie Zheng
age since eclosion measurement datum
age since sowing measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
MO_748 sowing
PERSON:Chris Stoeckert, Jie Zheng
age since sowing measurement datum
age since coitus measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
MO_783 coitus
PERSON:Chris Stoeckert, Jie Zheng
age since coitus measurement datum
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
In MageTab file, we use
initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.)
Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
MO_178 Age
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
discussed on Nov 15, dev call
All subtype will be defined by textual definition now.
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet.
life of bearer doesn't imply organism
this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature
age as a quality is dubious; we plan to revisit
stages in development are currently handled with controlled vocabulary, such as 2-somite stage
age measurement datum
age since fertilization measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
Definition of fertilization comes from GO.
MO_701 fertilization
PERSON:Chris Stoeckert, Jie Zheng
age since fertilization measurement datum
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
MO_710 birth
PERSON:Chris Stoeckert, Jie Zheng
age since birth measurement datum
genetic characteristics information
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)
MO_66 IndividualGeneticCharacteristics
Person: Chris Stoeckert, Jie Zheng
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
genetic characteristics information
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
MO_95 BiosourceType
PERSON: Chris Stoeckert, Jie Zheng
specimen with known storage state
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
MO_954 organism_part
PERSON: Chris Stoeckert, Jie Zheng
specimen from organism
tissue specimen
specimen collection time measurement datum
NIAID GSCID-BRC
Specimen Collection Date
A time measurement datum that is the measure of the time when the specimens are collected.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
collection date
specimen collection time measurement datum
selection criterion
A directive information entity which defines and states a principle of standard by which selection process may take place.
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
Person: Philippe Rocca-Serra
rats should be aged between 6 and 8 weeks and weight between 180-250grams
selection criterion
selection rule
conclusion based on data
Group:2013 Philly Workshop group
An information content entity that is inferred from data.
Group:2013 Philly Workshop group
conclusion based on 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.
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".
cell freezing medium
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.
PERSON: Matthew Brush
cell freezing medium
selection
A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
OBI
PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
Person: Philippe Rocca-Serra
selection
selection process
this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
categorical value specification
PERSON:Bjoern Peters
categorical value specification
A value specification that is specifies one category out of a fixed number of nominal categories
scalar value specification
1
1
scalar value specification
A value specification that consists of two parts: a numeral and a unit label
PERSON:Bjoern Peters
value specification
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.
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
value specification
PERSON:Bjoern Peters
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
molecular-labeled material
PERSON:Matthew Brush
OBI developer call, 3-12-12
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
molecular-labeled material
collection of specimens
Biobank
OBIB, OBI
A material entity that has two or more specimens as its parts.
Blood cells collected from multiple donors over the course of a study.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
collection of specimens
specimens derived from shared ancestor
A collection of specimens derived from one common specimen via one or more material processing process(es).
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Biobank
Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy.
Chris Stoeckert, Jie Zheng
Duke Biobank, OBIB, OBI
specimen family
specimens derived from shared ancestor
containing a specimen function
Duke Biobank, OBIB
A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay.
Biobank
Chris Stoeckert
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
containing a specimen function
specimen container
A container with the function of containing a specimen.
Biobank
COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
Chris Stoeckert
Duke Biobank, OBIB
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
Specimen containers are typically constructed or treated in a particular manner in order to perform their containing a specimen function. This will be a defined class so that any container (e.g., cryotube, vacutainer, conical test tube) with the function of containing a specimen will be inferred to be a specimen container.
specimen container
physical store
A container with an environmental control function.
Biobank
Chris Stoeckert
Duke Biobank, OBIB
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
a freezer. a humidity controlled box.
physical store
specimen family creation
Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum.
Biobank
For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Mathias Brochhausen, Chris Stoeckert, Jie Zheng
OBI, OBIB
specimen family creation
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
IHC slide staining
http://www.agilent.com/cs/library/technicaloverviews/public/08002_ihc_staining_methods.pdf
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.
Chris Stoeckert, Ned Haubein
H&E slide staining
http://www.histalim.com/accueil/activities/our-services/histology/hematoxylin-eosin-2/
H&E-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of H&E slide staining.
Chris Stoeckert, Ned Haubein
H&E-stained fixed tissue slide specimen
OBIB, OBI
IHC-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
Chris Stoeckert, Ned Haubein
IHC-stained fixed tissue slide specimen
OBIB, OBI
immunohistochemistry slide specimen
amniotic fluid specimen
A specimen that is derived from amniotic fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
amniotic fluid specimen
bile specimen
A specimen that is derived from bile.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
bile specimen
cerebrospinal fluid specimen
A specimen that is derived from cerbrospinal fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
cerebrospinal fluid specimen
feces specimen
A specimen that is derived from feces.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
feces specimen
stool specimen
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
digestive system fluid or secretion specimen
gastric fluid specimen
milk specimen
A specimen that is derived from milk.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
milk specimen
pericardial fluid specimen
A specimen that is derived from pericardial fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
pericardial fluid specimen
saliva specimen
A specimen that is derived from saliva.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
saliva specimen
sputum specimen
A specimen that is derived from sputum.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
sputum specimen
sweat specimen
A specimen that is derived from sweat.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
sweat specimen
synovial fluid specimen
A specimen that is derived from synovial fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
synovial fluid specimen
vitreous humor specimen
A specimen that is derived from vireous humor.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
vitreous fluid specimen
vitreous humor specimen
bone marrow specimen
A specimen that is derived from bone marrow.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
bone marrow specimen
placenta specimen
A specimen that is derived from placenta.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
placenta specimen
peritoneal fluid specimen
A specimen that is derived from peritoneal fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
peritoneal fluid specimen
pleural fluid specimen
A specimen that is derived from pleural fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
pleural fluid specimen
brain specimen
A specimen that is derived from brain.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
brain specimen
hair specimen
A specimen that is derived from hair.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
hair specimen
prostate gland specimen
A specimen that is derived from prostate gland.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
prostate gland specimen
skeletal muscle tissue specimen
A specimen that is derived from skeletal muscle.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
skeletal muscle tissue specimen
heart specimen
A specimen that is derived from heart.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
heart specimen
renal medulla specimen
A specimen that is derived from renal medulla.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
kidney medulla specimen
renal medulla specimen
adrenal gland specimen
A specimen that is derived from adrenal gland.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
adrenal gland specimen
breast specimen
A specimen that is derived from breast.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
breast specimen
mammary tissue specimen
urinary bladder specimen
A specimen that is derived from urinary bladder.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
urinary bladder specimen
tibial artery specimen
A specimen that is derived from tibial artery.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
tibial artery specimen
skin of body specimen
A specimen that is derived from skin.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
skin of body specimen
skin specimen
pancreas specimen
A specimen that is derived from pancreas.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
pancreas specimen
stomach specimen
A specimen that is derived from stomach.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
stomach specimen
pituitary gland specimen
A specimen that is derived from pituitary gland.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
pituitary gland specimen
adipose tissue specimen
A specimen that is derived from adipose tissue.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
adipose tissue specimen
cortex of kidney specimen
A specimen that is derived from cortex of kidney.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
cortex of kidney specimen
kidney cortex specimen
esophagus mucosa specimen
A specimen that is derived from esophagus mucosa.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
esophagus mucosa specimen
colon specimen
A specimen that is derived from colon.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
colon specimen
lung specimen
A specimen that is derived from lung.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
lung specimen
esophagus muscularis mucosa specimen
A specimen that is derived from esophagus muscularis mucosa.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
esophagus muscularis mucosa specimen
esophagus muscularis specimen
cerebral cortex specimen
A specimen that is derived from cerebral cortex.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
brain cortex specimen
cerebral cortex specimen
thyroid gland specimen
A specimen that is derived from thyroid gland.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
thyroid gland specimen
cerebellum specimen
A specimen that is derived from cerebellum.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
brain cerebellum specimen
cerebellum specimen
tibial nerve specimen
A specimen that is derived from tibial nerve.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
tibial nerve specimen
coronary artery specimen
A specimen that is derived from coronary artery.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
coronary artery specimen
spleen specimen
A specimen that is derived from spleen.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
spleen specimen
aorta specimen
A specimen that is derived from aorta.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
aorta specimen
blood plasma specimen
PERSON: Philippe Rocca-Serra
03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
PERSON: Maura Gasparetto
PERSON: Melanie Courtot
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.
WEB: http://en.wikipedia.org/wiki/Blood_plasma
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
blood plasma specimen
plasma
blood serum specimen
PERSON: Philippe Rocca-Serra
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
PERSON: Maura Gasparetto
PERSON: Melanie Courtot
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.
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood serum specimen
organism
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.
GROUP: OBI Biomaterial Branch
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.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
organism
plant
virus
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
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.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
specimen
cultured cell population
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
PERSON:Matthew Brush
PERSON:Matthew Brush
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.
cultured cell population
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.
cell culture sample
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).
data transformation
Philippe Rocca-Serra
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Branch editors
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
data transformation
data transformation objective
Modified definition in 2013 Philly OBI workshop
An objective specification to transformation input data into output data
James Malone
PERSON: James Malone
data transformation objective
normalize objective
averaging data transformation
James Malone
An averaging data transformation is a data transformation that has objective averaging.
PERSON: James Malone
averaging data transformation
pool of specimens
GROUP: CEBS
PERSON: Jennifer Fostel
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
pool of specimens
edited document
A document which is the output of a document editing process
Person:Bjoern Peters
Philippe Rocca-Serra
The OBI manuscript is (much) edited imformation
edited document
filtration
OBI-Branch: adapted from wikipedia and wordnet
Philippe Rocca-Serra
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
centrifugation
Philippe Rocca-Serra
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
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
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
staining
Philippe Rocca-Serra
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
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.
staining
storage
OBI-Branch
Philippe Rocca-Serra
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
storage
document editing
Philippe Rocca-Serra and OBI consortium
adapted from wikipedia
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL.
Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
document editing
is a planned process with specified input original document and specified output edited document
digital curation
Philippe Rocca-Serra
wikipedia
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
digital curation
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
Person: Jennifer Fostel
Melanie Courtot
Trish Whetzel
centrifuge
http://en.wikipedia.org/wiki/Centrifuge
microtome
PERSON: Daniel Schober
PERSON: Phillippe Rocca-Serra
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.
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
microtome
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.
PERSON: Chris Stoeckert
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.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
study design
eligibility criterion
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
Person: Philippe Rocca-Serra
an eligibility criterion (rule) is_a selection criterion which
defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
eligibility criterion
eligibility rule
inclusion criteria
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
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) .
Person: Philippe Rocca-Serra
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 criteria
inclusion rule
exclusion criterion
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
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.
Person: Philippe Rocca-Serra
an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
exclusion criterion
human subject enrollment
As with group assignment, should the specified output here be an organism which bears a role
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
Bjoern Peters
IEDB
criteria come from plan / clinical trial branch
enlisting familiy members of HIV patients into a study
human subject enrollment
collecting specimen from organism
IEDB
PERSON:Bjoern Peters
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
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
material component separation
Bjoern Peters
IEDB
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
material component separation
pooling specimens
2
OBI branch derived
PlanAndPlannedProcess Branch
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
physical combination of several instances of like material
pooling specimens
sample pooling
material portioning
OBI branch derived
PERSON:Bjoern Peters
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
aliquoting
apportioning
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
maintaining cell culture
OBI branch derived
PlanAndPlannedProcess Branch
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
maintaining cell culture
establishing cell culture
PERSON:Matthew Brush
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).
establishing cell culture
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.
PERSON:Matthew Brush
addition of molecular label
labeling
OBI developer call, 3-12-12
PERSON:Matthew Brush
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
addition of molecular label
dialysis
OBI branch derived
PERSON:Kevin Clancy
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
donor
A T cell line from a PPD(+) donor.
Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
donor role
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
IEDB
IEDB
donor
target of material addition
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
A cell culture into which a mixture of peptides is being added.
A material entity into which another is being added in a material combinatino process
IEDB
target of material addition
clinical history
A series of statements representing health-relevant qualities of a patient and of a patient's family.
clinical history
phenotype
phenotype
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
disease
Albert Goldfain
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
disorder
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
Albert Goldfain
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
diagnosis
Albert Goldfain
The representation of a conclusion of a diagnostic process.
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
treatment
http://code.google.com/p/ogms/issues/detail?id=35
Albert Goldfain
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
health care encounter
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
diagnostic process
An interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these.
http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
Albert Goldfain
biobank
Mathias Brochhausen
A biobank is a collections of samples of biological substances
(e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data.
definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
human biobank
Deutscher Ethikrat: Human biobanks for research. Opinion. Berlin, 2010. http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
A human biobank is a collections of samples of human body substances
(e.g. Tissue, blood, DNA) which are linked to personal data and socio
deographic information about the donors of the material. They have a dual
nature as collections of samples and data."
settlement part of address of sample collection or study contact
Mathias Brochhausen
Sample Collection/Study contact city
The part of a sample collection or study contact's adress denoting a settlement.
biobank proper name
Mathias Brochhausen
An identifier in natural language referring to a biobank.
Name of biobank
ISO 3166-1 alpha-2 code
An identifier that consists of two letters, is part of the ISO 3166-1, and designates countries, dependent territories, and special areas of geographical interest.
Mathias Brochhausen
Two-letter country codes defined in ISO 3166-1, part of the ISO 3166 standard published by the International Organization for Standardization (ISO), to designate countries, dependent territories, and special areas of geographical interest.
http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2
biobank idenfier with ISO 3166-1 alpha-2 code
A biobank identifier that has an ISO 3166-1 alpha-2 code as a part.
Biobank ID
Mathias Brochhausen
Textual string of letters starting with the country code (according to standard ISO1366 alpha2) followed by the underscore “_” and post-fixed by a biobank ID or name specified by its juristic person (nationally specific).
obsolete_sample collection or study identifier
true
Mathias Brochhausen
A sample collection or study proper name that is centrally registered and unique within one framework.
Sample Collection/Study ID
ISO 3166-1 alpha-2 code for sample collection or study contact
Mathias Brochhausen
Sample Collection/Study contact country
The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address.
biobank organization
An organization bearing legal personality that ownes or adminstrates a biobank.
An organization bearing legal personality that ownes or adminstrates a biobank.
Mathias Brochhausen
biobank juristic person
contacting
Contacting is the process of one human being starting a communication process with another human being. Contacting can be done using all modes of communication used by humans.
Mathias Brochhausen
A planned process that involves a human being and is intended to initiate a communication with another human being.
contact role
A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process.
Mathias Brochhausen
biobank contact person
A human being that is member of a biobank organization and bears the organization contact role.
Mathias Brochhausen
name of biobank contact person
A personal name that designates the person acting as contact for a sample collection or a study.
Biobank contact person
Mathias Brochhausen
email address of biobank contact person
An email address for the purpose of contacting a biobank contact person.
Biobank contact email
Mathias Brochhausen
postal address of biobank contact person
Mathias Brochhausen
Postal address used as a directive for deliveries to the biobank contact person.
department
An organization with a specific responsibility that is a part of a larger organization with a specific responsibility.
http://en.wikipedia.org/wiki/Department
department of biobank contact
A department that has a contact person for a biobank as an organizational member.
Mathias Brochhausen
Biobank contact department
unique resource locator
http://en.wikipedia.org/wiki/Uniform_resource_locator
A CRID that constitutes a reference to an Internet resource.
Mathias Brochhausen
uri
biobank's unique resource locator
Mathias Brochhausen
A unique resource locator referring to the homepage of a biobank.
Biobank URL
telephone number
Mathias Brochhausen
A telephone number is a textual entity consisting of a sequence of digits used to call from one telephone line to another in a public switched telephone network.
MB: This class should probably be a subclass to CRID. However, the textual definition of CRID right now states that each instance has the CRID identifier as a part. This is not the case for telephone numbers. Therefore, they cannot be subsumed under CRID now. I am looking into changing IAO accordingly. Once that is done, the class ought to be a subclass of CRID.
http://en.wikipedia.org/wiki/Telephone_number
telephone number of biobank contact
A telephone number that is contact information about a biobank contact person.
Biobank contact phone
Mathias Brochhausen
post-office box number
Mathias Brochhausen
A centrally registered identifier denoting a post-office box.
post-office box
Mathias Brochhausen
http://en.wikipedia.org/wiki/Post-office_box
A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable.
telephone number of sample collection or study contact
A telephone number that is contact information about a sample collection or study contact person.
Mathias Brochhausen
Sample Collection/Study contact phone
postal code
Mathias Brochhausen
A postal code is a textual entity that is a series of letters and/or digits and is part of a postal address for the purpose of sorting mail.
MB: This class should probably be a subclass to CRID. However, the textual definition of CRID right now states that each instance has the CRID identifier as a part. This is not the case for postal codes. Therefore, they cannot be subsumed under CRID now. I am looking into changing IAO accordingly. Once that is done, the class ought to be a subclass of CRID.
http://en.wikipedia.org/wiki/Postal_code
postal code of biobank contact
Biobank contact ZIP
Mathias Brochhausen
The postal code that is part of the postal address of the biobank contact person.
ISO 3166-1 alpha-2 code for biobank contact person
Mathias Brochhausen
Biobank country code
The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address.
settlement part of address
A textual entity that is part of a postal address and denotes a human settlement for the purpose of delivering mail.
Mathias Brochhausen
settlement part of address biobank contact
Mathias Brochhausen
Biobank contact city
The part of a biobank contact's adress denoting a settlement.
intra-settlement specification part of address
A textual entity that is part of a postal address and specifies the location inside the settlement (which is specified by another part of the address). This can be a street name and a house number, or just a number or a post-office box number.
Mathias Brochhausen
intra-settlement specification part of address of biobank contact
Biobank contact address
Mathias Brochhausen
An intra-settlement specification part of address that is part of a biobank contact's postal address.
hosted study collection
A object aggregate that consists of specimens, participates in a study and is part of a biobank.
Hosted studies
Mathias Brochhausen
name of hosted study collection
Mathias Brochhausen
The proper name that designates a hosted study collection.
email address of sample collection or study contact
Mathias Brochhausen
An email address for the purpose of contacting a sample collection or study contact person.
Sample Collection/Study contact email
sample collection or study aim description
A textual entity describing a study aim or a sample collection.
Mathias Brochhausen
Sample collection or study description
study proper name
A proper name that designates a study.
Mathias Brochhausen
Study name
name of sample collection responsible or principal investigator
A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study.
Mathias Brochhausen
Sample Collection Responsible / Principal Investigator
name of sample collection or study contact person
Mathias Brochhausen
A personal name that designates the person acting as contact for a sample collection or a study.
Sample Collection/Study contact person
department of sample collection or study contact
Mathias Brochhausen
A department that has a contact person for a sample collection or a study as an organizational member.
Sample Collection/Study contact department
street
A street is a thoroughfare in a built environment.
Mathias Brochhausen
intra-settlement specification part of address of sample collection or study contact
Mathias Brochhausen
An intra-settlement specification part of address that is part of a sample collection or study contact's postal address.
Sample Collection/Study contact address
postal code for sample collection or study contact
Mathias Brochhausen
Postal code that is part of the address of a human being serving as sample collection or study contact.
Sample Collection/Study contact ZIP
biobank location ISO 3166-1 alpha-2 code
An ISO 3166-1 alpha-2 code that designates the country a biobank is located in.
Mathias Brochhausen
Biobank country code
CTEP organization identifier
An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program.
Mathias Brochhausen
biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code.
Mathias Brochhausen
obsolete_bone marrow specimen
true
Bone marrow contains two types of stem cells: haematopoietic (which can produce blood cells) and stromal (which can produce fat, cartilage and bone).
A specimen that refers to the tissue at the center of large bones which is the place where new blood cells are produced.
http://www.who.int/transplantation/activities/GlobalGlossaryonDonationTransplantation.pdf
Alice Nzinga
fixed tissue specimen
A processed specimen that is the output of a fixation process.
Alice Nzinga
Mathias Brochhausen
fixed tissue specimen
fixed tissue block specimen
A fixed tissue specimen that is in block form.
fixed tissue slide specimen
A fixed tissue specimen that is placed in a slide.
fixed tissue slide specimen
flash frozen specimen
A frozen specimen that has been instantly/quickly frozen by subjecting the specimen to cryogenic temperatures, or in direct contact with liquid nitrogen at -320.8F 0r -196C.
http://en.wikipedia.org/wiki/Flash_freezing
fresh tissue specimen
A fresh specimen that is in a tissue form.
frozen tissue block specimen
A frozen specimen is a tissue sample preserved in a block.
frozen tissue slide specimen
A frozen specimen that has been sliced from a tissue block into thin layers that are placed on a glass to be examined under a microscope.
microdissected specimen
A specimen that has been procured from a histology slide under direct microscopic visualization.
Alice Nzinga
http://www.ncbi.nlm.nih.gov/pubmed/11269646
survey data
A data set that contains the outcome of a survey.
Alice Nzinga
Mathias Brochhausen
sampling specimens for biobank
Mathias Brochhausen
The process of collecting or selecting an aggregate of specimens into a biobank.
biobank contact role
A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.
A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study.
sample collection or study contact role
sample collection or study contact person
A human being acting as bearing the contact role for a sample collection or a study.
study principle investigator or responsible
The principle investigtor or responsible person for a study or a sample collection.
specimen disease state datum
A data item that indicates the pathological assessment of a specimen.
diseased state specimen datum
A specimen disease state datum item that specifies that the specimen in question consists of a disorder.
mixed state specimen datum
A specimen disease state datum that specifies that the specimen in question consists of partially normal tissue and a disorder.
normal state specimen datum
A specimen disease state datum that specifies that the specimenin questions consists of normal tissue.
obsolote_unknown state specimen data
true
A specimen disease state data of the procured specimen that is unclear.
This is a temporary state.
fixation
A material processing that uses chemical process by which biological tissues are preserved from decay. Fixation terminates any ongoing biochemical reactions and may increase stability of the treated tissues.
The choice of fixation depends on the type of study.
http://en.wikipedia.org/wiki/Fixation_%28histology%29
http://sharedresources.fhcrc.org/training/tips-about-fixation-and-formalin
addition of molecular label
labeling
OBI developer call, 3-12-12
PERSON: Matthew Brush
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
addition of molecular label
age interval information
1
Alice Nzinga
An information content entity that is about a data set that has age information and specifies the range of age information in that data set.
Example: age interval is 18-65
Martin Fransson
Mathias Brochhausen
average age
1
Alice Nzinga
An average value of age for a certain group of individuals.
Mathias Brochhausen
patient registry data
A data set of collected secondary data related to patients with a specific diagnosis, condition, or procedure and plays an important role in post marketing surveillance of pharmaceuticals.
Alice Nzinga
It can be said to be a formal record of an internationally agreed minimum amount of information about clinical trial.
Martin Fransson
patient register data
obsolete_survey data
true
A data set that contains additional information about a group of individuals and is gathered through a survey.
Alice Nzinga
The equivalent class restriction includes data combination since the the output of survey execution is from one participant, while the survey data is the combination of data gathered from multipe participants or multiple executions of the survey.
date of data entry
A data item that indicates the time when data about the sample collection was reported into a database.
Alice Nzinga
It is denoted by Date in ISO-standard (8601) time format.
date of data update
A data item that indicates the time when data about the sample collection was last updated in a database.
Alice Nzinga
It is expressed as a Date in ISO-standard (8601) time format.
end date of sampling for biobank
A data item that indicates the time when the sampling of specimens for a biobank ended.
Alice Nzinga
It is denoted by Date in ISO-standard (8601) time format.
start date of sampling for biobank
A data item that indicates the time when the sampling of specimens for a biobank started.
Alice Nzinga
It is denoted by Date in ISO-standard (8601) time format.
comorbidity
A diagnosis that is the outcome of a diagnostic process targeting a second or additional health problem.
Alice Nzinga
It is argued that Comorbidity occurs due to a disposition established by a prior infection with a pathogenic organism of a different kind.
Mathias Brochhausen
amended from http://en.wikipedia.org/wiki/Comorbidity
secondary infection, nosocomial infection
primary diagnosis
A diagnosis that is the main reason for the inducement of medical care.
Alice Nzinga
Hint:
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
main diagnosis
count of current sampled human study participant
A count that is about the aggregate of individuals who have contributed biological specimens in a study.
Alice Nzinga
count of current total human study participant
A count that is about the aggregate of individuals who have been recruited to participate in a study.
Alice Nzinga
physiological measurement data
A measurement datum that contains the assessment information about the functioning of a major organ system, the extent of disease or disability,as well as the provision and/or response to therapeutic interventions.
Alice Nzinga
http://www.improvement.nhs.uk/physiologydiagnostics/documents/WhatisPhysiologicalMeasurement.pdf
Examples: Audiology, Cardiac Physiology, GI Physiology, Neurophysiology, Ophthalmic and Vision Science, Respiratory and Sleep Physiology, Urodynamics, Vascular Technology
Mathias Brochhausen
storage temperature setting
A setting datum that specifies the temperature inside a container participating in a storage process.
Alice Nzinga
Examples: -18 °C to -35 °C, -60 °C to -85 °C, Liquid nitrogen, Room temperature etc
Mathias Brochhausen
omics experiment on specimen
A tentative procedure that is aimed at discovering some characteristic of a large familiy of cellular molecules, having named by appending suffix "-omics."
Alice Nzinga
An objective specification that aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
Mathias Brochhausen
Technologies that measure some characteristic of a large family of cellular molecules, such as genes, proteins, or small metabolites, have been named by appending the suffix "-omics," as in "genomics." Omics refers to the collective technologies used to explore the roles, relationships, and actions of the various types of molecules that make up the cells of an organism.
http://en.wikipedia.org/wiki/Omics
interrelated experiments.
number of sampled human study participants objective
Alice Nzinga
An objective specification that specifies the number of individuals to participate in a study and provide biological specimens to the study.
Mathias Brochhausen
number of total human study participant objective
Alice Nzinga
An objective specification that specifies the total number of individuals who are planned to participate in study.
case control study design
A study design that compares two groups of subjects; those with the disease or condtion under study and a similar group of subjects who do not have the condition.
Alice Nzinga
cross sectional study design
A study design in which all participants or a representative subset of participants are examined at only a single time for characteristics of a interest (e.g. a specific disease).
Alice Nzinga
longitudinal study design
A study design that involves repeated observations of the same entity over time. In the biobank context, longitudinal studies sample a group of people in a given time period, and study them at intervals by the acquisition and analyses of data and/or samples over time.
Alice Nzinga
cohort study design
A longitudinal study that aims to study a case-defined population who presently have a certain condition or recepient of a particular treatment that are followed over time and are compared with a similar group who do not have condition.
panel study design
A longitudinal study that samples a cross-section and studies it at regular intervals.
population based study design
A study design that is multidisciplinary done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
Alice Nzinga
quality control study design
A study design where some aspect of the experiment is quality controlled for the purposes of quality assurance.
Alice Nzinga
twin study design
A study design usually in behavior genetics which aids the study of individual differences between genetically identical twins by highlighting the role of environmental and genetic causes on behavior.
Alice Nzinga
survey plan specification
A plan specification that is realized by process of gathering information (e.g. by asking questions).
Alice Nzinga
Mathias Brochhausen
medical record
It is a chronological written account of examination, treatment, medical history or complaints.
Martin Fransson
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 used interchangeably with health record and medical chart.
https://en.wikipedia.org/wiki/Medical_record
sample medical record
A medical record of a specimen donor.
Alice Nzinga
sample handling summary
A document that outlines the procedures employed to preserve and protect the material collected during specimen collection as an indication of sample quality.
Alice Nzinga
It could be argued as to why this class was not created as an 'objective specification'. However, the emphasis here is to 'a briefing of how the specimen in the sample collection have been handled as an indication of specimen quality.'
It could be freeze chain, freze time, SPREC compliant, etc.
age interval information for sampled donors
1
Alice Nzinga
Age interval information that is age information of specimen donors.
http://www.abta.org/Dictionary/67
sampled group age interval
donor patient registry data
Alice Nzinga
Registry data for a patient who participates as a donor in a study.
study subject survey data
A survey data for a specimen donor.
Alice Nzinga
Examples: Individual Disease History, Individual History of Injuries, Medication, Perception of Health, Women's Health, Reproductive History, Familial Disease History, Life Habits/Behaviors, Sociodemographic Characteristics, Socioeconomic Characteristics, Physical Environment, Mental Health, Other.
Mathias Brochhausen
sample collection data entry
A planned process that involves the initial entering of data about sample collection into a database.
sample collection data update
A planned process which involves editing of specimen collection data into a database after its initial entry.
survey execution
A planned process that realizes the concretization of a survey to generate an output(survey data.)
temperature regulating
As per placing the term as a planned process, it can be argued that nature does play a role in the final output of the actual temperature.
A planned process that aims to control or maintain the temperature of a material entity to a given or required measurement datum.
comment from tissue procurement
A textual entity that states additional information about the specimen or donor that is deemed relevant for the specimen collection process.
Alice Nzinga
specimen measurement
3mm X 3mm X 3mm
A measurement datum that is the result of measurement of the three dimensions of a specimen.
Alice Nzinga
Mathias Brochhausen
date of specimen collection
A data item that indicates the time when the collection of a specimen occurred.
Alice Nzinga
It is denoted by Date in ISO-standard (8601) time format.
Mathias Brochhausen
date of specimen preparation
specimen meeting specification
All specimens that meet the set parameters to be procured on.
Mathias Brochhausen
adherance to specification
surgical procedure
A planned process that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, or to help improve bodily function or appearance.
http://en.wikipedia.org/wiki/Surgery
mastectomy / craniotomy / liver resection e.t.c.
specimen preparation contact
A personal name that designates the person who prepared the specimen.
Alice Nzinga
time in formalin measurement
15min
A time measurement datum that states the duration during which a specimen was submerged in formalin.
Alice Nzinga
specimen surgical removal
A collecting specimen from organism process that involves removing the specimen from an individual through a surgical procedure.
specimen freezing
A freezing storage for the specimen.
specimen ID
A proper name that identifies a specimen and is usually in form of a label included in the specimen cassette.
Alice Nzinga
http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf
case ID
Alice Nzinga
An identifier that refers to a specimen donor who is participating in specimen collection process for tissue procurement purposes and is usually assigned at the time of donor procurement.
http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf
specimen measurement specification
A specification (often abbreviated as spec) may refer to an explicit set of requirements to be satisfied by a material, design, product, or service.
Alice Nzinga
An directive information entity that states the technical standard measurement set and values that determines if a specimen qualifies for procurement or not.
http://en.wikipedia.org/wiki/Specification_(technical_standard)
time of specimen freezing
A data item that reports the time when a specimen was frozen.
Alice Nzinga
Mathias Brochhausen
time of surgical removal of specimen
A data item that reports the time when a specimen was collected by a surgical procedure.
Alice Nzinga
Mathias Brochhausen
normal specimen
A specimen that is normal.
obsolete_cerebrospinal fluid specimen
true
Abbreviated as 'CSF'.
A specimen that refers to a portion of a fluid largely secreted by the choroid plexuses of the ventricles of the brain, filling the ventricles and the subarachnoid cavities of the brain and spinal cord, collected from an organism.
Alice Nzinga
http://www.ncbi.nlm.nih.gov/books/NBK398/
obsolete_faeces specimen
true
A specimen that comprises of a portion of faeces collected from an organism.
Alice Nzinga
obsolete_saliva specimen
true
A specimen consisting of a portion of saliva collected from an organism.
Alice Nzinga
It is a clear, tasteless, odorless, slightly acidic (pH 6.8) viscid fluid, secreted from the parotid, sublingual, and submandibular salivary glands and the mucous glands of the oral cavity.
hosting biobank
A biobank that collects and stores specimen during specimen collection primarily for the purposes of some study.
Alice Nzinga
specimen donor
A Homo sapiens who contributes specimen.
Alice Nzinga
Mathias Brochhausen
sample donor
sample handling
A planned process of preparing and submitting specimens to storage.
http://www.exchangenetwork.net/standards/SampleHandling_01_06_2006_Final.pdf
specimen handling
start of sampling specimens for biobank
Mathias Brochhausen
The process boundary marking the beginning of a sampling of specimens into a biobank.
end of sampling specimens for biobank
Mathias Brochhausen
The process boundary marking the end of a sampling of specimens into a biobank.
human health care role
Mathias Brochhausen
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
William R. Hogan
health care role
health care provider role
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
Mathias Brochhausen
William R. Hogan
nurse role
A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
Mathias Brochhausen
based on: http://en.wikipedia.org/wiki/Nursing
nurse
collection of organisms
An object aggregate of organisms.
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
collection of humans
An object aggregate all of whose components are human beings.
role in human social processes
A role inhering in an entity realized by social interactions in human society.
Mathias Brochhausen
Previous definition: A role played by an entity in human social processes.
aggregate of organizations
2
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
It is often convenient to group organizations together that otherwise might not even interact with one another.
William R. Hogan
Amanda Hicks
legal person role
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Mathias Brochhausen
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.
OMB ethnic identity datum
Amanda Hicks
An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
racial identity datum
A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
racial identification process
ethnic identity datum
Amanda Hicks
An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
ethnic identification process
hispanic or latino identity datum
Amanda Hicks
An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
not hispanic or latino identity datum
Amanda Hicks
An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
identity datum
Amanda Hicks
An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
gender identity datum
Amanda Hicks
A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
identification process
Amanda Hicks
gender identification process
American Indian or Alaska Native identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
Amanda Hicks
Asian identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
Amanda Hicks
black or African American identity datum
Amanda Hicks
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
Native Hawaiian or other Pacific Islander identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
Amanda Hicks
white identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
Amanda Hicks
OMB racial identity datum
Amanda Hicks
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
age
biological sex
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
biological sex
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
height
A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
length
A 1-D extent quality which is equal to the distance between two points.
length
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
mass
weight
A physical quality inhering in a bearer that has mass near a gravitational body.
viability
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.
volume
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
volume
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
quality of a single physical entity
physical object quality
A quality which inheres in a continuant.
alive
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
frozen
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
frozen
organismal quality
A quality that inheres in an entire organism or part of an organism.
organismal quality
collection of organisms
organism collection
group of organism
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
insulin
An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof.
INS
molecular label role
MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (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.
OBI developer call, 3-12-12
molecular label role
molecular tracer role
molecular label
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
OBI developer call, 3-12-12
molecular tracer
region
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
region
sequence
pituitary gland
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].
pituitary gland
organ part
A multicellular structure that is a part of an organ.
cardinal organ part
amniotic fluid
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.
amniotic fluid
blood
A fluid that is composed of blood plasma and erythrocytes.
blood
breast
The upper ventral region of an animal's torso.
breast
renal medulla
renal medulla
the inner portion of the kidney consisting of the renal pyramids
organism substance
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.
organism substance
material anatomical entity
Anatomical entity that has mass.
material anatomical entity
anatomical cluster
Anatomical group that has its parts adjacent to one another.
anatomical cluster
tissue
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.
tissue
multi-tissue structure
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.
multi-tissue structure
stomach
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.
stomach
aorta
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
aorta
heart
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
heart
brain
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].
brain
cerebral cortex
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.
cerebral cortex
female gonad
female organism genitalia gonad
female organism genitalia gonada
female organism reproductive system gonad
female organism reproductive system gonada
female reproductive system gonad
female reproductive system gonada
genitalia of female organism gonad
genitalia of female organism gonada
gonad of female organism genitalia
gonad of female organism reproductive system
gonad of female reproductive system
gonad of genitalia of female organism
gonad of reproductive system of female organism
gonada of female organism genitalia
gonada of female organism reproductive system
gonada of female reproductive system
gonada of genitalia of female organism
gonada of reproductive system of female organism
ovary
ovum-producing ovary
reproductive system of female organism gonad
reproductive system of female organism gonada
the gonad of a female organism which contains germ cells
uterus
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
vagina
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].
adipose tissue
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
adipose tissue
strand of hair
A filament, mostly protein, that grows from follicles found in the dermis[WP].
strand of hair
rectum
terminal portion of intestine
the terminal portion of the intestinal tube, terminating with the anus
pleural fluid
Transudate contained in the pleural cavity.
pleural fluid
sweat
Secretion produced by a sweat gland.
sweat
synovial fluid
Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae.
synovial fluid
right lobe of liver
The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
liver right lobe
lobus hepaticus dexter
right liver lobe
right lobe of thyroid gland
A lobe of thyroid gland that is in the right side of a thyroid gland.
lobus dexter (glandula thyroidea)
right thyroid lobe
thyroid gland right lobe
left lobe of thyroid gland
A lobe of thyroid gland that is in the left side of a thyroid gland.
left thyroid lobe
lobus sinister (glandula thyroidea)
thyroid gland left lobe
skeletal muscle tissue
Muscle tissue that consists primarily of skeletal muscle fibers.
skeletal muscle tissue
body of pancreas
The body of the pancreas is a subsection of the pancreas organ in the human body. It is somewhat prismatic in shape, and has three surfaces: anterior, posterior, and inferior. It is at the same level as the transpyloric plane. [WP,unvetted].
pancreas body
pancreatic body
caecum
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
caecum
cecum
intestinum crassum caecum
colon
Last portion of the large intestine before it becomes the rectum.
colon
ascending colon
Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified]
colon ascendens
transverse colon
The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
colon transversum
descending colon
The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
colon descendens
sigmoid colon
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
body of stomach
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
corpus gastricum (ventriculare)
gastric body
stomach body
cortex of kidney
Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
cortex of kidney
right adrenal gland
An adrenal gland that is in the right side of the abdomen
glandula suprarenalis dexter
right suprarenal gland
left adrenal gland
An adrenal gland that is in the left side of the abdomen
glandula suprarenalis sinister
left suprarenal gland
urinary bladder
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
urinary bladder
pancreas
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
pancreas
peritoneal fluid
Transudate contained in the peritoneal cavity.
peritoneal fluid
tibial nerve
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].
tibial nerve
cerebrospinal fluid
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
cerebrospinal fluid
gastrocnemius
The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg.
gastrocnemius muscle
m. gastrocnemius
m.gastrocnemius
ascending aorta
The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]
ascending thoracic aorta
pars ascendens aortae
coronary artery
An artery that supplies the myocardium.
coronary artery
vitreous humor
A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina
vitreous humor
minor salivary gland
One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP].
lower lip
Lip that covers the lower portion of the mouth.[TAO].
lower jaw lip
saliva
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
saliva
milk
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
milk
bile
bile
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.
placenta
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.
placenta
feces
Portion of semisolid bodily waste discharged through the anus[MW,modified]
feces
cerebellum
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].
cerebellum
thyroid gland
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].
thyroid gland
lung
Respiration organ that develops as an oupocketing of the esophagus.
lung
right cardiac atrium
A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
cardiac right atrium
heart right atrium
right atrium
right atrium of heart
right cardiac atrium
cardiac atrium
Cardiac chamber in which blood enters the heart.
atria
atrium
atrium of heart
cardiac atria
heart atrium
heart left ventricle
A cardiac ventricle that is in the left side of the heart.
cardiac left ventricle
left cardiac ventricle
left ventricle
left ventricle of heart
skin of body
The organ covering the body that consists of the dermis and epidermis.
skin of body
spleen
spleen
the organ that functions to filter blood and to store red corpuscles and platelets
liver
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].
kidney
A paired organ of the urinary tract which has the production of urine as its primary function.
ileum
the portion of the small intestine that extends from the jejunum to the colon
right ovary
An ovary that is part of a right side of organism [Automatically generated definition].
left ovary
An ovary that is part of a left side of organism [Automatically generated definition].
peritoneum
A serous membrane that lines the peritoneal cavity[VHOG,modified].
prostate gland
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.
prostate gland
adrenal gland
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].
adrenal gland
bone marrow
bone marrow
the soft tissue that fills the cavities of bones
pericardial fluid
Transudate contained in the pericardial cavity.[FMA]
pericardial fluid
esophagus mucosa
A mucosa that is part of a esophagus [Automatically generated definition].
esophagus mucosa
omentum
A fold of peritoneum originating at the stomach and supporting the viscera.
fallopian tube
Initial section of the oviduct through which the ova pass from the ovary to the uterus
mammalian oviduct
uterine tube (sensu Mammalia)
esophagus muscularis mucosa
A muscularis mucosa that is part of a esophagus.
esophagus muscularis mucosa
greater omentum
The greater omentum (also the great omentum, omentum majus, gastrocolic omentum, epiploön, or, especially in animals, caul) is a large fold of peritoneum that hangs down from the stomach, and extends from the stomach to the posterior abdominal wall after associating with the transverse colon.
digestive system fluid or secretion
digestive system fluid or secretion
sputum
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
sputum
tibial artery
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.
tibial artery
esophagogastric junction
The junction between the esophagus and the stomach epithelium
cardioesophageal junction
gastroesophageal junction
lingula of left lung
Anterioinferior portion of left upper lung lobe
left pulmonary lingula
lingula of lung
lingula of the lung
body of uterus
The part of the uterus above the isthmus and below the orifices of the uterine tubes.
corpus uteri
uterine body
uterine corpus
splenic flexure of colon
The splenic (or left colic) flexure is a sharp bend between the transverse and the descending colon in the left upper quadrant of humans. The left colic flexure is near the spleen, and hence called the splenic flexure. There are two colic flexures in the transverse colon — the other being the hepatic flexure in the right upper quadrant.
flexura coli splenica
left colic flexure
splenic flexure
splenic flexure of colon
hepatic flexure of colon
Hepatic (or the right colic) flexure is the sharp bend between the ascending and the transverse colon. The right colic flexure is adjacent to the liver, and is therefore also known as the hepatic flexure. Thus, the left colic flexure is also known as the splenic flexure (as it is close to the spleen). The hepatic flexure lies in the right upper quadrant of the abdomen in humans.
flexura coli heaptica
hepatic flexure
hepatic flexure of colon
right colic flexure
esophagogastric junction muscularis mucosa
gastro-esophageal junction muscularis mucosa
muscularis mucosa from the lowest portion of the esophagus, just proximal to the stomach.
life-death temporal boundary
A life cycle temporal boundary that marks the end of the life cycle of the organism.
end of life cycle
moment of death
time of death
suprapubic skin
Area of skin in the hypoastric region of the abdomen.
rectosigmoid junction
An anatomical junction that is between the sigmoid colon and rectum.
length unit
A unit which is a standard measure of the distance between two points.
length unit
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
mass unit
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
temperature unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
temperature unit
concentration unit
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
concentration unit
Laboratory
An organizational unit (as opposed to the physical facility) that performs research, provides services, or processes materials
Laboratory
ethnic group
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)
An ethnic group is a population whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait.
Ethnicity
race
African American
A term used in the United States to categorize a population group comprised of persons having origins in any of the black racial groups of Africa. Includes population subgroups (e.g., Kenyan, Nigerian, Haitian). The concept refers also to individuals who classify themselves as described.
Afro American
BLACK OR AFRICAN AMERICAN
Black
Black Populations
American
Asian
Asians
Denotes a person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including Cambodia, China, India, Japan, Korea, Malaysia, Mongolia, Pakistan, the Philippine Islands, Thailand, and Vietnam.
Asian Indian
Asian Indians
Hindu
In North America the term is used to distinguish a person having origins in the original peoples of the Indian sub-continent from Native Americans.
Indian
Chinese
Denotes the inhabitants of China, a person from there, or their descendants elsewhere.
European-American
Japanese
Denotes the inhabitants of Japan, a person from there, or their descendants elsewhere.
JPT
Latino
A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race. An arbitrary ethnic classification.
Hispanic
Hispanic Populations
Hispanic or Latino
Hispanics or Latinos
Latino Population
Spanish Origin
Hispanic
A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race. An arbitrary ethnic classification.
Hispanic Populations
Hispanic or Latino
Hispanics or Latinos
Latino Population
Spanish Origin
smoking behavior
Inhaling and exhaling the smoke of tobacco or something similar to tobacco.
smoking
chewing tobacco behavior
Mastication of tobacco, correlated with an increased risk of oral cancers.
date of birth
The point in time at which an individual was born.
date of diagnosis
The point at which a clinical diagnosis is made.
Obsolete Class
geographic location
A reference to a place on the Earth, by its name or by its geographical location.
geographic location
example to be eventually removed
example to be eventually removed
failed exploratory term
Person:Alan Ruttenberg
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
failed exploratory term
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
PERSON:Alan Ruttenberg
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."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
core
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
core
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
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 imported
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.
term split
universal
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
Alan Ruttenberg
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.
universal
defined class
"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.
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
Alan Ruttenberg
defined class
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
Alan Ruttenberg
named class 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
Alan Ruttenberg
Terms with this status should eventually replaced with a term from another ontology.
group:OBI
to be replaced with external ontology term
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
axiom holds for all times
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
relation has no temporal argument
## Elucidation
This is used when the first-order logic form of the relation is
binary, and takes no temporal argument.
## Example:
Class: limb
SubClassOf: develops_from some lateral-plate-mesoderm
forall t, t2:
forall x :
instance_of(x,Limb,t)
implies
exists y :
instance_of(y,LPM,t2)
develops_from(x,y)
degree Celsius
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
C
degree C
degree Celsius
pH
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
pH
To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
Person:Alan Ruttenberg