A subset of OBI contains all terms representing NIAID GSCID/BRC Project, Sample and Sequencing Assay Core Standards, This OBI view contains NIAID GSCID and BRC community preferred labels and field IDs assigned by NIAID metadata working group. The details of NIAID GSCID and BRC metadata standards are available on: http://www.niaid.nih.gov/labsandresources/resources/dmid/metadata/Pages/default.aspx.
The view was generated from OBI release version 20150413 using ontoDog.
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.
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
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
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
example of usage
has curation status
OBI_0000281
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition
textual 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 OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
editor note
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.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
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
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
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
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
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
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
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)
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).
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
IEDB alternative term
An alternative term used by the IEDB.
IEDB
IEDB alternative term
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
temporal interpretation
https://code.google.com/p/obo-relations/wiki/ROAndTime
temporal interpretation
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.
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.
label
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
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])
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
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
provides_service_consumer_with
provides_service_consumer_with
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
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
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
supplies
A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
GROUP: Relations branch
supplies
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.
inheres in
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
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
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 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)
concretizes
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).
concretizes
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
role_of
this investigator role is a role of this person
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)
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)
temporal relation
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
move to BFO?
Allen
temporal relation
starts
inverse of starts with
Chris Mungall
Allen
starts
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
entity
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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
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])
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
independent continuant
(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]
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
(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]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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
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.
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]
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]
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.
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
realizable entity
(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]
(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]
RealizableEntity
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
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])
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
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
specifically dependent continuant
(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
SpecificallyDependentContinuant
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
Specifically dependent continuant 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.
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.
sdc
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
role
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.
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
site
Site
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
a hole in the interior of a portion of cheese
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
Manhattan Canyon)
a rabbit hole
an air traffic control region defined in the airspace above an airport
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)
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.
process boundary
ProcessBoundary
p-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])
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])
process boundary
the boundary between the 2nd and 3rd year of your life.
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
immaterial entity
immaterial
ImmaterialEntity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
gross anatomical part
Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
gross anatomical part
peptide
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
peptide
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acid
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
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
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
ribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
ribonucleic acid
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
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
environmental material
Material in or on which organisms may live.
environmental material
CS20
Environmental Material
NIAID GSCID-BRC
geographic location
A reference to a place on the Earth, by its name or by its geographical location.
geographic location
CS13
NIAID GSCID-BRC
Specimen Collection Location - Location
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
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
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
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
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
publication
A document that has been accepted by a publisher
A journal article or book
PERSON: Lawrence Hunter
publication
publication about an investigation
A publication that is about an investigation
Most scientific journal articles
PERSON: Lawrence Hunter
publication about an investigation
scientific publication
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
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
assigning a centrally registered identifier
assigning a CRID
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
Person:Alan Ruttenberg
Person:Bjoern Peters
Person:Melanie Courtot
a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
assigning a centrally registered identifier
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
human pathogenicity disposition
A disposition to initiate processes that result in a disorder in a human organism.
CS19
Human Pathogenicity of Suspected Organism(s) in Specimen
NIAID GSCID-BRC
human pathogenicity disposition
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
human
human being
man
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
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
biological feature identification objective
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")
reporting party role
MO:submitter mapped to this term. So, alternative term 'submitter' was added.
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
reporting party
submitter
Jennifer Fostel
OBI
The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
a study personnel role played by a party who reports the outcome of a study component
reporting party role
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
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
OBI branch derived
PlanAndPlannedProcess Branch
sample preparation for assay
study
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
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
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
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.
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
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
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
extract
GROUP: OBI Biomatrial Branch
PERSON: Philippe Rocca-Serra
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extract
extracted material
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
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
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
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 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
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
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.
sample from organism
5/29: This is a helper class for now
a material obtained from an organism in order to be a representative of the whole
sample from organism
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
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 sample role
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
material sample role
material sample
A material entity that has the material sample role
OBI: workshop
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
material sample
sample
sample population
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
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
sequence feature annotation
Bjoern Peters
Bjoern Peters
Information about a sequence region
place holder for sequence ontology term
sequence feature annotation
infectious agent
CS17, CS18
IEDB
IEDB
NIAID GSCID-BRC
Suspected Organism(s) in Specimen
infectious agent
is a material entity bearing the disposition to infect an organism
service consumer role
A biologist who uses a sequencing services fulfills the role of a service consumer
OBI
Person:Helen Parkinson
a role which inheres in a person who uses a service
service consumer role
service provider role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
PERSON:Helen Parkinson
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
service provider role
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
GROUP: OBI
Person:Chris Stoeckert
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
sequence data
individual organism identifier
PERSON: Chris Stoeckert, Jie Zheng
CS1
MO_169 Individual
NIAID GSCID-BRC
Specimen Source ID
a CRID symbol used to distinguish one individual organism from another.
individual organism identifier
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 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
CS6
NIAID GSCID-BRC
Specimen Source Age - Value
age measurement datum
service
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
Carlo; Matt
OBI workshop San Diego 2011
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
service
tissue specimen
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
MO_954 organism_part
PERSON: Chris Stoeckert, Jie Zheng
CS16
NIAID GSCID-BRC
Specimen Type
tissue specimen
material maintenance service
A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Matthew Brush
material maintenance service
model organism colony maintanance
sequence assembly algorithm
NIAID GSCID-BRC
An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
Assembly Method
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
SA6
sequence assembly algorithm
material service
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
PERSON: Carlo Torniai
PERSON: Carlo Torniai
PERSON: Matthew Brush
material service
material analysis service
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Matthew Brush
Services performing DNA sequencing or Cell Analysis
material analysis service
material storage service
A service that offers liquid nitrogen stroage.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Matthew Brush
material storage service
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
GenBank ID
GenBank Record ID
NIAID GSCID-BRC
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
SA10
investigation description
study description
NIAID GSCID-BRC
A textual entity that describes an investigation.
CP3
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Project Description
investigation description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
CS15
NIAID GSCID-BRC
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Specimen ID
specimen ID
specimen identifier
PubMed ID
NIAID GSCID-BRC
A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
CP12
NIAID GSCID-BRC
PMID
Person: Chris Stoeckert, Jie Zheng
PubMed ID
PubMed Identifier
Publication Citation
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
average depth of sequence coverage
NIAID GSCID-BRC
An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
Genome Coverage
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
SA7
average depth of sequence coverage
specimen collection time measurement datum
NIAID GSCID-BRC
A time measurement datum that is the measure of the time when the specimens are collected.
CS10
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Specimen Collection Date
collection date
specimen collection time measurement datum
latitude coordinate measurement datum
NIAID GSCID-BRC
A measurement datum that is the measure of the latitude coordinate of a site.
CS11
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Specimen Collection Location - Latitude
latitude
latitude coordinate measurement datum
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
CS12
NIAID GSCID-BRC
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Specimen Collection Location - Longitude
longitude
longitude coordinate measurement datum
investigation title
study title
A textual entity that denotes an investigation.
CP1
NIAID GSCID-BRC
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person:Chris Stoeckert, Jie Zheng
Project Title
investigation title
organism identification objective
A biological feature identification objective to identify the organism species in a specimen.
Penn Group
Person: Chris Stoeckert, Jie Zheng
organism identification objective
organism identification assay
NIAID GSCID-BRC
An assay that identifies the organism species in a specimen.
CS21
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Organism Detection Method
Person: Chris Stoeckert, Jie Zheng
organism identification assay
sequence annotation algorithm
An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation.
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
sequence annotation algorithm
Bioinformatics Resource Center
NIAID GSCID-BRC
An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
BRC
Bioinformatics Resource Center
Bioinformatics Resource Center
CP20
NIAID GSCID-BRC
Person: Chris Stoeckert, Jie Zheng
Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
country name
NIAID GSCID-BRC
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
CS14
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Specimen Collection Location - Country
Website: http://en.wikipedia.org/wiki/Country
country name
investigation identifier
A CRID symbol used to identify an investigation.
NIAID GSCID-BRC
CP2
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zhneg
Project ID
investigation identifier
grant identifier
NIAID GSCID-BRC
A CRID symbol used to identify a grant.
CP11
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Supporting Grants/Contract ID
grant identifier
grant
AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
Discussed on Feb 13, 2012 dev call. Details see the tracker:
https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
Group: OBI
OBI
grant
contact representative role
A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
Person: Chris Stoeckert
Discussed on May 7, 2012 dev call
propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ?
Whether it works for communicating author in manuscript or not?
Tracker:
https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178
NIAID GSCID-BRC
contact representative role
specimen collector role
NIAID GSCID-BRC
Penn Group
An Investigation agent role borne by a person or organization which
is realized in a specimen collection process.
Person: Jie Zheng, Chris Stoeckert
specimen collector role
organization of specimen provider principal investigator
NIAID GSCID-BRC
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
CP14
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Sample Provider PI's Institution
organization of specimen provider principal investigator
organization of Bioinformatics Resource Center contact person
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center
NIAID GSCID-BRC
Bioinformatics Resource Center Contact's Institution
CP22
NIAID GSCID-BRC
organization of Bioinformatics Resource Center contact person
target material in specimen specification
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
A plan specification which specifies the type of material that will be assayed in an investigation.
NIAID GSCID-BRC metadata working group
CP6
NIAID GSCID-BRC
Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome.
Target Material
target material in specimen specification
Bioinformatics Resource Center contact person
Bioinformatics Resource Center Contact Name
CP21
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
A person who is the contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center contact person
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
specimen-based scope of investigation specification
CP5
NIAID GSCID-BRC metadata working group
Sample Scope
Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic.
NIAID GSCID-BRC
A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
specimen-based scope of investigation specification
specimen repository organization
PERSON: Chris Stoeckert, Jie Zheng
An organization that provides a service to store and distribute specimens
CS22
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
NIAID GSCID-BRC
Specimen Repository
specimen repository organization
email address of Bioinformatics Resource Center contact person
NIAID GSCID-BRC metadata working group
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC
An email address of the person who is contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact's email
CP23
NIAID GSCID-BRC
email address of Bioinformatics Resource Center contact person
sequencing facility contact person
NIAID GSCID-BRC metadata working group
A person who is the contact representative at the sequencing facility
CP17
NIAID GSCID-BRC
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
Sequencing Facility Contact Name
sequencing facility contact person
specimen provider principal investigator
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC
CP13
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
A person who is a principal investigator and provides the specimen
Sample Provider Principal Investigator (PI) Name
specimen provider principal investigator
email address of specimen collector
An email address of the person collecting the specimen
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC
CS27
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Specimen Collector's email
email address of specimen collector
sequencing facility organization
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC
An organization that provides sequence determination service
NIAID GSCID-BRC metadata working group
CP16
NIAID GSCID-BRC
Sequencing Facility
sequencing facility organization
specification of data to be generated in an investigation
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC
NIAID GSCID-BRC
Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype
NIAID GSCID-BRC metadata working group
An objective specification which indicates the type of data that will be generated and submitted to a database.
CP9
Project Objectives
specification of data to be generated in an investigation
organization of specimen collector
An organization that is the affiliation of the person collecting the specimen
CS26
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
Specimen Collector's Institution
organization of specimen collector
email address of sequencing facility contact person
NIAID GSCID-BRC metadata working group
An email address of the contact representative at the sequencing facility
CP19
NIAID GSCID-BRC
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
Sequencing Facility Contact's email
email address of sequencing facility contact person
specimen collector
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
A person who collects the specimen
CS25
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Specimen Collector Name
specimen collector
investigation assay specification
A plan specification which indicates the assay type used to obtain data.
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
NIAID GSCID-BRC
Some examples of Project Method are Sequence, Array, Mass Spectrometry
PERSON: Chris Stoeckert, Jie Zheng
CP8
Project Method
investigation assay specification
organization of sequencing facility contact person
PERSON: Chris Stoeckert, Jie Zheng
An organization that is the affiliation of the contact representative at the sequencing facility
NIAID GSCID-BRC
CP18
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Sequencing Facility Contact's Institution
organization of sequencing facility contact person
comment on investigation
PERSON: Chris Stoeckert, Jie Zheng
A textual entity that is about any of the aspects of an investigation worth noting
CS24
Comments
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
NIAID GSCID-BRC
comment on investigation
target capture specification
Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey
A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen.
CP7
NIAID GSCID-BRC
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Target Capture
target capture specification
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
CS23
NIAID GSCID-BRC
Specimen Repository Sample ID
specimen identifier assigned by specimen repository
specimen identifier assigned by sequencing facility
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
A specimen identifier which is assigned by a sequencing facility
NIAID GSCID-BRC
SA1
Sample ID - Sequencing Facility
specimen identifier assigned by sequencing facility
sample preparation for sequencing assay
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
A sample preparation for assay that preparation of nucleic acids for a sequencing assay
NIAID GSCID-BRC
Nucleic Acid Preparation Method
PERSON: Chris Stoeckert, Jie Zheng
SA3
sample preparation for sequencing assay
email address of specimen provider principal investigator
NIAID GSCID-BRC
PERSON: Chris Stoeckert, Jie Zheng
An email address of the principal investigator providing the specimens for the investigation
CP15
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
Sample Provider PI's email
email address of specimen provider principal investigator
sequencing service
Person: Jie Zheng
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
Adpated from 'DNA sequencing service'
NIAID GSCID-BRC
sequencing service
conclusion based on data
An information content entity that is inferred from data.
Group:2013 Philly Workshop group
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
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.
grant agency
An organization that provides funding support for projects such as investigations.
NIAID GSCID-BRC
PERSON: Jie Zheng, Chris Stoeckert
'funding organization'
http://vivoweb.org/ontology/core#FundingOrganization
CP10
funding organization
Grant Agency
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
grant agency
sequence annotation
NIAID GSCID-BRC metadata working group
Annotation Method
NIAID GSCID-BRC
PERSON: Jie Zheng, Chris Stoeckert
A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
NIAID GSCID-BRC
SA9
sequence annotation
sequence annotation provider
A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence.
PERSON: Jie Zheng, Chris Stoeckert
NIAID GSCID-BRC
NIAID GSCID-BRC metadata working group
Annotation Provider
NIAID GSCID-BRC
SA8
sequence annotation provider
sequence assembly name
PERSON: Jie Zheng, Chris Stoeckert
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
A textual entity that is used to denote a sequence assembly.
Assembly Name
NIAID GSCID-BRC
SA5
sequence assembly name
sequence annotation reporting role
NIAID GSCID-BRC metadata working group
PERSON: Jie Zheng, Chris Stoeckert
A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence.
NIAID GSCID-BRC
sequence annotation reporting role
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.
CS3, CS4
NIAID GSCID-BRC
Specimen Source Species
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.
CS2
GROUP: OBI Biomaterial Branch
NIAID GSCID-BRC
Specimen Category
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
extraction
A material separation in which a desired component of an input material is separated from the remainder
Person:Bjoern Peters
Philippe Rocca-Serra
nucleic acid extraction using phenol chloroform
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity.
'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
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
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
CP4
NIAID GSCID-BRC
Project Relevance
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
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
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
sequencing assay
NIAID GSCID-BRC
OBI branch derived
PlanAndPlannedProcess Branch
SA4
Sequencing Technology
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has_output should be sequence of input; we don't have sequence well defined yet
sequencing assay
the use of a chemical or biochemical means to infer the sequence of a biomaterial
nucleic acid extraction
NIAID GSCID-BRC
Nucleic Acid Extraction Method
OBI branch derived
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
PlanAndPlannedProcess Branch
SA2
a material separation to recover the nucleic acid fraction of an input material
nucleic acid extraction
requested by Helen Parkinson for MO. Could be defined class
infection
IEDB
IEDB
infection
the detrimental process in which an infectious agent colonizes or replicates in a host environment
disposition to infect an organism
IEDB
IEDB
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
disposition to infect an organism
pathologic process
IEDB
IEDB
abnormal, harmful processes caused by or associated with a disease
pathologic process
disease
disease
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
CS9
NIAID GSCID-BRC
Specimen Source Disease
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
CS5
NIAID GSCID-BRC
Specimen Source Gender
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
quality of a single physical entity
organismal quality
A quality that inheres in an entire organism or part of an organism.
organismal quality
CS8
NIAID GSCID-BRC
Specimen Source Health Status
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
antithrombin III is a protein
protein
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
sequence_assembly
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
sequence_assembly
assembly
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
assembly
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
CS7
NIAID GSCID-BRC
Specimen Source Age - Unit
example to be eventually removed
example to be eventually removed
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
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