Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.
Next generation biobanking ontology(NGBO).
term source
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
expand assertion to
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has associated axiom(nl)
Person:Alan Ruttenberg
has associated axiom(fol)
has axiom label
term replaced by
Add as annotation triples in the granting ontology
Use on obsolete terms, relating the term to another term that can be used as a substitute
Use on obsolete terms, relating the term to another term that can be used as a substitute Add as annotation triples in the granting ontology
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
An entity responsible for making contributions to the content of the resource.
Contributor
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the content of the resource.
Creator
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the resource.
Date
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
An account of the content of the resource.
Description
Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
The topic of the content of the resource.
Subject and Keywords
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
Title
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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
Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000063, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. For a full definition, refer to the inverse of this property, BFO_0000060. (Allyson Lister)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
is preceded by
preceded_by
preceded by
precedes
The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'.
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Modified by Allyson Lister from the preceded_by (which is the inverse of precedes / 'followed by') definition within RO: http://www.obofoundry.org/ro/ro.owl
Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000060, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. (Allyson Lister)
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
has temporal occupant
[copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001
history of
member of
has measurement unit label
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
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.
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
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
Alan Ruttenberg
is quality measurement of
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
has measurement datum
x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context..
designates
p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
is designated by
A relation that is used to follow traceability of specimen activity
trace_from
A relation that is used to track specimen activity
track_to
A relation that relates a container to a measurement datum that specifies the maximum capacity of the container.
has maximum capacity
A relation that relates a container to a measurement datum that specifies the actual amount of material in the container.
has actual load
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
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.
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
is_specified_input_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_manufactured_by
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Liju Fan
has_make
has_manufacturer
is_specified_output_of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
has organization member
Relating an organization to a legal person or organization.
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
has performer
performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system)
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
owns
a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
Mathias Brochhausen
A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl
administrates
a is contact information for b, if a is a information content entity, b is a human being or an organization and a identifies a physical location or electronic resource that allows to initiate communication with a.
is contact information about
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
is owned by
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
true
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
'inheres in at all times'
inheres_in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
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).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contained_in
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
aligned with
A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
has component
A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
Chris Mungall
has phenotype
phenotype of
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in
temporal relation
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
starts
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
has output
Any relationship between an exposure event or process and any other entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.
g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
ubiquitously expressed in
expresses
ubiquitously expresses
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
has member is a mereological relation between a collection and an item.
has member
output of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
A relation that holds between a disease or an organism and a phenotype
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
causal relation between material entities
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Groups both positive and negative correlation
The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
causes or contributes to condition
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
condition ameliorated by
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
condition exacerbated by
Do not use this relation directly. It is intended as a grouping for a more specific relations
A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
disease has basis in dysfunction of (disease to anatomical structure)
A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
disease has basis in disruption of (disease to process)
A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
causal relationship with disease as subject
A relationship between a disease and a process where the disease process disrupts the execution of the process.
disease causes disruption of (disease to process)
disease causes dysfunction of (disease to anatomical entity)
A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
TODO: complete range axiom once more of CARO has been mireoted in to this ontology
This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of
This relation groups relations between diseases and any other kind of entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes)
'is related to' is the top level relation in SIO
is related to
has attribute
is attribute of
is annotation of
document x is annotated with the keywords 'ontology','semantic web'
has annotation
has identifier
is identifier for
has unique identifier
is unique identifier for
Microsoft version 2007 is directly preceded by Microsoft version 2003.
Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software.
'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s.
directly followed by
Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification.
userEmailId
userID
userPassword
userName
A persistent, unique identifier of a molecular sequence database entry.
Damion Dooley
sequence accession
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
an edge of a cube-shaped portion of space.
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
Endothelial cell of or involving the cerebrum and the blood vessels supplying it.
Cancer cell of the blood-forming tissues in which large numbers of immature, abnormal red blood cells are found in the blood and bone marrow.
Cancer cell of the major organ of respiration the lung.
A malignant tumour cell of glandular origin in the prostate. Over 95% are adenocarcinomas.
A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die.
stationary phase culture
A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes.
logarithmic phase culture
A rare type of hepatocellular carcinoma arising from the cholangioles, composed of tumor cells resembling the epithelial cells of the cholangioles arranged in cords consisting of two layers of cells surrounding a minute lumen.
Infiltrating ductal carcinoma is one of several recognized specific patterns of cancer of the breast. It is so named because it begins in the cells forming the ducts of the breast. It is the most common form of breast cancer, comprising 65-85% of all cases.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line.
A cell found in the embryo before the formation of all the gem layers is complete.
A female germ cell that has entered meiosis.
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system.
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4,CD5,CD8 alpha chain, CD14, CD19, CD20, integrin alpha-M, neural cell adhesion molecule 1, lymphocyte antigen 6G, lymphocyte antigen 76.
A progenitor cell committed to the erythroid lineage.
A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).
Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors.
A stem cell that can give rise to mulitple lineages of cells.
A stem cell that can give rise to multiple lineages of cells.
A precursor cell with a limited number of potential fates.
An embryonic (precursor) cell of the myogenic lineage that develops from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes.
An embryonic cell that becomes a cell of muscle fiber.
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
A connective-tissue cell of mesenchymal origin that secretes proteins and especially molecular collagen from which the extracellular fibrillar matrix of connective tissue forms.
A large, flat, oval cell found in connective tissue and responsible for the formation of fibers.
A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone.
A neurectoderm derived cell that lines the neural lumen. [ JB:jb GOC:tfm PMID:9550134 ]
A cell that is usually found in a two-dimensional sheet with a free surface.
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
Cell that cover the surface of the body and line its cavities.
Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH).
The endothelial cells that line the vasculature.
A flattened epithelial cell of mesenchymal origin that lines the serous cavity.
A cell which moves among different tissues of the body, via blood, lymph, or other medium.
A cell found predominately in the blood.
Cells of the pancreas that secrete digestive enzymes, the archetypal secretory cell upon which much of the early work on the sequence of events in the secretory process was done.
A leukocyte with abundant granules in the cytoplasm.
A polymorphonuclear white blood cell with granule-containing cytoplasm.
A polymorphonuclear white blood cell with granule-containing cytoplasm.nIn humans the granulocytes are also classified as polymorphonuclear leucocytes and are subdivided according to the staining properties of the granules into eosinophils, basophils and neutrophils, some invertebrate blood cells are also referred to, not very helpfully, as granulocytes.
Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement.
Neurons which activate muscle cells (MSH).
Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
The main type of cell found in the inside lining of blood vessels, lymph vessels, and the heart.
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. (Reichenbach and Wolburg)
MERGED DEFINITION:nTARGET DEFINITION: The delicate network of branched cells and fibers that supports the tissue of the central nervous system.n--------------------nSOURCE DEFINITION: The cells of the supportive tissue of the central nervous system (neuroglia). These non-neural cells are of three kinds: astrocytes, oligodendrocytes (collectively termed macroglia) and microglia.
The delicate network of branched cells and fibers that supports the tissue of the central nervous system.
A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from "star" cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and "reactive astrocytes" (along with microglia) respond to injury (MSH).
A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury.
cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and
A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.
A class of large neuroglial (macroglial) cells in the central nervous system. Oligodendroglia may be called interfascicular, perivascular, or perineuronal (not the same as satellite cells, perineuronal of ganglia) according to their location. They form the insulating myelin sheath of axons in the central nervous system (MSH).
A central nervous system macrophage found in the parenchyma of the central nervous system.
A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.
A small, migratory, phagocytic, interstitial cell of hematopoietic origin found in the central nervous system. Microglial cells are of various forms and may have slender branched processes.
MERGED DEFINITION:nTARGET DEFINITION: The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system. They are of various forms and may have slender branched processes. They are migratory and act as phagocytes to waste products of nerve tissue. n--------------------nSOURCE DEFINITION: One of the small interstitial phagocytic cells of the microglia.
The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system. They are of various forms and may have slender branched processes. They are migratory and act as phagocytes to waste products of nerve tissue.
A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of tryglycerides.
A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
An epidermal cell that produces melanin.
A cell that specializes in controlled release of one or more substances.
A cell of the epithelial lining that produce and secrete mucins.
A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl.
A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
A neuron that has the specialized function to produce and secrete hormones, and that constitutes, in whole or in part, an endocrine organ or system.
Neuroendocrine cells are cells that receive neuronal input (neurotransmitters released by nerve cells) and, as a consequence of this input, release message molecules (hormones) to the blood. An example of a neuroendocrine cell is the cell of the adrenal medulla which releases adrenalin to the blood. The major center of neuroendocrine integration in the body is found in the hypothalamus and the pituitary gland. Here hypothalamic neurosecretory cells release factors to the blood.
Neuroendocrine cells are cells that receive neuronal input (neurotransmitters released by nerve cells) and, as a consequence of this input, release message molecules (hormones) to the blood. In this way they bring about and integration between the nervous system and the endocrine system, a process known as neuroendocrine integration. An example of a neuroendocrine cell is the cell of the adrenal medulla (innermost part of the adrenal gland) which releases adrenalin to the blood. The adrenal medullary cells are controlled by the sympathetic division of the autonomic nervous system. These cells are modified postganglionic neurons. Autonomic nerve fibers lead directly to them from the central nervous system. The major center of neuroendocrine integration in the body is found in the hypothalamus and the pituitary gland. Here hypothalamic neurosecretory cells release factors to the blood. Some of these these factors, release at the median eminence, control the secretion of pituitary hormones, while others (the hormones oxytocin and vasopressin) are released directly to the peripheral circulation.
A cell that composes the bulk of the islets of Langerhans and secretes insulin.
A cell that secretes insulin and is located towards the center of the islets of Langerhans.
A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules.
The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament. [ GOC:tfm ISBN:0721662544 ]
A mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle.
A mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle. This cell has as part of its cytoplasm myofibrils organized in various patterns.
Mature contractile cells, commonly known as myocytes, that form one of three kinds of muscle. The three types of muscle cells are skeletal (muscle fibers), cardiac (myocytes, cardiac), and smooth (myocytes, smooth muscle). They are derived from embryonic (precursor) muscle cells called myoblasts (MSH).
A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
Non-striated, elongated, spindle-shaped cells found lining the digestive tract, uterus, and blood vessels. They are derived from specialized myoblasts (myoblasts, smooth muscle) (MSH).
A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
A mechanoreceptor cell located in the organ of Corti that is sensitive to auditory stimuli and in the vestibular apparatus that is sensitive to movement of the head. In each case the accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
A cell whose function is determined by the generation or the reception of an electric signal.
A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier.
A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons.
A cell of the middle germ layer of the embryo.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
A red blood cell. In mammals, mature erythrocytes are non-nucleated, biconcave disks containing hemoglobin whose function is to transport oxygen.
Any of the hemoglobin-containing cells that carry oxygen to the tissues and are responsible for the red color of vertebrate blood.
A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
A mononuclear phagocyte which differentiates from monocytes, is typically resident in a particular tissue, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells (Cell Ontology).
Relatively long-lived phagocytic cell of mammalian tissues, derived from blood monocyte. Macrophages from different sites have distinctly different properties. Main types are peritoneal and alveolar macrophages, tissue macrophages (histiocytes), Kuppfer cells of the liver, and osteoclasts. In response to foreign materials may become stimulated or activated. Macrophages play an important role in killing of some bacteria, protozoa, and tumour cells, release substances that stimulate other cells of the immune system, and are involved in antigen presentation. May further differentiate within chronic inflammatory lesions to epithelioid cells or may fuse to form foreign body giant cells or Langhans' giant cells.
A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive.
Immunologically important lymphocyte that is not thymus-dependent, is either short-lived and naive or long-lived and of memory phenotype, and resembles the bursa-derived lymphocyte of birds in that it is responsible for the production of immunoglobulins.
A cell of a filament of a fungal mycelium.
One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor.
A cell of the strip of specialized ectoderm flanking each side of the embryonal neural plate, which after the closure of the neural tube, forms a column of isolated cells along the dorsal aspect of the neural tube. Most of the cranial and all of the spinal sensory ganglion cells arise by differentiation of neural crest cells.
An embryonic cell that develops into a nerve cell or neuron.
A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling.
hair follicle dermal papilla cell
A cell which is part of an extraembryonic structure associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface.
A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
An epithelial cell of the integument (the outer layer of an organism).
The cell protoplasm after removal of the cell wall.
A blood cell especially of an invertebrate animal.
blood cell (sensu Nematoda and Protostomia)
polygonal cell
A cell whose nucleus has two haploid genomes.
A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids.
A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response.
Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451.
A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.
A special type of cell that is a key regulator of the immune system, acting as a professional antigen-presenting cell, APC, capable of activating naive T cells and stimulating the growth and differentiation of B cells. Dendritic cells are found, for example, in the lymph nodes and spleen. As an APC, a dendritic cell can retain antigen for long periods on its surface, present the antigen to a T or B cell and so influence their behavior.
Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum.
A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.
A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors.
An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix.
paneth cell
A precursor cell destined to differentiate into smooth muscle myocytes.
A myoblast that differentiates into skeletal muscle fibers.
skeletal muscle myoblast
A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo. It It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.
A grayish or reddish granular cell with specialized processes that is the fundamental functional unit of nervous tissue.
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
The basic cellular units of nervous tissue. Neurons are polarized cells with defined regions consisting of the cell body, an axon, and dendrites, although some types of neurons lack axons or dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells.
An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared.
A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
The earliest cytologically identifiable precursor in the thrombocytic series.
The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm.
A large cell that has a lobulated nucleus, is found especially in the bone marrow, and is the source of blood platelets.
A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata-1, Gata2 but do express C/EBPa, and Pu.1.
A progenitor cell that has plasma membrane part CD123, CD34, and CD45RA, lacks plasma membrane part CD19 and CD3, and is committed to the granulocyte and monocyte lineages.
An immature erythrocyte showing a basophilic reticulum under vital staining.
An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
A mononuclear phagocytic leukocyte, 13 to 25 mm in diameter, with an ovoid or kidney-shaped nucleus, containing lacy, linear chromatin and abundant gray-blue cytoplasm filled with fine reddish and azurophilic granules. Formed in the bone marrow from promonocytes, monocytes are transported to tissues such as the lung and liver, where they develop into macrophages.
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
A follicle cell that migrates from the anterior pole of the egg chamber, between the nurse cells, to the anterior of the oocyte where they participate in formation of the micropyle. About 6-10 border cells per egg chamber migrate as a tightly associated cluster.
An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen.
The reproductive cell in multicellular organisms.
A projection neuron in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region.
An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm.
A neuron that uses GABA as a vesicular neurotransmitter
A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source.
see PMID:21177950, The making of a photosynthetic animal.
A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver.
Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen.
Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament.
*Slender, contractile, mesenchymal-like cell found in close association with capillary walls. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. (From OBO Cell Type Ontology). *A flattened, or elongated, stellate-shaped solitary cell with multiple cytoplasmic processes encircling the capillary endothelium and contacting a large abluminal vessel area. It may be equivalent to the vascular smooth muscle cell, although this identify has not been conclusively determined yet (Armulik et al., Circ Res 97: 512, 2005).
A slender, contractile, mesenchymal-like cell found in close association with capillary walls. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. (From Stedman, 26th ed).
An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells.
A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
A neuron that releases dopamine as a neurotransmitter.
Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle.
A stem cell that can give rise to cell types of the body other than those of the germ-line.
A nucleated cell of the myeloid or lymphoid lineages, found in blood or other tissue.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
Any of the blood cells that are colorless, lack hemoglobin, contain a nucleus, and include the lymphocytes, monocytes, neutrophils, eosinophils, and basophils.
A myocyte located in the heart. The contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
A striated muscle cell found in the heart. They develop from cardiac myoblasts.
Striated muscle cells found in the heart. They are derived from cardiac myoblasts (myoblasts, cardiac (MSH).
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
Any of the immature blood cells that develop in the bone marrow, such as those involved in hematopoiesis.
A immature or mature cell in the lineage leading to and including erythrocytes.
A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
A nucleated precursor of an erythrocyte.
Granular leukocytes characterized by a relatively pale-staining, lobate nucleus and cytoplasm containing coarse dark-staining granules of variable size and stainable by basic dyes.
Granular leukocytes with a nucleus that usually has two lobes connected by a slender thread of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and stainable by eosin.
A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling.
A tissue-resident macrophage of the renal glomerular mesangium.
A dendritic cell type of distinct morphology, localization, and surface marker expression from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.
A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen.
A terminally differentiated cell of the B lymphocyte lineage that produces antibodies; plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern.
A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
An immature B cell is a precursor B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation.
A precursor B cell is a B cell with the phenotype CD10-positive (P08473/NEP_HUMAN; PIRSF001194).
A precursor B cell is a B cell with the phenotype CD10-positive.
A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative.
A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
A progenitor cell of any hematopoietic lineage, potentially multipotent.
hematopoietic multipotent progenitor cell
lymphoid lineage restricted progenitor cell
A progenitor cell of any myeloid lineage, potentially multipotent.
A progenitor cell restricted to the myeloid lineage.
myeloid lineage restricted progenitor cell
gastrointestinal tract (lamina propria) macrophage
mucosa-associated lymphoid tissue macrophage
gut-associated lymphoid tissue macrophage
nasal and broncial associated lymphoid tissue macrophage
CD11c-negative plasmacytoid dendritic cell
immature CD11c-low plasmacytoid dendritic cell
mature CD11c-low plasmacytoid dendritic cell
immature CD11c-negative plasmacytoid dendritic cell
CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor
mature CD11c-negative plasmacytoid dendritic cell
CD8_alpha-negative CD11b-negative dendritic cell
CD4-positive CD11b-positive dendritic cell
CD8_alpha-positive CD11b-negative dendritic cell
immature CD8_alpha-negative CD11b-negative dendritic cell
mature CD8_alpha-negative CD11b-negative dendritic cell
immature CD8_alpha-positive CD11b-negative dendritic cell
mature CD8_alpha-positive CD11b-negative dendritic cell
Kit and Sca1-positive hematopoietic stem cell
CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor
CD115-positive monocyte OR common dendritic progenitor
CD34-positive, CD38-negative hematopoietic stem cell
CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor
An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism.
CD34-positive, CD38-positive granulocyte monocyte progenitor
Kit-positive granulocyte monocyte progenitor
CD34-positive, GlyA-negative erythroid progenitor cell
CD34-negative, GlyA-negative proerythroblast
Kit-low, CD34-positive eosinophil progenitor cell
CD34-positive, CD38-positive eosinophil progenitor cell
Kit-negative, Ly-76 high basophilic erythroblast
Kit-negative, Ly-76 high polychromatophilic erythroblast
CD71-low, GlyA-positive polychromatic erythroblast
Kit-negative, Ly-76 high orthochromatophilic erythroblasts
CD71-negative, GlyA-positive orthochromatic erythroblast
CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell
Kit-positive megakaryocyte progenitor cell
CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell
CD34-negative, CD41-positive, CD42-positive megakaryocyte cell
CD9-positive, CD41-positive megakaryocyte cell
Fc-epsilon RIalpha-low mast cell progenitor
Fc-epsilon RIalpha-high basophil progenitor cell
hematopoietic lineage restricted progenitor cell
hematopoietic oligopotent progenitor cell
Slamf1-negative multipotent progenitor cell
Slamf1-positive multipotent progenitor cell
CD34-positive, CD38-negative multipotent progenitor cell
Kit-positive, integrin beta7-high basophil mast progenitor cell
CD14-positive, CD16-negative classical monocyte
CD8alpha-positive thymic conventional dendritic cell
Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH.
A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. [ GOC:tfm ISBN:0618947256 ]
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
IgG-positive double negative memory B cell
IgG-negative double negative memory B cell
IgD-positive CD38-positive IgG memory B cell
IgD-negative CD38-positive IgG memory B cell
B220-positive CD38-positive naive B cell
B220-positive CD38-negative unswitched memory B cell
B220-low CD38-negative unswitched memory B cell
B220-positive CD38-positive unswitched memory B cell
B220-low CD38-positive unswitched memory B cell
IgG-negative class switched memory B cell
CD38-negative IgG-negative class switched memory B cell
CD38-positive IgG-negative class switched memory B cell
CD24-positive CD38-negative IgG-negative class switched memory B cell
CD24-negative CD38-negative IgG-negative class switched memory B cell
B220-positive CD38-positive IgG-negative class switched memory B cell
B220-low CD38-positive IgG-negative class switched memory B cell
An endothelial cell found in capillaries.
A cell derived from a promyelocyte. It differentiates into a metamyelocyte. It has a diameter of 10-18 micrometer, and an oval or round nucleus with finely granulated chromatin.
A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses.
A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known.
A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta.
An epithelial cell of the large intestine.
A PP cell located in the islets of the pancreas.
Totipotent cell cultured from early embryo. Have the advantage that following modification in vitrothey can be used to produce chimeric embryos and thus transgenic animals.
An epithelial cell of the mammary gland.
An undifferentiated fibroblast that can be stimulated to form a fat cell.
A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage.
A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1.
A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative.
fetal liver hematopoietic progenitor cell
A keratocyte is a specialized fibroblast residing in the stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate.
An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. [ PMID:18403190 GOC:tfm ]
An epithelial cell located in the inner portion of the thymus where the T lymphocytes become mature and are released into the circulation.
An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output.
An endo-epithelial cell of the respiratory tract.
Epithelium of the respiratory portion of the bronchial tree.
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells.
A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast.
A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi. [ PMID:16397499 GOC:tfm PMID:17851544 GOC:hjd PMID:15987436 ]
The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons.
Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell
CD8_alpha-negative plasmactyoid dendritic cell
CD8_alpha-positive plasmactyoid dendritic cell
langerin-negative dermal dendritic cell
CD8alpha-negative thymic conventional dendritic cell
lymphoid MHC-II-negative classical monocyte
lymphoid MHC-II-negative non-classical monocyte
langerin-positive lymph node dendritic cell
langerin-negative, CD103-negative lymph node dendritic cell
CD103-positive, langerin-positive lymph node dendritic cell
CD103-negative, langerin-positive lymph node dendritic cell
CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell
CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell
A mesenchymal stem cell that is part of the bone marrow. [ GOC:tfm ]
mesenchymal stem cell of the bone marrow
fibroblast of dermis
lung fibroblast
An epithelial cell of the intestine. [ GOC:tfm ]
An endothelial cell of the umbilical vein. [ GOC:tfm ]
An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial. [ GOC:tfm PMID:20807818 PMID:9020076 ]
A basal cell in the respiratory tract. [ PMID:20699479 GOC:tfm ]
Ghrelin secreting cells found in the found in the exocrine pancreas.
Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. [ PMID:18356246 PMID:16550043 GOC:tfm ]
Any endothelial cell of artery that is part of a coronary artery. [ GOC:TermGenie ]
Any osteoblast that is part of a skull. [ GOC:TermGenie ]
Any leukocyte that is part of a spleen. [ GOC:TermGenie ]
Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology.
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
A specimen barcode is a specimen identification number formatted as an optical machine-readable representation.
WEB: http://en.wikipedia.org/wiki/Barcode
A reference to a place on the Earth, by its name or by its geographical location.
Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community
GENEPIO
reference genome identifier
help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users.
A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them.
Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature.
Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/
de-identified data
sequence identifier
/^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ])) ?(:<LDU>[0-9][ABCEGHJKLMNPRSTVWXYZ][0-9])$/i, $FSA $LDU
A Canadian postal code is a postal code that pertains to a geographic region of Canada.
Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account.
Canada postal code
The location of a sequence feature as defined by its start and end position on some reference coordinate system.
1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.
sequence feature location
The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system
In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences.
In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus).
1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.
genomic feature location
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
GROUP: OBI
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
software interpreter
R program, Perl interpreter, Java virtual machine
A software interpreter is a software application that executes some specified input software.
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
person:Chris Stoeckert
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
PERSON:Chris Stoeckert
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI Plan and Planned Process branch
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
GROUP: IAO
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
batch number
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
text
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
document part
An abstract, introduction, method or results section.
an information content entity that is part of a document
methods section
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
A part of a publication about an investigation that is about the study design of the investigation
experimental
experimental procedures
experimental section
methods
results section
The section labelled 'results' in a typical scientific journal article
A part of a publication about an investigation that is about a study design execution
results
A scalar measurement datum that is the result of measuring a temporal interval
Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards
time measurement datum
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
a planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software method
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software module
A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
software library
A software application is software that can be directly executed by some processing unit.
software application
A software script is software whose instructions can be executed using a software interpreter.
software script
case report section
The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
A part of a document about the medical history of a specific patient as it relates to the topic of the document.
PERSON: Bill Baumgartner
case presentation
case report
consent section
The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
A part of a document about the consent process that was used to enroll patients in a study.
consent
ethical approval section
The section labelled 'ethical approval' in a typical scientific journal article.
A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
ethical approval
materials section
The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
A part of a document about the materials required to reproduce the content of the document.
materials
requirements section
The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
requirements
statistical analysis section
The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
A part of the document used to describe the statistical methodologies employed in the work presented in the document.
statistical analysis
A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
identifier
proper name
A personal name is a proper name identifying an individual person.
Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
personal name
A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject.
an informed consent form that has been filled with all required contents.
an informed consent form that has been partically filled with required contents.
a one-dimensional temporal region that is a period of an informed consented study
informed consented study period
a temporal interval that represent the time of someone (for example the study subject) participating the study or the research.
YL, MH, AK, EE, YH
participation duration
Total length of time of subject's participation in a clinical study; from the time of enrollment to the completion of follow-up.
This duration is different with the 'planned duration of study subject participation'
actual duration of study subject participation
a termporal interval that represents a period of time during which a signed informed consent form is stored.
WEB: http://answers.hhs.gov/ohrp/questions/7223
storage duration of signed informed consent form
a participation time that is the total length of time of subject's participation in a research study; from the time of enrollment to the completion of follow-up.
The term definition is adapted from NCIt definition of "Planned Duration of Study Subject Participation" (C70707) with modification. Compared to the NCIt definition, the ICO definition specifies research research study instead of a clinical study.
planned duration of study subject participation
A realizable entity that represents the eligibility of a candidate according to a study protocol.
eligibility of candidate participation
A disposition whose realization negatively regulates an immune response.
immunosuppressive disposition
Any system designed to expedite the sorting and delivery of mail by assigning a series of alphanumeric codes to each delivery area. Also used to refer to any individual delivery area code.
The street name and building number where a person or organization can be found.
A system designed to expedite the sorting and delivery of mail by assigning a series of numbers to each delivery area in the United States. Also used to refer to any individual delivery area code.
A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others.
A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network.
A text string identifier for a location to which e-mail can be delivered.
Damion Dooley's note: It can also be used as an authorization token in some identification processes.
A description of an individual's current and past experience with alcoholic beverage consumption.
Data item which represents a normalized probability of observing the new amino acid at that position and ranges from 0 to 1.
SIFT score impact
A processed specimen which is the output of preparing a DNA sample for further analysis.
DNA processed specimen
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change
PS1 criteria
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history
PS2 criteria
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls
PS4 criteria
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation
PM1 criteria
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or ExAC
PM2 criteria
Assumed de novo, but without confirmation of paternity and maternity
PM6 criteria
For recessive disorders, detected in trans with a pathogenic variant
PM3 criteria
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants
PM4 criteria
ACMG guidelines for classification of variants of strong variants classification
ACMG strong variants classification
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product
PS3 criteria
ACMG guidelines for classification of variants of moderate classification
ACMG moderate classification criteria
ACMG guidelines for classification of variants of very strong classification
ACMG very strong classification criteria
ACMG guidelines for classification of variants of spporting classification
ACMG supporting classification criteria
inferred from the College of American Pathologists (CAP) requirements
Information content entity that is a standard way that information is encoded for storage in a computer file.
data file format
inferred from https://en.wikipedia.org/wiki/Variant_Call_Format
A file format which represent represent the format of a text file used in bioinformatics for storing gene sequence variations
VCF format
A file format which represent a text-based format for storing biological sequences aligned to a reference sequence
SAM format
A file format which represent represent a text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes
FASTA format
A file format which represent text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores
FASTQ format
A fixed tissue slide specimen that is contain unstained tissue section(s)
inferred from KFMC SOP
unstained fixed tissue slide
A file format which represent a binary file format designed for storing a genome consists of multiple chromosomal sequences
2bit format
A file format which represent a data format allows display of continuous-valued data in track format
bed graph format
A file format which represent represent format provides a flexible way to define the data lines that are displayed in an annotation track
bed format
A file format which represent binary format for storing sequence data.
BAM format
A standard operating procedure for shipping and receiving of sample
shipping and receiving of samples SOP
A reference genome datum which represent reference genome edition
reference genome version number
inferred from College of American Pathologists (CAP) requirments
A reference genome datum which represent a location where reference genome can be accessed online
reference genome URI
Information about data storage location information content entity which represent any physical hardware such as external hard drives, flash drives, and CD
information about local data storage
Information about data storage location information content entity which represent information about the basic containers that hold your data in cloud storage
information about cloud storage bucket
A personal name that designates the human being donated specimen
name of specimen donor
A document which represent a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes.
material transfer agreement
inferred from ISBER
A document information content entity established between organisations that governs the transfer of one or more data sets from the owner/provider to a third party
data transfer agreement
An assay kit processed material comprises a sterile device for collecting a sample, a collection and dispersing device for depositing and holding the sample, a device for transferring the sample, and a container for storing the sample to be tested. There may also be a labeling system for identifying the sample and for diluting the sample
specimen collection kit
A container which used to ship temperature sensitive products such as foods, pharmaceuticals, organs, blood, biologic materials, and chemicals. They are used as part of a cold chain to help maintain product freshness and efficacy.
insulated shipping container
A one-dimensional temporal region that is a period of an duration of standard operation procedure
When a procedure is discontinued or replaced, a paper or electronic copy is maintained for at least 2 years, recording initial date of use, and retirement date.
standard operating procedure actual use duration
A material processing process which attaches synthetic oligonucleotides of a known sequence to one or both ends of cDNA fragments
adapter ligation process
A specimen which is a recognizable part or product taken from specimen
specimen derivative
A data transformation which involeves curation, processing and analysis of complex biological data
bioinformatics analysis
A gene expression level analysis is a bioinformatics analysis that compares the RNA expression levels of multiple genes (profiling) and/or multiple samples (screening)
inferred from https://www.thermofisher.com/ca/en/home/life-science/gene-expression-analysis-genotyping/gene-expression-profiling.html
gene expression level analysis
Variant calling is the process by which we identify variants from sequence data.
variant calling assay
A genetic variation analysis which assign a formal classification to a detected genetic variant.
variant classification assay
A bioinformatics analysis which attempt to group biological sequences that are somehow related
sequence clustring
A file format which represent alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent at UCSC
axt file format
required quality check list for the procedure of paraffin embedding and/or fixation.
paraffin embedding and Fixation quality check report
a specimen which represent remaining portion of a specimen obtained for clinical purposes that is no longer needed for its original purpose and that would otherwise be discarded
CAP accreditation program, Biorepository checklist
remnant specimen
A specimen that derives from an organism and might contain infectious materials.
specimen with potentially infectious materials
A training manual is a book or booklet of instructions, designed to improve the quality of a performed task.
training manual
A data item infromation content entity that represent any data that could potentially identify a specific individual. Any information that can be used to distinguish one person from another and can be used for de-anonymizing anonymous data can be considered PII.
personally identifiable information
A sequencing assay which involves the determination of the arrangement of the amino acid sequence of a protein.
Dalia Alghamdi
protein sequencing
A database which represent libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.
biological database
A bioinformatics analysis data transformation which two or more things are positioned in a straight line or parallel to each other
alignment
A bioinformatics analysis that produces data structure that improves the speed of data retrieval operations on a database table at the cost of additional writes and storage space to maintain the index data structure
database index
A bioinformatics analysis which referes to the process of compressing to reduze the size of genome file
genome indexing
A measured expression level which refers to the characteristic of preferentially expressing a parental allele in the hybrid due to variations in regulatory sequences from the parental genomes.
ASE_SNP_CNV_Expression, Allele-Specific Expression
Allele-specific expression data
A measured expression level measurement datum which represent copy number variation (CNV) obtained by microarray
microarray CNV genotypes data
A measured expression level measurement datum which refers to represent small non-coding RNAs of 19-24 nucleotides in length that downregulate gene expression during various crucial cell processes such as apoptosis, differentiation and development.
microRNA expression data
A measured expression level which refers to activity (the expression) of thousands of genes at once, to create a global picture of cellular function.
gene expression profile data
A mesurement datum that represent all of the protein-coding regions of genes in a genome (known as the exome)
whole exome sequence data
A single molecule real time sequencing data is DNA sequence data generated from parallelized single molecule DNA sequencing method.
inferred from https://en.wikipedia.org/wiki/Single-molecule_real-time_sequencing
single molecule real time sequencing data
A DNA sequence data which represent the the complete DNA sequence of an organism's genome at a single time
whole genome sequence data
DNA sequence data which represent genomic DNA obtained from environmental samples
metagenomics sequence data
RNA sequence data which represent the complete complement of transcripts in a sample, at a given time
inferred from https://sequencing.roche.com/en/
whole transcriptome sequence data
Inffered from clinical lab standard operating procedure
16s RNA sequence data is used to identify bacteria at the species level in order to differentiate between closely related species.
RNA sequence data which is about the 16s gene of one or more organisms.
16s RNA sequence data
A genetic variation analysis which involves identifying biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.
Bioinformatics operations, data types, formats, identifiers and topics ontology (operation_3226)
variant prioritisation
An assay which attempt to select highly confident variants and remove the ones that are falsely called
genetic variants filtration assay
A sequence alignment which align every residue in every sequence
global sequence alignment
A sequence alignment which align dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context
local sequence alignment
A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
replace with OBIws
multiple sequence alignment
A sequence alignment bioinformatics analysis which identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid)
pairwise sequence alignment
A bioinformatics analysis which attempt to searching sequence databases by using alignment to a query sequence
sequence similarity search
appropriate command line flags for running bioinformatics pipline, for example, bwa - Burrows-Wheeler Alignment Tool options found here: http://bio-bwa.sourceforge.net/bwa.shtml
A symbol that is used to specify options for command line programs.
command line argument command line parameter
command line flag
Functional annotation is a bioinformatics analysis consists of attaching biological information to genomic elements such as: biochemical function, biological function, involved regulation and interactions and expression
functional annotation
A planned process which ensure data have undergone data cleansing to ensure they have data quality, that is, that they are both correct and useful.
data validation
A data validation process that checks that the data is in a specified format (template), e.g., dates have to be in the format DD/ MM/YYYY is correct
format validation
A data validating whech validate sequencing quality scores and measure the probability that a base is called incorrectly.
sequence data quality validation
inffered from the College of American Pathologists (CAP) requirments
A processed material which contain a set of articles or equipment needed for a specific purpose.
assay kit
A process material which contains DNA fragments that represent the entire genome of an organism.
DNA library
An assay kit used for the technique of isolating DNA in a biological sample
DNA extraction assay kit
A data item which represent datum related to reference genome used as a standard for comparison in basic research and clinical settings
reference genome datum
A URL at which the data file file is stored.
data file URL
A database is an information content entity that describe a structured set of data held in a computer, especially one that is accessible in various ways.
database
An assay kit processed material that include a set of articles or equipment needed for library construction
library construction kit
A report that represent the process of data collection and analysis through which the degree of conformity to predetermined standards and criteria are exemplified
quality assesment report
A material processing that has as its input a specimen and as its output a sample derivative.
sample derivative from specimen creation process
A data item that represent sort of archive that contains one or more files that have been reduced in size through file compression process
inferred from https://support.microsoft.com/en-us/windows/zip-and-unzip-files-8d28fa72-f2f9-712f-67df-f80cf89fd4e5
compressed file
A bioinformatics analysis which analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
Bioinformatics operations, data types, formats, identifiers and topics EDAM
genetic variantion analysis
An assay which represent the process of targeting detected known disease causing genetic variant for validation purposes
validation of known variant assay
A validation of known variant assay which permits the direct detection of any point mutation in human DNA by analyzing the PCR products in an ethidium bromide-stained agarose or polyacrylamide gel
allele specific PCR
A molecular quality that represent the number of copies of a particular gene varies from one individual to the next (germline mutation)
inferred from https://www.genome.gov/genetics-glossary/Copy-Number-Variation
copy number variation
A molecular quality that describe changes in copy number that have arisen in somatic tissues.
Li, W., Lee, A. & Gregersen, P.K. Copy-number-variation and copy-number-alteration region detection by cumulative plots. BMC Bioinformatics 10, S67 (2009). https://doi.org/10.1186/1471-2105-10-S1-S67
copy number alteration
Secure file transfer is a planned process that represent data sharing via a secure, reliable delivery method. It is used to safeguard proprietary and personal data in transit and at rest. Most secure file sharing methods use standard protocols, including: Secure File Transfer Protocol (SFTP)
secure file transfer process
A data transfer protocol is a network protocol that provides file access, file transfer, and file management over any reliable data stream
secure file transfer protocol
A protocol plan specification which describes the process of data transfer between two entities
data transfer protocol
A data transfer protocol, and extension of the Hypertext Transfer Protocol (HTTP). It is used for secure communication over a computer network, and is widely used on the Internet
hypertext transfer protocol secure
A protocol plan specification which describes the process of generating a collection of DNA fragments for sequencing
library preparation protocol
Protocol for acceptence or rejcetion must be based on metrics and quality control parameters established during test optimization and utilized during validation
result acceptance or rejection protocol
A protocol which describe the criteria for acceptance or rejection of a specimen
specimen acceptance or rejection protocol
Sequencing quality scores measure the probability that a base is called incorrectly.
to review
sequencing quality scores
A biological database that contains genes nomenclature created by the HUGO Gene Nomenclature Committee (HGNC) that sets the standards for human gene nomenclature.
HUGO gene nomenclature committee gene name
A specimen that is divided into separate parts which are typically stored in separate containers as individual samples
aliquot
A protocol that ensure that biospecimens can be tracked accurately from the collection site through biospecimen arrival and subsequent
specimen tracking protocol
Each freezer, refrigerator, room temperature stor- age cabinet, or other unit appropriate to the collec- tions should have a unique identifier.
storage unit identifier
A data item which represent the availability of other specimen from the same donor
Availability of other specimen from the same donor
An identifier which denotes number assigned by a shipper of specimen.
specimen shipment identifier
A version number denotes standard operating procedure
standard operating procedure version number
A unique SOP name which captures the essence of the practice described.
standard operating procedure title
A temperature which represent specimen temperature during shipment.
specimen shipping temperature
A specimen shipping tempruture which represent a Refrigerated temperature (2 to 8°C) - wet ice or gel packs (conditioned at –15°C, designed for refrigerated temperatures, or phase change material rated for refrigerated transport).
refrigerated specimen temperature
A planned process with the objective to destroy an entire collection or specific specimen.
specimen destruction assay
A specimen culling is the process of reviewing and eliminating specimens in a collection or an entire collection either by destruction or transfer to a new custodian
specimen culling
A data item representing a variant’s significance in relation to a disease or phenotype.
clinical variant interpretation
A clinical variant interpretation that represents a sequence variant that is previously reported and is a recognized cause of the disorder.
disease causing mutation predisposing variant sasceptibility gene susceptibility gene mutation
pathogenic variant
A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which is expected to cause the disorder.
likely pathogenic variant
A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which may or may not be causative of the disorder.
variant of unknown significance
A clinical variant interpretation that represents a sequence variant that is previously unreported and is probably not causative of disease
likely benign variant
inferred from College of American Pathologists (CAP) requirements
A clinical variant interpretation that represents a sequence variant previously classified or reported as a recognized neutral variant
benign variant
A genomic feature location which represent the expression quantitative trait loci are genomic loci that explain all or a fraction of variation in expression levels of mRNAs
expression quantitative trait loci
RNA sequence data that represent the sequence of single-stranded RNA molecule that is complementary to one of the DNA strands of a gene. The mRNA is an RNA version of the gene that leaves the cell nucleus and moves to the cytoplasm where proteins are made.
messenger RNA sequence data
inferred from use case discussion
A data item which indicates availability of specimen associated data
measurement datum availability statement
A material processing which capture specific regions of interest after library preparation for next generation sequencing.
target region enrichment assay
A bioinformatics analysis which involves any edit or change to a molecular sequence file.
raw sequence file editing
An assay which generate OMICS data through a wet bench process such as sequencing techniques.
omics data generation assay
A protocol that describe the process of assigning a formal classification to the detected variant
interpretation of clinical variant protocol
inffered from College of American Pathologists (CAP) requirment
A protocol which describes the guidance for the interpretation of sequence variants suggested by The American College of Medical Genetics and Genomics (ACMG).
ACMG guidelines for classification of variants
inffered from whole exome sequencing clinical report
An algorithm which perform mapping of low-divergent sequences against a large reference genome, such as the human genome.
Burrows-Wheeler Aligner algorithm
A protocol which describes the process of attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments as a prepration for sequencing
adapter ligation protocol
A protocol which describe the process of validation of known variant
inferred from Rodenburg RJ. The functional genomics laboratory: functional validation of genetic variants. J Inherit Metab Dis. 2018;41(3):297-307. doi:10.1007/s10545-018-0146-7
validation of known variant protocol
A protocol which describes the process of Allele-specific polymerase chain reaction (PCR)
allele specific PCR protocol
A protocol plan specification which describes the process of reducing the likelihood that the data can identify an individual.
data anonymization protocol
Bioinformatics analysis which performs gapped alignment for single-end reads, supports paired-end mapping, generates mapping quality, and gives multiple hits if required
inferred from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/
BWA assembly process
A software designed to extract meaningful information from the mass of molecular biology data
bioinformatics analysis software
A data item that represent information on data storage.
data storage datum
An objective specification to determine attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments
inferred from https://www.cytivalifesciences.com/en/us/solutions/genomics/knowledge-center/glossary/adapter-ligation
ligation objective
A protocol which describes the workflow to capture specific regions of interest after library preparation for NGS and has many advantages over whole genome sequencing (WGS).
target enrichment protocol
inferred from the College of American Pathologists (CAP) requirements use case clinial report
A data item that which represent information about subset of genes or specific regions of interest of the genome.
inferred from https://www.bgi.com/us/sequencing-services/dna-sequencing/target-region-sequencing/
target sequence information
An information content entity that is about the location of data storage
information about data storage location
A library preparation material processing which uses bead-linked transposomes for a more uniform tagmentation reaction compared to in-solution tagmentation reactions
in-bead tagmentation library prepration
A personal name that designates the person who executed the sequencing run.
name of data generation assay executor
assay kit version
A personal name that designates the person who executed the bioinformatics analysis.
name of bioinformatics analysis executor
A data file which contain the output of data transformation process
output data file
A data file which contain the input for data transformation process
input data file
Information content entity about bioinformatics software
information about software
Information about software includes software name
bioinformatics software name
Information about software includes information on software version number.
software version number
Information about software includes information on software parameter value.
software parameter value
Information about software includes information on software parameter name.
bioinformatics software parameter name
A time measurement datum of the bioinformatics analysis execution date.
bioinformatics analysis execution date
Information about software includes software description.
software description
Information about software includes software documentation URI
software Documentation URI
An identifier which denotes the bioinformatics analysis ID.
software run identifier
A description of the file that contain raw data generated by a measurement device.
data file description
A document part of relevant notes or instructions regarding data generation assay execution
assay execution note
A conclusion based on data about a permanent change in the DNA sequence that makes up a gene
detected gene mutation
Any data file as generated by some acquisition computer or console.
data file
A data item which represents the substitution of one or more amino acids.
amino acid substitution
A planned process of making the decision of the data transfer.
data transfer agreement document act
An Identifier of an oligonucleotide probe.
probe ID
A region of short stretches of single-stranded DNA or RNA used to detect the presence of complementary nucleic acid sequences (target sequences) by hybridization.
oligonucleotide probe
A data item that describe expression quantitative trait loci.
expression quantitative trait loci data
An assay kit used for the technique of target enrichment
target enrichment kit
A software pipeline that is composed of a wide array of software algorithms to process biological raw data.
bioinformatics pipeline
An information content entity about user authentication information.
This term is used for to store users information registered in a federated service https://github.com/Dalalghamdi/NGBOSemanticWebApplication
user information
A material entity that is bearer of a medication role.
medication material
A planned process for receiving specimens such as into a laboratory.
specimen receiving
An adding a material entity into a target process where a collected specimen is added to a specimen container. (note, not used for other specimen process that produce new specimens)
adding specimen into a container
An adding specimen into a container process that spots the blood from an organism on the blood spot card.
blood spotting
A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets.
buffy coat specimen
A blood specimen that is located on a blood spot card.
A specimen that located in a blood spot card via blood spotting process.
blood specimen on blood spot card
A duration time of smoking about how long a person has been smoking regularly. (better to have criteria of regularly mean, such as smoke everyday)
duration time of smoking regularly
A time measurement datum which is the start date of a smoking behavior.
smoking start date
A time measurement datum about how long a person has been smoking.
duration time of smoking
A time measurement datum which is the end date of a smoking behavior.
smoking end date
A time measurement datum that states the duration during which a specimen was submerged in fixative.
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
An identifier that refers to a collection packet used in a specimen collection process.
A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations.
A standard operating procedure for the transportation of specimens.
A standard operating procedure for collecting specimens from organism.
A standard operating procedure for properly and completely filling out a case report form.
A specimen from organism that is collected with a collection packet that is designed to collect specimens of a particular type for a particular purpose.
specimen collected with specific collection packet
A time measurement datum that states the duration during which the specimen donor's body was refrigerated.
time donor body refrigerated measurement
A time measurement datum of the period between organ resection and the time of first clamping perfomed in vivo.
A time measurement datum of the duration of fasting by the specimen donor prior to surgery.
Duration of fasting by specimen donor prior to surgery
BPV SOP governing receipt and dissection of surgical tissue in the Tissue Bank
A standard operating procedure for the receipt and dissection of surgical tissue in a biobank.
receipt and dissection of surgical specimen SOP
A personal name that designates the person who received a specimen in the biobank.
name of biobank person receiving specimen
Parent Tissue Specimen ID of required study tumor tissue received in Tissue Bank from the Pathology Gross Room
A specimen ID denoting a specimen that is used to create a specimen family.
A personal name that designates the person who performed the dissection of a surgical specimen to create a specimen family.
A quality that inheres in buffered formalin by virtue of its usage and processing.
A standard operating procedure for collection and processing of blood specimens.
blood specimen collection and processing SOP
A personal name that designates the person who performed the collection of a blood specimen.
A personal name that designates the person who received a blood specimen in the laboratory.
name of person receiving blood specimen in laboratory
A specimen barcode that is associated with a vacutainer.
A personal name that designates the person who stored a specimen.
An identifier that specifically identifies a particular conical centrifuge tube.
A specimen barcode that is associated with a blood plasma specimen.
A specimen barcode that is associated with a cryovial.
A personal name that designates the person who processed a blood specimen to generate aliquots of blood plasma specimens.
name of person processing blood plasma specimen aliquots
A personal name that designates the person who transferred blood plasma specimens to freezer.
name of person transferring blood plasma specimens to freezer
Whole Cell Pellet Aliquot Specimen Barcode ID
A specimen barcode that is associated with a cell pellet specimen.
A personal name that designates the person who performed processing of the blood cell pellet specimen.
name of person processing blood cell pellet specimen
A role borne by an organization that is the provider of a specimen that is transported to another organization.
A role borne by an organization that is the recipient of a specimen that is transported from another organization.
A personal name that designates the person who is responsible for the transport of a specimen to another organization.
name of person responsible for specimen shipment
name of person responsible for specimen transport
A personal name that designates the person who verified the specimen transport was according to best practice, international standards, and industry regulations as trained by the IATA.
name of IATA-trained person verifying specimen shipment
name of IATA-trained person verifying specimen transport
A personal name that designates the person who performed a quality control inspection of the specimen that is to be transported to another organization.
name of quality control inspector of specimen
A personal name that designates the person who performed the data entry process for filling in a tissue recovery case report form.
name of data entry person for tissue recovery form
A personal name that designates the person who is the leader of the team responsible for entering the tissue recovery form data.
name of team leader for filling out tissue recovery form
A standard operating procedure for fixation of a tissue to the state where it is completely infiltrated with a suitable histological wax and can be embedded ready for section cutting on the microtome for a formalin-fixed paraffin-embedded (FFPE) process.
An information content entity that indicates whether duration of the alcohol stage followed that prescribed in the FFPE tissue processing SOP.
adherence of alcohol stage duration to FFPE tissue processing SOP
A time measurement datum that is the result of measuring the duration of the alcohol stage in a formalin-fixed paraffin-embedded (FFPE) process.
An information content entity that indicates whether duration of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
adherence of dehydration process duration to FFPE tissue processing SOP
A time measurement datum that is the result of measuring the duration of the dehydration process in the formalin-fixed paraffin-embedded (FFPE) process.
An information content entity that indicates whether temperature of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
adherence of dehydration process temperature to FFPE tissue processing SOP
An information content entity that indicates whether the number of stages and replicates followed that prescribed in the FFPE tissue processing SOP.
adherence of stage and replicate numbers to FFPE tissue processing SOP
An information content entity that indicates whether the duration in clearing agent followed that prescribed in the FFPE tissue processing SOP.
adherence of duration in clearing agent to FFPE tissue processing SOP
A time measurement datum that is the result of measuring the duration in clearing agent in the formalin-fixed paraffin-embedded (FFPE) process.
An information content entity that indicates whether the temperature of clearing agent followed that prescribed in the FFPE tissue processing SOP.
adherence of temperature of clearing agent to FFPE tissue processing SOP
An information content entity that indicates whether the paraffin impregnation method followed that prescribed in the FFPE tissue processing SOP.
adherence to paraffin impregnation method in FFPE tissue processing SOP
An information content entity that indicates whether the paraffin temperature followed that prescribed in the FFPE tissue processing SOP.
adherence of paraffin temperature to FFPE tissue processing SOP
A standard operating procedure for the paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue.
A time measurement datum that is the result of measuring the total time that freshly poured blocks were cooled in the formalin-fixed paraffin-embedded (FFPE) process.
total time FFPE freshly poured blocks were cooled
A standard operating procedure for the handling, tracking, and storing of a formalin-fixed paraffin-embedded (FFPE) tissue block.
FFPE tissue block handling, tracking, and storage SOP
An information content entity that indicates whether the FFPE tissue block storage SOP was followed.
adherence to FFPE tissue block storage SOP
A personal name that designates the person who performed a specimen slide preparation.
name of specimen slide preparation technician
A standard operating procedure for the preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
An age that inheres in a microtome blade.
A microtome blade age that indicates that the microtome blade is as new as possible.
A standard operating procedure for the hematoxylin and eosin (H&E) staining and slide mounting of a formalin-fixed paraffin-embedded (FFPE) tissue section.
FFPE tissue section H&E staining and mounting SOP
A time measurement datum that is the result of measuring the duration in an oven for the hematoxylin and eosin staining of a formalin-fixed paraffin-embedded (FFPE) tissue section.
FFPE tissue section H&E staining in oven duration
A planned process involving the manual performance of the FFPE tissue section H&E deparaffinization protocol.
manual FFPE tissue section H&E deparaffinization
A planned process involving the manual performance of the FFPE tissue section H&E staining protocol.
A planned process involving the manual performance of the FFPE tissue section H&E clearing protocol.
A planned process involving the manual performance of the FFPE tissue section H&E cover slip protocol.
manual FFPE tissue section H&E cover slipping
A specimen barcode associated with the specific chart (key) used to randomly assign specimens to one of several distinct experimental protocols.
An identifier that specifically identifies a particular component of a collection packet.
A specimen ID that specifically identifies a particular tissue cassete used in a formalin-fixed paraffin-embedded (FFPE) process.
A time measurement datum that is the result of measuring the duration of the the planned delay of placing the tissue cassette in fixative in the formalin-fixed paraffin-embedded (FFPE) process.
placement of tissue cassette in FFPE fixative delay duration
A time measurement datum that is the result of measuring the time between FFPE tissue processor cycle completion and embedding in a formalin-fixed paraffin-embedded (FFPE) process.
measurement of time between FFPE tissue processor cycle completion and embedding
A personal name that designates the person who performed the dissection of a normal tissue adjacent to a tumor for a formalin-fixed paraffin-embedded (FFPE) process.
name of dissector of normal adjacent tissue to tumor for FFPE
An identifier that specifically identifies a particular specimen image.
name of submitter of pathology case summary report.
A personal name that designates the person who served as the reviewer for quality assurance purposes of a pathology case summary report.
name of reviewer of pathology case summary report.
An information content entity that is an indicator of whether the local pathology review of a formalin-fixed paraffin-embedded (FFPE) hematoxylin and eosin (H&E)-stained tumor tissue slide confirmed the histological type.
confirmation of histologic type of FFPE H&E tumor slide
A personal name that designates the person who served as the pathologist reviewing a specimen slide at an organization conducting specimen collection from organisms.
name of reviewing pathologist at organization conducting specimen collection
A personal name that designates the person who performed the data entry process for filling in a local pathology review form.
name of data entry person for local pathology review form
A personal name that designates the person who received a specimen in a pathology gross room from an associated operating room (OR).
name of person in gross room receiving OR specimen
A specimen transport SOP governing the transport of tissue from the operating room (OR) to the pathology gross room.
specimen transport from OR to gross room SOP
A personal name that designates the person who performed the gross evaluation of a resected tissue specimen.
name of performer of gross evaluation of resected tissue specimen
An information content entity that is an indicator of whether a tumor specimen was obtained and processed with a particular FFPE fixation delay protocol other than meeting the top priority for tissue procurement.
additional tumor specimen was obtained and processed with a particular FFPE fixation delay protocol
An centrally registered identifier symbol assigned by an Institutional Review Board (IRB) that identifies a particular protocol at a given site.
identification number of a protocol at a particular site
A personal name that designates who performed the screening of a potential specimen donor for a research study.
name of person screening specimen donors
A personal name of an individual with research obtainer role who approaches a person's legal representative and informs them of key facts about potential risks and benefits, and asks them for authorization for post-mortem specimen donation for research for the person they legally represent.
Research authorization obtainer for post-mortem specimen donation
name of person obtaining authorization from legally authorized representative for post-mortem specimen donation
An identifier that uniquely identifies a particular legally authorized representative in a research study.
identifier for legally authorized representative
A relationship that may be biological or legal, between the specimen donor and the legally authorized representative who signed the research authorization.
relationship between person signing research authorization and specimen donor
A time measurement datum that is the result of measuring the time elapsed since radiation therapy prior to surgery.
time since radiation therapy was received prior to surgery
A time measurement datum that is the result of measuring the time elapsed since chemotherapy prior to surgery.
time since chemotherapy was received prior to surgery
A time measurement datum that is the result of measuring the time elapsed since immunotherapy prior to surgery.
time since immunotherapy was received prior to surgery
A time measurement datum that is the result of measuring the time elapsed since hormonal therapy prior to surgery.
time since hormonal therapy was received prior to surgery
An Alcohol Use History in which there is no alcohol consumption.
An Alcohol Use History in which there was alcohol consumption in the past but is currently a non-drinker of alcohol.
An Alcohol Use History in which alcohol consumption was equal to or less than 2 drinks per day for men and 1 drink or less per day for women.
An Alcohol Use History in which alcohol consumption was more than 2 drinks per day for men and more than 1 drink per day for women.
greater than moderate alcohol consumption history
A time measurement datum that is the result of measuring the duration of greater than moderate alcohol consumption (more than 2 drinks per day for a man or more than 1 drink per day for a woman) prior to study enrollment.
duration of greater than moderate alcohol consumption prior to enrollment
Less than 100 cigarettes smoked in lifetime
A Smoking History in which there was no or an insignificant level of smoking.
A Smoking History in which there is current smoking either on a daily or non-daily basis.
A Smoking History in which there is no current smoking and has not been smoking for more than 15 years.
current reformed smoker for more than 15 years history
A Smoking History in which there is no current smoking and has not been smoking for less than 15 years.
current reformed smoker for less than 15 years history
A time measurement datum that is the result of measuring the duration of use of hormonally based birth control prior to enrollment in a study.
duration of hormonal birth control use prior to enrollment
A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally based birth control.
time since last usage of hormonal birth control
A time measurement datum that is the result of measuring the duration of hormone replacement therapy prior to enrollment in a study.
duration of hormone replacement therapy prior to enrollment
A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally replacement therapy.
time since last usage of hormone replacement therapy
A clinical history in which there is a history of sepsis.
A clinical history in which there is a history of pneumonia.
A clinical history in which there is a history of open wounds.
A clinical history in which there is a history of a high unexplained fever .
clinical history of high unexplained fever
A clinical history in which there is a history of positive blood cultures.
clinical history of positive blood cultures
A clinical history in which there is a history of abnormal white blood cell levels.
clinical history of abnormal white blood cell levels
A clinical history in which there is a history of fungal infections.
A clinical history in which there is a history of the presence of ascites fluid.
A clinical history in which there is a history of cellulitis.
A clinical history in which there is a history of receiving a blood transfusion while in another country.
clinical history of blood transfusion in foreign country
A clinical history in which there is a history of receiving a human tissue or organ transplant .
clinical history of human tissue transplant
A clinical history in which there is a history of receiving an animal tissue or organ xenotransplant.
clinical history of animal tissue xenotransplant
A clinic history in which there is a history of a recent of smallpox vaccination.
clinical history of smallpox vaccination
A clinical history in which there is a history of contact with someone who recently had smallpox.
a clinical history of contact with someone with smallpox
The patient had a clinical history of dialysis treatment three times a week for longer than one month.
A clinical history in which there is a history of significant regular dialysis treatment.
A clinical history in which there is a current diagnosis of cancer at death.
A clinical history in which there is a history of cancer diagnosis in the preceding five years.
A clinical history in which there is a history of cancer diagnosis within a specified time frame.
clinical history of cancer within a time period before death
A clinical history in which there is a history of tuberculosis .
A clinical history in which there was active meningitis at death.
A clinical history in which there was active encephalitis at death.
A clinical history in which there is a history of long term steroid use.
clinical history of long term steroid use
A clinical history in which there is a history of osteomyelitis.
A clinical history in which there is a history of unexplained seizures.
clinical history of unexplained seizures
A clinical history in which there is a history of unexplained weakness and fatigue described as flu-like symptoms.
clinical history of unexplained weakness and fatigue
A clinical history in which there is a history of exposure to toxic substances that may have led to chronic conditions.
A clinical history in which there is a history of an animal bite in the last 12 months, from an animal suspected to have rabies.
A clinical history in which there is a history of an animal bite in recent past, from an animal suspected to have rabies.
A clinical history in which there is a history of clotting disorders, such as hemophilia, requiring treatment with human-derived clotting factors.
A clinical history in which there is a history of growth hormone use.
A clinical history in which there is a history of the donor not being able to be tested for Human Immunodeficiency Virus (HIV) because of hemodilution.
clinical history of inability to have Human Immunodeficiency Virus testing due to hemodilution
A clinical history in which there is a history of unexplained weight loss.
clinical history of unexplained weight loss
A clinical history in which there is a history of night sweats.
A clinical history in which there is a of blue or purple spots on the skin or mucus membranes (typical of Kaposi's sarcoma).
clinical history of blue or purple spots on skin or mucous membranes
A clinical history in which there is a history of unexplained lymphadenopathy lasting more than one month.
A clinical history in which there is a history of unexplained lymphadenopathy of a specific duration.
clinical history of unexplained lymphadenopathy
A clinical history in which there is a history of fever of at least 38.6 Celsius for more than 10 days.
A clinical history in which there is a history of fever of at least 38.6 Celsius for a specified duration.
A clinical history in which there is are active signs of unexplained persistent cough and/or shortness of breath.
clinical history of an unexplained cough or shortness of breath
A clinical history in which there is a history of opportunistic infections.
clinical history of opportunistic infections
A clinical history in which there is a history of sexually transmitted diseases
clinical history of sexually transmitted disease
A clinical history in which there is a history of drug abuse.
A clinical history in which there is a history of a Severe Acute Respiratory Syndrome (SARS) diagnosis.
clinical history of Severe Acute Respiratory Syndrome
A clinical history in which there is a history of recent contact with someone who has Severe Acute Respiratory Syndrome (SARS).
clinical history of exposure to Severe Acute Respiratory Syndrome
A clinical history in which there is a history of West Nile Virus (WNV) infection.
A clinical history in which there is a history of contact with a human or animal who has West Nile Virus (WNV).
clinical history of West Nile Virus exposure
A clinical history in which there is a history of current gonorrhea infection or treatment for gonorrhea in the last 12 months.
A clinical history in which there is a history of active gonorrhea infection or treatment for gonorrhea in the recent past.
A clinical history in which there is a history of current syphilis infection or treatment for syphilis in the last 12 months.
A clinical history in which there is a history of active syphilis infection or treatment for syphilis in the recent past.
A clinical history in which there is a history of Hepatitis B infection.
A clinical history in which there is a history of Hepatitis C infection.
A clinical history in which there is a history of Human Immunodeficiency Virus (HIV).
clinical history of Human Immunodeficiency Virus
A clinical history in which there is a history of systemic lupus
A clinical history in which there is a history of sarcoidosis.
A clinical history in which there is a history of scleroderma.
A clinical history in which there is a history of Reye's Syndrome.
A clinical history in which there is a history of rheumatoid arthritis.
clinical history of rheumatoid arthritis
A clinical history in which there is a history of idiopathic heart disease.
clinical history of idiopathic heart disease
A clinical history in which there is a history of Alzheimer's Disease.
A clinical history in which there is a history of dementia with unknown cause that is not caused by a previous Cerebrovascular Accident (CVA) infection, head trauma or brain tumor).
clinical history of dementia of unknown cause
A clinical history in which there is a history of Multiple Sclerosis (MS).
A clinical history in which there is a history of Amyotrophic Lateral Sclerosis (ALS)
clinical history of Amyotrophic Lateral Sclerosis
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
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
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
chromatography column
Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
Frank Gibson
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
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.
liquid chromatography mass spectrometry platform
A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
software optimization objective
Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
measuring
scientific observation
OBI branch derived
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
GROUP:Role Branch
OBI, CDISC
CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
patient role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
protocol testing objective
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
measured expression level
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
sequence feature identification objective
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
molecular feature identification objective
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
hardware testing objective
Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
filter paper
a device manufacture with the intent to provide a porous unsized paper used for filtering.
protocol optimization objective
Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
microtiter plate
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
Melanie Courtot
microplate
methodology testing objective
Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
cellular feature identification objective
Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
hardware optimization objective
Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
software testing objective
Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
plan
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
AR, BP, JM, MC, PRS
branch derived
organism feature identification objective
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
mass analyzer
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
contain function
A contain function is a function to constrain a material entities location in space
heat function
A heat function is a function that increases the internal kinetic energy of a material
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
mechanical function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
environment control function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer
primer role
The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
The extraction of RNA from an input material that specifically isolates viral RNA
viral RNA extraction
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
PCR
polymerase chain reaction
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity.
This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term.
averaging objective
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
An assay with the objective to determine a sequence feature of DNA
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
needle
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule.
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
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
packed column
A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube.
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
organic acid column
An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant.
protein column
A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins.
refactor as defined class
normal phase column
A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column.
chromatography instrument
Any instrument that is used to carry out a chromatography experiment.
chromatography device, defined class?
cation exchange column
A cation exchange column is a chromatography column that is used in cation exchange chromatography.
capillary column
A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
reversed phase column
A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column.
chromatofocusing column
A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind.
trap column
A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector.
affinity column
An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
gel filtration column
A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
ion exchange column
An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
spin column
A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits.
high temperature column
A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
anion exchange column
An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
plunger column
A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column.
liquid chromatography column
A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix.
open tubular column
An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube.
glass column
A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
size exclusion column
A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
custom made column
A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group.
gel permeation column
A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size.
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
carbon nanotube column
Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well.
acquisition computer
A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
NMR instrument
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
a portion of urine collected from an organism
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
are we happy calling collection of urine a material separation?
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
fuzzy clustering objective
A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori.
blood drawn from a human for glucose assay
a material entity derived from a portion of blood collected from an organism
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
statistical hypothesis test objective
is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
average value
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
is an objective to obtain an output material that contains several input materials.
PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10.
adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
adapted from information provided by Solid web site
ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing).
A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase
Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing
A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material entity that has the material sample role
Application of the Bonferroni correction
A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
multiple comparison correction objective
the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality
An objective specification maintains some or all of the qualities of a material over time.
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
The SALK institute is a research organization.
An organization formed with a goal to have its members conduct investigations
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
A person or organization that has a manufacturer role
a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide
2010-01-31: Philippe Rocca-Serra placeholder
human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
A medical organization at which sick or injured people are given clinical care
modified from the wording of the wordnet definition
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
A RNA extraction process in which the desired output material is RNA in the organelle(s).
A RNA extraction process in which total cellular and organelle RNA are extracted.
A primer in a PCR reaction. A probe on an Affymetrix chip.
A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
A RNA extraction process in which the desired output material is RNA in the cytoplasm.
A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees.
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
A RNA extraction process in which the desired output material is RNA in the nucleus.
real time polymerase chain reaction assay
An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
quantitative real time polymerase chain reaction
A specimen that has been modified in order to be able to detect it in future experiments
A device with a separation function realized in a planed process
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
is realized in a planned process where the bearer participates
AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
A function that is realized when a reagent is automatically added to some research material.
PERSON: Nicole Vasilevsky, Matthew Brush
4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people?
A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package
An objective specification which is fulfilled by the provision of some training.
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent.
A sequencing centre has a service provision objective
An objective which is fulfilled by the provision of some service e.g. a training service
an objective which aims to create a device with a specified function
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
A device that is used to measure the pH (acidity or alkalinity) of a liquid.
A device that is used to isolate and collect RNA for subsequent molecular analysis.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
A device that is used to automatically stain tissue sections on slides or tissue specimens.
A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
A group of linked computers, working together closely so that in many respects they form a single computer.
A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations.
A device that is used to perform paraffin embedding of tissue specimens.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
nucleic acid extraction/purification instrument
A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
A device that is used to isolate and collect DNA for subsequent molecular analysis.
A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins.
A microinjection device that is used to measure very small volumes of liquids.
An device that is used to determine the order of amino acids in protein sequences.
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
genetic transformation objective
a material transformation objective aims to create genetically modified organism or cell
Person: Jie Zheng
suggested to be added by BP and AR during Oct 25, 2010 dev call
assay validation objective
an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
PERSON: Chris Stoeckert, Jie Zheng
GROUP: Penn Group
validation by real time PCR design
a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
MO_434 real_time_PCR_quality_control
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
discussed on Nov 15, dev call All subtype will be defined by textual definition now.
selective organism creation objective
an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29
An assay that determines the sequence of an RNA molecule.
SNP microarray
a DNA microarray used to detect polymorphisms in DNA samples
transcription profiling by tiling array assay
A transcription profiling by array assay that uses a tiling path array.
An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
transcription profiling by high throughput sequencing
tiling microarray
a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Person: Chris Stoeckert, Jie Zheng
Group: Penn Group
An assay that analyses the microRNA component of the transcriptome using a microRNA array.
A transcription profiling assay that uses reverse transcription PCR (RT-PCR).
A transcription profiling assay that uses array technology.
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
cell collecting
A planned process that collects cells from culture.
linear amplification
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
sequence assembly algorithm
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.
NIAID GSCID-BRC metadata working group
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
investigation description
A textual entity that describes an investigation.
project description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
specimen ID
sample identifier
average depth of sequence coverage
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.
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
collection date
organism identification objective
A biological feature identification objective to identify the organism species in a specimen.
Penn Group
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.
Bioinformatics Resource Center
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
Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
nano-cap analysis of gene expression assay
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846
A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE).
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160
A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
molecular function identification objective
is an objective specification which aims to discover molecular function realized by a molecular entity
PERSON:Philippe Rocca-Serra
OBI group
cellular structure feature identification objective
is an objective specification which aims to discover cellular structure properties
structural analysis by paired-end tag sequencing assay
Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419]
An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants.
transcript analysis by paired-end tag sequencing assay
Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299]
A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology.
transcription start site identification objective
A transcription profiling identification objective that aims to characterize the transcription start sites of genes.
paired-end library preparation
A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
DNase I hypersensitive sites sequencing assay
Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541]
An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I.
protein and RNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and RNA.
JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'.
formaldehyde-assisted isolation of regulatory elements assay
Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217]
An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity.
RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248]
An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing.
assay array
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
Illumina BeadChip
An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi
Illumina methylation BeadChip
A BeadChip made for an analyte assay that generates information about DNA methylation.
sequence assembly process
A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs).
PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly.
Alejandra Gonzalez-Beltran
reagent
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.
(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
organization of specimen provider principal investigator
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
organization of Bioinformatics Resource Center contact person
An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact's Institution
specimen repository organization
An organization that provides a service to store and distribute specimens
sequencing facility organization
An organization that provides sequence determination service
specification of data to be generated in an investigation
Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype
An objective specification which indicates the type of data that will be generated and submitted to a database.
organization of specimen collector
An organization that is the affiliation of the person collecting the specimen
organization of sequencing facility contact person
An organization that is the affiliation of the contact representative at the sequencing facility
Sequencing Facility Contact's Institution
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
DNA replication identification objective
A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time.
chromosome conformation identification objective
A molecular feature identification objective that aims to determine spatial organization of chromatin.
microRNA profiling by high throughput sequencing assay
Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767
A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology.
micrococcal nuclease digestion followed by high throughput sequencing assay
Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607]
An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease
A transcription profiling assay that quantifies the microRNA species within a biological sample.
selection
PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
Person: Philippe Rocca-Serra
selection process
OBI
a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
grant agency
An organization that provides funding support for projects such as investigations.
'funding organization' http://vivoweb.org/ontology/core#FundingOrganization
software pipeline
A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements.
WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29
sequence annotation
A sequence annotation bioinformatics analysis that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
target gene specification
http://www.ncbi.nlm.nih.gov/pubmed/25367129 "performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene)
is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey
PRS for OBI
target gene
An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric.
The best action to take is typically defined as the one that maximizes expected utility.
biodiversity assessment objective
biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level
Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710
A cancer therapeutic procedure that involves a surgical procedure as a main part.
A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
Illumina Infinium Human Methylation 450K BeadChip
surgical cancer treatment
specimen gross appearance of metastatic tumor
Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139
A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution.
A specimen gross appearance of a tumor that has spread from its original site by discontinuous (not direct) spread, e.g. by blood or lymphatics.
Illumina Infinium Human Methylation 27K BeadChip
specimen gross appearance of tumor center
Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850
A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis.
A specimen gross appearance of the most internal topographic location of the tumor.
Illumina Human 1M-Duo Infinium HD BeadChip
Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407
A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
A specimen gross appearance of the border of the tumor with non-tumorous tissue.
specimen gross appearance of tumor edge
Mouse 385K Whole Genome CGH Tiling Array
research authorization for post mortem specimen donation for a specific tissue or fluid
Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/
A research authorization documentation for postmortem specimen donation in which the authorization is for a specified tissue or biological fluid.
A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features.
Nimblegen Mouse 385K Whole Genome CGH Tiling Array
Mouse 3x720K Whole Genome CGH Tiling Array
Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584
A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features.
An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues.
Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array
0-non autolyis
Human 3x720K Whole Genome CGH Tiling Array
Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464
A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features.
An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues.
Nimblegen Human 3x720K Whole Genome CGH Tiling Array
1-slight autolysis
Human 2.1M Whole-Genome CGH Tiling Array v2.0
Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274
A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features.
An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues.
Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0
2-moderate autolysis
Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882
A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.
An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues.
3-severe autolysis
A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS).
A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants.
Affymetrix HT Human Genome U133 Plus 2 Array Plate Set
An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay
A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants.
Affymetrix HT Human Genome U133 Array Plate Set
An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories.
SAGE ditag library preparation
A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library.
Related tracker:https://sourceforge.net/p/obi/obi-terms/720/
serial analysis of gene expression assay
A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced.
translation-associated transcript leader sequencing assay
An RNA-seq assay that combines TL-seq with polysome fractionation
An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing.
Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528
A RNA-seq assay that sequences only mRNA protected by the ribosome during translation.
self-transcribing active regulatory region sequencing assay
Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765.
An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA.
self-transcribing active regulatory region sequencing
An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs).
Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615.
A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level.
A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
specimen container
COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
A container with the function of containing a specimen.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
Chris Stoeckert
Duke Biobank, OBIB
Biobank
Specimen containers are typically constructed or treated in a particular manner in order to perform their containing a specimen function. This will be a defined class so that any container (e.g., cryotube, vacutainer, conical test tube) with the function of containing a specimen will be inferred to be a specimen container.
Human 6x630K CGH Whole Genome Tiling Array
A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features.
Term request: https://sourceforge.net/p/obi/obi-terms/791/
Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group
NimbleGen Human 6x630K CGH Whole Genome Tiling Array
An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits.
bromouridine labeling and sequencing assay
An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs.
bromouridine pulse-chase and sequencing assay
An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time.
WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS.
A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.
Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later.
DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified.
A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons).
H&E-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of H&E slide staining.
Chris Stoeckert, Ned Haubein
OBIB, OBI
IHC-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
immunohistochemistry slide specimen
Illumina Genome Analyzer
A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.
Person: Chris Stoeckert, Jason Hilton
ENCODE project
Illumina HiSeq X Ten
A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann
HiSeq X Ten
Illumina Infinium Omni5Exome-4 Kit
An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation.
Illumina Infinium MethylationEPIC BeadChip
An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution.
Nanostring nCounter miRNA expression assay
A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification.
bromouride labeling and sequencing after UV exposure
An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions.
extrachromosomal circular DNA sequencing assay
An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods.
An organization that delivers messages, packages, and mail.
courier organization
A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item.
courier tracking number
An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories.
Leica Peloris rapid tissue processor
molecular analysis facility organization
An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs.
An organization that provides molecular analysis service.
A clinical history in which there is a diagnosis of cancer.
A clinical history in which there was no diagnosis of cancer.
A clinical history in which it is not known whether there was a diagnosis of cancer.
A clinical history in which there is a diagnosis of cancer in a blood relative.
A clinical history in which there is a diagnosis of cancer in the female sibling of a parent.
A clinical history in which there is a diagnosis of cancer in a male sibling.
A clinical history in which there is a diagnosis of cancer in a person's female child.
A clinical history in which there is a diagnosis of cancer in a male parent.
A clinical history in which there is a diagnosis of cancer in a female parent.
A clinical history in which there is a diagnosis of cancer in a female sibling.
A clinical history in which there is a diagnosis of cancer in a person's male child.
A clinical history in which there is a diagnosis of cancer in a male sibling of a parent.
A clinical history in which there is a diagnosis of cancer in a female parent of a parent.
A clinical history in which there is a diagnosis of cancer in a male parent of a parent.
A clinical history in which there is a diagnosis of cancer in a male child of a sibling.
A clinical history in which there is a diagnosis of cancer in a female child of a sibling.
A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays.
A clinical history in which there has been second hand exposure to tobacco smoking.
exposure to second hand smoke in household during childhood
An exposure to second hand smoke that occurred in the (patient's) household when the person was a child.
exposure to second hand smoke in current household
An exposure to second hand smoke in person's current household.
A clinical history in which a female has had a pregnancy.
A clinical history in which a woman has had gynecologic surgery in the past.
A gynecologic surgery history in which a woman has had a hysterectomy.
A gynecologic surgery history in which a woman has had a unilateral oophorectomy.
neither hysterectomy nor oophorectomy history
A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy.
A clinical history in which an individual has had hormonal replacement therapy in the past.
transcription start site mapping by primer extension assay
A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached.
precision nuclear run-on sequencing assay
An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends.
precision nuclear run-on and sequencing assay
alignment counting algorithm
An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts).
Stephen A. Fisher, Junhyong Kim, Dan Berrios
alignment counting application
A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes.
base calling application
A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis.
bcl2fastq software application
A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
reference genome-transcriptome alignment algorithm
An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome.
star algorithm
A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference.
microraft
A material separation device also commerically known as Isoraft, that is used to isolate single cells.
A specimen that is derived from amniotic fluid.
A specimen that is derived from cerbrospinal fluid.
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
A specimen that is derived from pericardial fluid.
A specimen that is derived from synovial fluid.
A specimen that is derived from vireous humor.
A specimen that is derived from bone marrow.
A specimen that is derived from placenta.
A specimen that is derived from peritoneal fluid.
A specimen that is derived from pleural fluid.
A specimen that is derived from prostate gland.
A specimen that is derived from skeletal muscle.
A specimen that is derived from renal medulla.
A specimen that is derived from adrenal gland.
A specimen that is derived from urinary bladder.
A specimen that is derived from tibial artery.
A specimen that is derived from pancreas.
A specimen that is derived from stomach.
A specimen that is derived from pituitary gland.
A specimen that is derived from adipose tissue.
A specimen that is derived from cortex of kidney.
A specimen that is derived from esophagus mucosa.
A specimen that is derived from esophagus muscularis mucosa.
A specimen that is derived from cerebral cortex.
A specimen that is derived from thyroid gland.
A specimen that is derived from cerebellum.
A specimen that is derived from tibial nerve.
A specimen that is derived from coronary artery.
A specimen that is derived from the atrium auricular region.
A specimen that is derived from the esophagogastric junction.
A specimen that is derived from minor salivary gland.
A specimen that is derived from omentum.
A specimen that is derived from female gonad.
A specimen that is derived from sigmoid colon.
A specimen that is derived from suprapubic skin.
A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed).
A data transformation in which data contained in 2 or more files are merged into a single file.
A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm.
Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819
A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013
An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing.
An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing.
A RNA extraction process in which only RNAs lacking a polyA tail are retained
Novel transcript forms were assessed by isoform sequencing.
A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms.
Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run.
The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed.
The results of a data transformation of sequence data in which files containing aligned sequence data are merged together
The results of a DNA methylation profiling assay
A data transformation in which subsequences of a molecular sequence are cut (removed).
A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.
Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.).
detection of pathogenic organisms objective
An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms.
insecticide resistance detection objective
An organism feature identification objective that aims to detect insecticide resistance of an insect.
A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.
blood plasma specimen
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
PERSON: Maura Gasparetto
plasma
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood serum specimen
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
bronchial alveolar lavage
solution containing lung derived T cells, eosinophils, and TNFa.
Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
BAL
GROUP: IEDB
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
feature extraction objective
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
differential expression analysis objective
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
PERSON: Elisabetta Manduchi
descriptive statistical calculation objective
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
Monnie McGee
PERSON: James Malone
PERSON: Monnie McGee
sequence analysis objective
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
survival analysis objective
A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation.
a data transformation objective of determining the concordance or agreement between human judges.
inter-rater reliability objective
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
PERSON: Tina Boussard
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
data visualization
data vector reduction objective
Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k.
Richard H. Scheuermann
PERSON: Richard H. Scheuermann
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
data normalization objective
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
correction objective
Type I error correction
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
background correction objective
A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
curve fitting objective
A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
center calculation objective
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
class discovery objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
discriminant analysis objective
unsupervised classification objective
class prediction objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
supervised classification objective
spread calculation objective
Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean
is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set
Awaiting English definition from Monnie McGee
scaling objective
Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
error correction objective
Application of a multiple testing correction method
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
James Malone, Helen Parkinson
sequence analysis data transformation
A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns.
cross validation objective
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
rotation estimation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
merging of columns from two different data sets
A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
combining objective
merging objective
A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables.
Calculation of characteristic path length in mass spectrometry
is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process.
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
OBI-Branch: adapted from wikipedia and wordnet
filtration
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
washing
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
nucleic acid hybridization
DNA Subtraction
PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81
a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library.
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
is a planned process with specified input original document and specified output edited document
document editing
Biofilm Flow Cell
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
Person:John Quinn
flow cell
fluid pressure regulator
LSR2 fluid pressure regulator
Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank.
Person: John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
DNA sequencer
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Trish Whetzel
arrayer
BioRobotics Microgrid II TAS, Affymetrix GMS 417
a device which deposits biological material onto a substrate in a defined pattern.
MO_697 arrayer
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
computer
Apple PowerBook, Dell OptiPlex
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
microarray
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
Daniel Schober
DNA microarray
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
PERSON: Daniel Schober
DNA Chip
DNA-array
protein microarray
The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
microscope slide
PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
human subject enrollment
enlisting familiy members of HIV patients into a study
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
As with group assignment, should the specified output here be an organism which bears a role
IEDB
criteria come from plan / clinical trial branch
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
physical combination of several instances of like material
sample pooling
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
pooling specimens
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
aliquoting
apportioning
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
cell culture splitting
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.
addition of molecular label
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
OBI developer call, 3-12-12
lavage
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
This is not washing, in which case the material of interest is not the resulting fluid
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
the use of a chemical or biochemical means to infer the sequence of a biomaterial
has_output should be sequence of input; we don't have sequence well defined yet
Sequencing Technology
SA4
NIAID GSCID-BRC
DNA polymerase amplification
The use of taq polymerase to amplify a DNA fragment during a PCR.
DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input
PERSON:Kevin Clancy
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
enzymatic DNA replication
the use of enzymes to duplicate DNA molecules
the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
requested by Helen Parkinson for MO
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
donor
A material separation where blood is taken from an organism.
blood harvesting
A cell culture into which a mixture of peptides is being added.
A material entity into which another is being added in a material combinatino process
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
A sequence data that is about the primary structure of RNA.
ITPPR
RNA sequence data
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data.
definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
biobank
An identifier in natural language referring to a biobank.
Name of biobank
biobank proper name
An identifier that consists of two letters, is part of the ISO 3166-1, and designates countries, dependent territories, and special areas of geographical interest.
Two-letter country codes defined in ISO 3166-1, part of the ISO 3166 standard published by the International Organization for Standardization (ISO), to designate countries, dependent territories, and special areas of geographical interest.
ISO 3166-1 alpha-2 code
A biobank identifier that has an ISO 3166-1 alpha-2 code as a part.
Biobank ID
Textual string of letters starting with the country code (according to standard ISO1366 alpha2) followed by the underscore “_” and post-fixed by a biobank ID or name specified by its juristic person (nationally specific).
biobank idenfier with ISO 3166-1 alpha-2 code
The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address.
Sample Collection/Study contact country
ISO 3166-1 alpha-2 code for sample collection or study contact
A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process.
contact role
A personal name that designates the person acting as contact for a sample collection or a study.
Biobank contact person
name of biobank contact person
A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable.
post-office box
The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address.
Biobank country code
ISO 3166-1 alpha-2 code for biobank contact person
A proper name that designates a study.
Study name
study proper name
A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study.
Sample Collection Responsible / Principal Investigator
name of sample collection responsible or principal investigator
Sample Collection/Study contact person
name of sample collection or study contact person
An ISO 3166-1 alpha-2 code that designates the country a biobank is located in.
biobank location ISO 3166-1 alpha-2 code
An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program.
CTEP organization identifier
A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code.
biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
fixed tissue specimen
A processed specimen that is the output of a fixation process.
Alice Nzinga
A fixed tissue specimen that is in block form.
fixed tissue block specimen
fixed tissue slide specimen
A fixed tissue specimen that is placed in a slide.
A specimen that has been procured from a histology slide under direct microscopic visualization.
microdissected specimen
A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.
A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study.
biobank contact role
sample collection or study contact role
A material processing that uses chemical process by which biological tissues are preserved from decay. Fixation terminates any ongoing biochemical reactions and may increase stability of the treated tissues.
The choice of fixation depends on the type of study.
fixation
adherance to specification
All specimens that meet the set parameters to be procured on.
specimen meeting specification
A personal name that designates the person who prepared the specimen.
specimen preparation contact
15min
A time measurement datum that states the duration during which a specimen was submerged in formalin.
time in formalin measurement
An identifier that refers to a specimen donor who is participating in specimen collection process for tissue procurement purposes and is usually assigned at the time of donor procurement.
case ID
A specimen that is normal.
normal specimen
sample donor
A Homo sapiens who contributes specimen.
specimen donor
A planned process of preparing and submitting specimens to storage.
specimen handling
sample handling
DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
William R. Hogan
health care role
human health care role
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
A role inhering in an entity realized by social interactions in human society.
Previous definition: A role played by an entity in human social processes.
role in human social processes
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
legal person role
A time quality inhering in a bearer by virtue of how long the bearer has existed.
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.
The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A physical quality inhering in a bearer that has mass near a gravitational body.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A physical quality of the thermal energy of a system.
Damion's Note: Future use might prefer: CMO_0000015 body temperature.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
An organism having both male and female sexual characteristics and organs.
A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
A quality that inheres in an entire organism or part of an organism.
A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content.
A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
A native plant cell (PO:0025606) which is diploid (2n), and undergoes meiosis (GO:0007126) to produce four haploid (1n) plant spores (PO:0025017).
A cell which is a plant structure (PO:0009011).
Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.
A native plant cell (PO:0025606) that is the larger cell of a microgametophyte (PO:0025280) in seed plants. It does not divide further and develops into a pollen tube cell (PO:0025195).
Cell that constitutes the central part of the root cap, arranged in longitudinal files.
A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).
A single meristematic cell (PO:0004010) at the tip of a plant structure where apical growth occurs.
Apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex, or protonema in bryophytes and some pteridophytes. Apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. The apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped (lenticular) with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo, or later.
An apical cell that is part of a whole plant in the gametophytic phase.
A meristematic apical cell that is part of a whole plant in the sporophytic phase.
Occurs in pteridophytes and the sporophyte of bryophytes.
molecular label role
a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
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
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
A pancreatic cell that produces and secretes hormones such as insulin and glucagon.
An Islet cell is a pancreatic cell that produces and secretes hormones such as insulin and glucagon.
The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO].
Editor notes - endocrine and exocrine pancrease are not co-associated in hagfishes or lampreys [PMID:20959416] - create a separate class for these?
A cell collecting process used to isolate PBMCs, including T cells, from whole blood using density gradient centrifugation (e.g., Ficoll-Paque).
peripheral blood mononuclear cell isolation
object quality
language entity
visual language entity
name
brand name
scientific name
description
label
first name
last name
legal name
version label
unique identifier
answer
A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource.
URL
numeric label
study design
annotation
history
a gene symbol is a short name assigned to a gene.
gene symbol
evolutionary lineage
family history
medical history
A malignant neoplasm characterized by a vascular proliferation which usually contains blunt endothelial cells. Erythrocyte extravasation and hemosiderin deposition are frequently present. The most frequent site of involvement is the skin; however it may also occur internally. It generally develops in people with compromised immune systems including those with acquired immune deficiency syndrome (AIDS).
A multicentric, malignant neoplastic vascular proliferation characterized by bluish-red cutaneous nodules, usually on the legs, toes, or feet, that slowly increase in size and number and spread to more proximal sites. The tumors have endothelium-lined channels and vascular spaces mixed with aggregates of spindle-shaped cells; they may remain confined to skin and subcutaneous tissue, but widespread visceral involvement may occur.
A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc.
An immature lymphocyte that has enlarged in response to antigenic stimulation.
Often referred to as a blast cell. Unlike other usages of the suffix -blast a lymphoblast is a further differentiation of a lymphocyte, T- or B-, occasioned by an antigenic stimulus. The lymphoblast usually develops by enlargement of a lymphocyte, active re-entry to the S phase of the cell cycle, mitogenesis and production of much m-RNA and ribosomes.
Cell coming from the intergument, organ that constitutes the external surface of the body. The intergument consists of the epidermis, dermis, and skin appendages.
A convenient source of human endothelial cells are those that line the large vein in the umbilical cord which is usually discarded together with the placenta after childbirth. The cells can be removed as a fairly pure suspension by mild enzymatic treatment of the vein followed by some mechanical distraction and will grow relatively easily in culture, retaining their differentiated characteristics for several passages.
nestin positive islet-derived progenitor cell
dendritic cell-derived intermediate cell
experimental cell is a cell which is experimentally derived such as a cell line cell, or a cell differentiated in culture. Experimentally derived cells may have diffrent properties from the cell from which they originally derived, such as through gene expression changes.
neural stem cells experimentally derived from ES cells
embryonic stem cell derived neuronal stem cell
A cell with empty-appearing cytoplasm when viewed with a light microscope.
An epithelial cell lining the thyroid follicle.
An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.
Any aspect of an individual's life, behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a disease, condition or injury.
Mikkelsen et al. (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560
Induced pluripotent stem cells (iPS cells or iPSCs) are a type of pluripotent stem cell artificially derived from a non-pluripotent cell. Various methods exist to revert cells to pluripotency such as reprogramming mediated through a mature metaphase II oocyte as in somatic cell nuclear transfer.
induced pluripotent stem cell
The point in time at which an individual was born.
date of birth
The point at which a clinical diagnosis is made.
date of diagnosis
A adult mesenchymal stem cell derived from adipose tisssue
adipose tissue derived mesenchymal stem cell
placental pericyte
The mural granulosa cells form during antral folliculogenesis, process in which a single antral cavity is formed, separating two functionally distinct granulosa cell populations. The mural granulosa cells line the wall of the follicle and are critical for steroidogenesis and ovulation.
Neuron class of two pharyngeal neurosecretory-motor neurons.
type of cells that make up muscle layers in the pharynx in worms such as C. elegans
disease cell type
Induced pluripotent stem cell line from a Caucasian male with type 2 diabetes, same donor as of MSLCL cell line.
Induced pluripotent stem cells derived from MSC658 fibroblasts.
lympoid tissue
utering smooth muscle cell
glial brain cell
mantle cell
merkel cell
address