Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Alan Ruttenberg
Allyson Lister
Barry Smith
Bill Bug
Bjoern Peters
Carlo Torniai
Chris Mungall
Chris Stoeckert
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Holger Stenzhorn
James A. Overton
James Malone
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jessica Turner
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philippe Rocca-Serra
Phillip Lord
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.
OWL-DL
An ontology for the annotation of biomedical and functional genomics experiments.
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
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
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID range allocated
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
Add as annotation triples in the granting ontology
retired from use as of
relates a class of CRID to the date after which further instances should not be made, according to the central authority
In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA tools project (http://isa-tools.org)
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An alternative term used by the Functional Genomics Data (FGED) Society.
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
An entity responsible for making contributions to the content of the resource.
Contributor
Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
The extent or scope of the content of the resource.
Coverage
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
Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).
An unambiguous reference to the resource within a given context.
Resource Identifier
Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.
A language of the intellectual content of the resource.
Language
Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.
An entity responsible for making the resource available
Publisher
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 related resource.
Relation
Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
Information about rights held in and over the resource.
Rights Management
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
Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.
The nature or genre of the content of the resource.
Resource Type
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
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. 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 succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
has measurement unit label
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
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.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
is quality measurement of
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
is quality measured as
A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
Person:Bjoern Peters
is quality specification of
inverse of the relation of is quality specification of
quality is specified as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
has measurement datum
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
replaced by: http://purl.obolibrary.org/obo/BFO_0000058
obsolete_is_concretization_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
replaced by: http://purl.obolibrary.org/obo/BFO_0000059
obsolete_is_concretized_as
A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
replaced by: http://purl.obolibrary.org/obo/BFO_0000086
obsolete_has_quality
has_specified_output
The inverse property of is_specified_output_of
Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
obsolete_is_realized_by
A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
obsoleted_has_specified_output_information
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.
has_make
has_manufacturer
Relation between an independent continuant and a function.
replaced by: http://purl.obolibrary.org/obo/BFO_0000085
obsolete_has_function
some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
obsoleted_is_reagent_in
example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes.
Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm]
replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'
obsolete_realizes
see example_of_usage for is_reagent_in
Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
obsoleted_utilizes_reagent
some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
Relationship between a device and a protocol application in which it participates
obsoleted_is_device_for
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
see example_of_usage for is_device_for
Relationship between protocol application and an intrument in which it participates
obsoleted_utilizes_device
position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity
A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition)
is_proxy_for
A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
obsoleted_has_specified_input_information
A relation between a continuant C and a role R. The reciprocal relation of role_of.
replaced by: http://purl.obolibrary.org/obo/BFO_0000087
obsolete_has_role
2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 . Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the
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
A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
Is the inverse relation of has_specfied_input_information
A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole.
JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
is grain of
A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use
5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship.
A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
A relationship between two material entitites that each have disposition to form a complex with the other.
This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other
has organization member
Relating an organization to a legal person or organization.
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
has performer
A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process.
OBI
The 'has 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).
A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc.
The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
is a relationship between a process and a preceding occurrent that directly caused the later one to occur
A relationship between two material entities that form a complex based on a selective, non-covalent interaction.
The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope.
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
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
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
surrounded by
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
starts
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values.
has_feature_value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
has representation
12th arrondissement of Paris
I feel sick to my stomach every Tuesday
'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text.
Further processing may enable the value to be represented in a component data structure such as an OBI value specification.
A planned process that has specified output a software product and that involves the creation of source code.
Mathias Brochhausen
William R. Hogan
A planned process resulting in a software product involving the creation of source code.
software development
A measurement datum that is the output of counting.
count
The planned process of finding the number of elements in a finite set of objects.
counting
software source code version control repository
A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based
source code repository
process of compiling software
A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
compiling software
creating a data set
A planned process that has a data set as its specified output.
data set creation
dataset creation
dataset creating
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
obsolete dependent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
specifically dependent continuant
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]
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of love, an obligation between one person and another.
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies.
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.
An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways.
An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.
A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides.
The nitrogen oxoanion formed by loss of a proton from nitrous acid.
A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma.
A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.
A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases.
A glycine derivative having methyl and amidino groups attached to the nitrogen.
A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species.
A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain.
An aldohexose used as a source of energy and metabolic intermediate.
An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5..
A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin.
The carbon oxoanion resulting from the removal of a proton from carbonic acid.
A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses
An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups.
Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids.
A halide anion formed when chlorine picks up an electron to form an an anion.
A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics.
A sodium salt of the conjugate of any bile acid with either glycine or taurine.
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 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17.
A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups.
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group.
An inorganic chloride salt having sodium(1+) as the counterion.
An oxopurine that is the final oxidation product of purine metabolism.
A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile.
A racemate comprising equimolar amounts of (R)- and (S)-lactic acid.
A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands.
A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring.
A monoatomic monocation obtained from sodium.
A monoatomic monocation obtained from potassium.
The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second).
An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions.
A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy.
A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A cobalt group element atom of atomic number 45.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A carboxylic acid containing one or more amino groups.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
polymer
Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids.
A phosphorus oxoanion that is the conjugate base of phosphoric acid.
A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units.
The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
A class of lipoproteins of small size (4-13 nm) and dense (greater than 1.063 g/ml) particles. They are synthesized in the liver without a lipid core, accumulate cholesterol esters from peripheral tissues and transport them to the liver for re-utilization or elimination from the body (the reverse cholesterol transport).
A class of lipoproteins of small size (18-25 nm) and low density (1.019-1.063 g/ml) particles with a core composed mainly of cholesterol esters and smaller amounts of triglycerides. The surface monolayer consists mostly of phospholipids, a single copy of apolipoprotein B-100, and free cholesterol molecules. The main function of LDL is to transport cholesterol and cholesterol esters from the liver. Excessive levels are associated with cardiovascular disease.
A class of lipoproteins of large size (30-80 nm), very low density (0.93-1.006 g/ml) particles with a core composed mainly of triglycerides and a surface monolayer of phospholipids and cholesterol into which are imbedded the apolipoproteins B, E, and C. VLDL facilitate the transport of endogenously made triglycerides to extrahepatic tissues.
Any magnesium ion that is positively charged.
A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem.
A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis.
A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small.
A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL).
Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL).
A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.
A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.
A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.
A 3,1-benzoxazin-1,4-dione having an N-methyl substituent.
A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.
A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
A hydrate that is the monohydrate form of tacrolimus.
An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species.
A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids.
A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group.
A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.
Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence.
confocal laser scanning fluorescence microscopy
fluorescence confocal scanning laser microscopy
scanning confocal fluorescence microscopy
Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series.
liquid chromatography tandem mass spectrometry
liquid chromatography tandem mass spectroscopy
liquid chromatography-tandem mass spectroscopy
liquid chromatography-tandem mass spectrometry
cell line cell
细胞系细胞
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分
'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time.
mortal cell line cell
非永生细胞系细胞
A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence.
immortal cell line cell
永生细胞系细胞
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。
cell line
细胞系
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。
培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。
immortal cell line
A cell line that is expected to be capable of indefinite propagation in an vitro culture.
mortal cell line
A cell line is able to support only a limited number of passages in vitro.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A 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 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.
A flattened epithelial cell of mesenchymal origin that lines the serous cavity.
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
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.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
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 lymphocyte of B lineage that is capable of B cell mediated immunity.
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. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
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.
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
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.
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 late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative.
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
Any of the immature or mature forms of a granular leukocyte that in its mature form has 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. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive.
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.
Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking.
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.
A T cell that expresses an alpha-beta T cell receptor complex.
CD8-positive, alpha-beta cytotoxic T cell
A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative.
A leukocyte with a single non-segmented nucleus in the mature form.
A neoplastic cell that is capable of entering a surrounding tissue
A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare.
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 that is part of the nervous system.
A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface.
A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.
A complex of two or more molecular entities that are not covalently bound.
Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.
Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
core promoter sequence-specific DNA binding
Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
The synthesis of an RNA transcript from an RNA template.
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
antibody-dependent cellular cytotoxicity
Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells.
An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
cytokine production involved in immune response
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels.
A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.
A process involving any mechanism for tolerance induction in B cells.
A process involving any mechanism for tolerance induction in T cells.
An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
cytokine production involved in inflammatory response
The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein.
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
Catalysis of the reaction: acetylcholine + H2O = choline + acetate.
Catalysis of the reaction: acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + hydrogen peroxide.
L-alanine:2-oxoglutarate aminotransferase activity
Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate.
Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
L-aspartate:2-oxoglutarate aminotransferase activity
Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate.
Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion.
Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
glutamate dehydrogenase [NAD(P)+] activity
Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+.
Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
isocitrate dehydrogenase [NAD(P)+] activity
Catalysis of the reaction: isocitrate + NAD(P)+ = 2-oxoglutarate + CO2 + NAD(P)H.
Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate.
Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication.
A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
cellular response to DNA damage stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
vascular endothelial growth factor production
The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative.
An immune response mediated by immunoglobulins, whether cell-bound or in solution.
Catalysis of the hydrolysis of amylose or an amylose derivative.
Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
The covalent alteration of one or more amino acid residues within a histone protein.
hydrolase activity, acting on ester bonds
Catalysis of the hydrolysis of any ester bond.
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
Binding to a specific domain of a protein.
Assembly of actin filaments by the addition of actin monomers to a filament.
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
connective tissue growth factor production
The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
granulocyte macrophage colony-stimulating factor production
The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
OBSOLETE. The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A.
transforming growth factor beta1 production
The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
transforming growth factor beta2 production
The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
transforming growth factor beta3 production
The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
Any process in which a macromolecule is transported to, or maintained in, a specific location.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far.
chemokine (C-X-C motif) ligand 9 production
The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
helper T cell enhancement of adaptive immune response
Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
helper T cell enhancement of T cell mediated immune response
Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.
helper T cell enhancement of B cell mediated immune response
Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.
The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 20 production
The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The expansion of a T cell population by cell division. Follows T cell activation.
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.
Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
macrophage migration inhibitory factor production
The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 17 production
The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Catalysis of the reaction: L(or D)-glutamine + D-glutamyl-peptide = NH3 + 5-glutamyl-D-glutamyl-peptide.
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
Catalysis of the hydrolysis of a carboxylic ester bond.
A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain.
actin polymerization-dependent cell motility
A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell.
transforming growth factor beta production
The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3.
monocyte chemotactic protein-1 production
The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 4 production
The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
macrophage inflammatory protein-1 gamma production
The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
macrophage inflammatory protein-1 alpha production
The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 5 production
The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 1 production
The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
granulocyte colony-stimulating factor production
The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor superfamily cytokine production
The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
chemokine (C-C motif) ligand 22 production
The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor (ligand) superfamily member 11 production
The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Cell killing caused by the membrane attack complex formed following complement activation.
histamine secretion mediated by immunoglobulin
Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface.
The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus.
The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.
chemokine (C-C motif) ligand 19 production
The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 21 production
The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-X-C motif) ligand 12 production
The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-X-C motif) ligand 13 production
The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-X-C motif) ligand 16 production
The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor.
The appearance of XCL1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
conditional specification
A directive information entity that specifies what should happen if the trigger condition is fulfilled.
PlanAndPlannedProcess Branch
OBI branch derived
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
narrative object
Examples of narrative objects are reports, journal articles, and patents submission.
A narrative object is an information content entity that is a set of propositions.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
person:Chris Stoeckert
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
obsolete_digital entity
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
obsolete2_digital entity
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
A report that is published in a journal.
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
binary digital entity
MS Word document, ZIP file, DICOM file, JPEG file
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
digital_entity
obsolete2_binary digital entity
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
programming language
R, Perl, Java
A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
integer numeral
A numeral that denotes an integer
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
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
time trigger
obsolete_study interpretation
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
text based digital entity
XML file, C++ source code file
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
obsolete2_text based digital entity
rule
example to be added
A rule is an executable which guides, defines, restricts actions.
MSI
PRS
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
obsolete2_report figure
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
software interpreter
R program, Perl interpreter, Java virtual machine
A software interpreter is a software application that executes some specified input software.
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
density plot
Density plot of SSC-H and FSC-H.
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
PERSON:Chris Stoeckert
report element
A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
2009-03-16: needs some more work (clarify relations).
2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
PERSON: Allyson Lister
obsolete_report element
binary executable
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
person:Jennifer Fostel
obsolete2_binary executable
source code module
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
report table
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
obsolete_report table
data format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
digital document
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
obsolete2_digital document
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
batch number
A settings datum is a datum that denotes some configuration of an instrument.
2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
setting datum
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
Need to rework digital entity. Digital quality was suggested by Barry.
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/10/23 Alan Ruttenberg: We need to work on the definition still
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:James Malone
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
obsolete_survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
A textual entity intended to identify a particular publication.
author identification
L. Hunter
A textual entity intended to identify a particular author
institutional identification
University of Colorado Denver School of Medicine
A textual entity intended to identify a particular institution
caption
Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
A textual entity that describes a figure
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
table
| T F --+----- T | T F F | F F
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
table of abbreviations
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
A table where the constituent texts are abbreviations and their expansions
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
publication
A journal article or book
A document that has been accepted by a publisher
publication about an investigation
Most scientific journal articles
A publication that is about an investigation
scientific publication
patent
US Patent 6,449,603
A document that has been accepted by a patent authority
document part
An abstract, introduction, method or results section.
An information content entity that is part of a document.
abstract
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
introduction to a publication about an investigation
Section labelled 'introduction' of a typical scientific journal article
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
background
introduction
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
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
discussion
discussion section
references section
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
A part of a document that has citations as parts
author list
Lawrence Hunter and Kevin Brettonel Cohen
A part of a document that enumerates the authors of the document
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
A part of a document that has parts that are institution identifications associated with the authors of the document
author contributions section
LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
A part of a publication that is about the specific contributions of each author
author contributions
contributions by the authors
acknowledgements section
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
Part of a publication that is about the contributions of people or institutions other than the authors.
acknowledgements
acknowledgments
footnote
The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
endnote
supplementary material to a document
A part of a document that is segregated from the rest of the document due to its size
additional information
appendix
supplemental information
supplementary material
supporting information
table of contents
A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
table of figures
A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
running title
A shorter version of a document title
copyright section
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
A document part that describes legal restrictions on making or distributing copies of the document
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
AR notes: We need to discuss whether it should include site.
cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
three dimensional cartesian spatial coordinate datum
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
hypothesis textual entity
A textual entity that expresses an assertion that is intended to be tested.
A scalar measurement datum that is the result of measuring a temporal interval
time measurement datum
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
postal address
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Chris Stoeckart
author role
A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
data item extraction from journal article
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
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Melanie Courtot
assigning a centrally registered identifier
Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
A planned process in which a CRID registry associates an information content entity with a CRID symbol
associating information with a CRID in the CRID registry
associating information with a centrally registered identifier in its registry
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
centrally registered identifier registry
Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
looking up a centrally registered identifier
time stamped measurement datum
pmid:20604925 - time-lapse live cell microscopy
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
time sampled measurement data set
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
PERSON: Michel Dumontier
software method
A software module is software composed of a collection of software methods.
PERSON: Melanei Courtot
software module
A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
software library
A software application is software that can be directly executed by some processing unit.
software application
A software script is software whose instructions can be executed using a software interpreter.
software script
abbreviation textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
A textual entity listing abbreviations and their expansions that are used in a document.
PERSON: Bill Baumgartner
abbreviations section
The section labelled 'abbreviations' in a typical scientific journal article.
A part of a document where abbreviations and their long-forms used within the document are listed.
abbreviations
abbreviations list
abbreviations used
list of abbreviations
list of abbreviations used
author information section
The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author information
authors’ information
author information textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author summary section
The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
author summary
summary
synopsis
Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
author summary textual entity
From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
availability section
The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
availability
availability textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
case report section
The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
A part of a document about the medical history of a specific patient as it relates to the topic of the document.
case presentation
case report
case report textual entity
Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
conclusion section
The section labelled 'conclusion' in a typical scientific journal article.
A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
concluding remarks
conclusion
conclusions
findings
conflict of interest section
The section labelled 'conflict of interest statement' in a typical scientific journal article.
A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
competing interests
conflict of interest
conflict of interest statement
declaration of competing interests
disclosure of potential conflicts of interest
SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
conflict of interest textual entity
consent section
The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
A part of a document about the consent process that was used to enroll patients in a study.
consent
consent textual entity
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
A textual entity that documents the consenting process used to enroll patients in a study.
ethical approval section
The section labelled 'ethical approval' in a typical scientific journal article.
A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
ethical approval
ethical approval textual entity
From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
A textual entity that documents the ethical approval of some study design.
figures section
The section labelled 'figures' in a typical scientific journal article.
A part of a document that contains one or more figures.
figures
funding source declaration section
The section labelled 'funding' in a typical scientific journal article.
A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
funding
funding information
funding sources
funding statement
funding/support
source of funding
sources of funding
funding souce declaration textual entity
From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
A textual entity documenting the source of funding that supported some study.
funding source declaration textual entity
future directions section
The section labelled 'future directions' in a typical scientific journal article.
A part of a document detailing extensions of the described work that may be implemented at some future point in time.
future challenges
future considerations
future developments
future directions
future outlook
future perspectives
future plans
future prospects
future research
future research directions
future studies
future work
future directions textual entity
Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
genome announcement section
The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
A document part announcing the publication of a novel draft genome sequence.
genome announcement
genome announcement textual entity
Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
A textual entity that describes the generation and public release of a novel, draft genome sequence.
keyword textual entity
From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
A textual entity listing keywords indicating the major theme(s) of a document.
keywords section
The section labelled 'keywords' in a typical scientific journal article.
A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
keywords
study limitations section
The section labelled 'limitations' in a typical scientific journal article.
A part of a document about biases or short comings related to the study design and execution.
limitations
study limitations
Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
study limitations textual entity
Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
A textual entity addressing a shortcoming or bias of a study design or execution.
materials section
The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
A part of a document about the materials required to reproduce the content of the document.
materials
notes section
The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
footnotes
notes
patients section
The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
A part of a document about the patients that participated in a study.
patients textual entity
Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
A textual entity expressing information regarding the patients used in a study.
pre-publication history section
The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
notice of republication
pre-publication history
pre-publication history textual entity
From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
related work section
The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
A part of a document about work in other publications that is relevant to the content of the document.
related literature
related work
related work textual entity
Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
requirements section
A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
requirements
requirements textual entity
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
A textual entity that expresses the requirements necessary to use a resource, e.g. software.
statistical analysis textual entity
From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
A textual entity documenting statistical analysis tools and techniques employed.
statistical analysis section
The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
A part of the document used to describe the statistical methodologies employed in the work presented in the document.
statistical analysis
tables section
The section labelled 'tables' in a typical scientific journal article.
A part of a document that contains one or more tables.
tables
An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
postal code
A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
Postal delivery route
A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
ZIP code
zone improvement plan code
database extract, transform, and load process
A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
ETL
identifier
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
taxonomic bridge ontology module
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by OWL profile
EL++ ontology module
pathogenic disposition
A disposition to initiate processes that result in a disorder.
pathogen
A material entity with a pathogenic disposition.
antibacterial
A material entity bearing an antibacterial disposition.
infection
A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
human pathogenicity disposition
A disposition to initiate processes that result in a disorder in a human organism.
post-transfusion hepatitis non A non B virus
human immunodeficiency virus type 1 HIV 1
human immunodeficiency virus type 1 HIV1
human immunodeficiency virus type 1, HIV-1
human immunodeficiency virus type I HIV-1
human immunodeficiency virus type-1 HIV-1
human immunodeficiency virus type 2 HIV-2
human immunodeficiency virus type 2, HIV-2
The process efficacy of a limb coordination.
The process efficacy of a upper limb coordination.
The process efficacy of a lower limb coordination.
The stability of a multicellular organism.
The functionality of a peripheral nervous system.
The functionality of a tendon of biceps brachii.
Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
Person charged with serving as CSO, FDA official who coordinates the review
the role of a human being that is realized by enforcing regulations to ensure consumer safety
OBI, CDISC
role of being consumer safety officer
fluorescent reporter intensity
A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
regulator role
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.
regulation-assigned role
Approval letter
Regulation-assigned role is a regulatory role defined by legislation or governmental orders
Person: Jennifer Fostel
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution
contract research organization role
list-mode data file
An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.
A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people.
A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
classified data set
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
reference substance role
haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization
cytological stain role
Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material..
9Mar09 after discussion with process branch changed definition to include use of centrifuge;
centrifuge pellet role
a worker role comprised of handling the administrative duties of a trial or study.
clinical research coordinator role
Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.
supernatant role
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.
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
drug role
http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.
a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism
Role Branch
A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument
xenotransplantation
is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
physical document
a book is a physical document
A physical document is an object serving as a record of information by means of symbolic marks.
waiting
A planned process where an agent does not take any new actions towards a particular objective for a period of time until a set of conditions is met.
BP: I have doubts about the utility of this.
We need a better handling/modeling of time (January 2008)
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.
A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
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.
A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
ratio of collected to emitted light
A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
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.
The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive
Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB.
notified body role
allotransplantation
is the transplantation of organs between members of the same species.
A processed material which measures gamma radiation
a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study.
trial monitor role
MMS mutagen
a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response
positive reference substance role
polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties
adapted from Wikipedia before possible import from CHEBI
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
a study personnel role played by a party who reports the outcome of a study component
MO:submitter mapped to this term. So, alternative term 'submitter' was added.
reporting party role
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
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.
Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
measuring
scientific observation
quantitative confidence value
A data item which is used to indicate the degree of uncertainty about a measurement.
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
study
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
unplanned occurrence effecting an investigation
Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
a process which is external in origin to the investigation that has an impact on the outcome.
eMedical record
An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
culture medium
electronic case report tabulation
An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators.
Polystyrene tubes can be used to contain tissue culture cells during centrifgation
A polystyrene tube is a test tube made of polystyrene
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
role of regulator of chemical manufacturer
EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm
a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances
One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009
detector reagent role
CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA
WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional
role of certified IRB professional
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
GROUP:Role Branch
CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
patient role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
protocol testing objective
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
participant under investigation role
obsolete_role of being first subject treated
Rat 1A; first enrolled patient to receive treatment
First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study
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.
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
responsible party role
a responsible party role played by a person responsible for the overall conduct of a study
CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
principal investigator role
transplantation
a protocol application to replace an organ or tissue of an organism
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
bromophenol blue has a pH indicator dye role
phenol red in RPMI; pH=4 indicator dye (also carries reference role)
the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity
pH indicator dye role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
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.
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker role
An assay where the output data is a datum with one of two values denoting success and failure.
gene list
Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.
number of particles in subset
A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
number of lost events electronic
74, 0, 14 events lost due to data acquisition electronic coincidence.
A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
calibration substance role
pH buffer used to calibrate a pH meter bears a calibration substance role
A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance
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.
Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
Label role is a role which inheres in a material entity and which is realized in a detection of label assay
Subject at time = 0; subject before a stress test.
a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
baseline participant role
role of independent data monitoring committee
a trial monitor role charged recommending whether to continue, modify, or end the trial
a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
pathologist role
supernatant collection system harvesting frame
A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.
A device manufacture with the intent to provide a porous unsized paper used for filtering.
cell co-culturing
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008
the role of a organization that is realized by members reviewing study designs for their agreement with regulations
CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial.
role of Institutional Review Board
eSource document
an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures
a role realized when a participant serves as reference to itself
crossover population role
Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment.
complete nutrient role
radiolabel role
a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection
radiolabel
cDNA library
PMID:6110205. collection of cDNA derived from mouse splenocytes.
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
GROUP: PSI
PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction
clonal cDNA library
electronic case report form
An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11.
Pill consisting of inert materials
a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance
CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product.
placebo role
autotransplantation
is the transplantation of tissue from one part of \nthe body to another in the same individual. )
parameter threshold
A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
The group of randomized participants that are assigned to a treatment arm of the trial
a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
study group role
p-value
PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
May be outside the scope of OBI long term, is needed so is retained
WEB: http://en.wikipedia.org/wiki/P-value
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
NMR 3D molecular structure determination assay
Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013).
A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample.
An assay that produces a picture of an entity.
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.
a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
role of pathology review board
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.
According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial
impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who
role of impartial witness
chromatin immunoprecipitation
Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method.
An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics.
Bjoern Peters, Randi Vita, James A. Overton
ChIP
A member of a dose-time group; a patient in a given arm of a trial
a reference participant role realized by equivalent treatment of participants
biological replicate role
Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material.
An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.
Wikipedia, feb 29, 2008
19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment.
nutrient role
Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study)
Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role.
a worker role of providing medical care either within or outside the study timeline
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.
analytical cytology data file
FCS file, ACS file, foo.fcs, foo.asc
A digital entity intended to capture data in analytical cytology domain.
Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
proxy respondent role
fluorescence compensation matrix
A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix.
Saline solution
a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response
negative reference substance role
role of legally acceptable representative
Parent of minor patient; Definition of legally acceptable representative An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE
a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial.
legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary]
investigation results report
An investigation report is a report on the results of an investigation.
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.
Saline treated rat; one of three identically-treated subjects
a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
reference subject role
A dye role that is realized when used to detect live cells in an experiment
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178
vital dye role
115 patients received ipilimumab and blinded medication
Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance
a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows
sub-investigator role
data encoding
storage of measurement results from an assay into a text file, such as
a documenting process to encode an information entity into a digital document
We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE
enzymatic cleavage
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
a material processing that digests the fraction of input material that is susceptible to that enzyme
hardware optimization objective
Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
Place holder class, Utility class to gather the defined classes
a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9]
trial statistician role
standard error
A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
see P-Value
A role of a material entity that is being recognized in whole or in part by receptors of the immune system such as antibodies or T cell receptors.
An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens
9Mar09 waiting for discussion with immunology terms
antigen role
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.
sponsor role
a responsible party role involved with any of the following activities: initiating, managing and funding a study
CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment.
feed role
Aliquots of a tissue subjected to parallel assays
technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
technical replicate role
dye role
A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest.
A substance used to color materials www.answers.com/topic/dye 19feb09
cluster
Cluster of the lymphocytes population.
A data set which is a subset of data that are a similar to each other in some way.
In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.
WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
cohort role
artificially induced nucleic acid hybridization
www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
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
Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458
A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.
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.
number of lost events computer
0, 125, 787 events lost due to computer busy.
A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
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)
role of regulator of consumables and medical devices
FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html
a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
analyte role
Stage II breast cancer, The timepoint of recovery from a disease
a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
disease stage
is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
intraperitoneal injection
precipitate
Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038
a precipitate is a material entity which is output of a precipitation process
precipited material
protein-protein interaction detection assay
An assay that determines interactions between proteins, such as protein-protein binding.
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors
Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902
enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
adverse event trigger
revisit?
eluate
Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
eluted material
drug added to a buffer contained in a tube; substance injected into an animal;
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
9 March 09 from discussion with PA branch
material to be added role
is the serous membrane that forms the lining of the abdominal cavity
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
histological sample preparation
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer.
a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns.
BP: 10/22/122: After changing the parent class to drawing a conclusion *based on data* it is no longer clear that this class is needed; minimally it needs a better definition to distinguish it. Proposal is to obsolete.
wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
inductive reasoning
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.
hypothesis driven investigation
is an investigation with the goal to test one or more hypothesis
hypothesis generating investigation
is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
The ion source of a Voyager-DE??? STR Biospectrometry Workstation
An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
record function
A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
magnify function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
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.
Electrospray ionization in mass spectrometry
a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation.
2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
ionize process
excitation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
freeze function
A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
perturb function
A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
mechanical function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
gas filter function
A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture
liquid filter function
A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture
transfer function
A transfer function is a function to displace a material from one location to another.
electricity supply function
the function of supplying current during a neuroscience experiment.
An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
power supply
ionization function
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
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.
connection function
A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another.
An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated.
A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid
energy supply function
An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
information processor function
An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
data processor function
signal conversion function
A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon.
A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
signal amplification function
A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
image acquisition function
An image acquisition function is a function to acquire an image of a material
An image creation device is a device which captures a digitized image of an object
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
display function
A display function is a function to present information by translating that information through some lookup process into visual form.
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.
sort function
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
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
PCR product
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
is double stranded DNA that is the specified output of a polymerase chain reaction
We are using PCR and not the written out words, as this is the most common used.
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
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid template role
recombinant plasmid
a plasmid in which extraneous DNA has been inserted.
pBluescript plays the role of a cloning vector
A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/
cloning vector role
Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs.
a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
cell cycle synchronization
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
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
cloning insert role
measuring glucose concentration in blood serum assay
Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319.
An assay that determines the concentration of glucose molecules in a blood serum sample
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
A material entity that has undergone a process of digestion with trypsin
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
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.
Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
injection
enzyme
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
The administration of a substance into the peritoneum of an organism
intraperitoneal administration
plasmid
plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
A process in which an input substance is injected into a organ section.
injection into organ section
polyacrylamide gel
Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
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
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
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.
agarose gel
Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
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
The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
The patients was weighed and mass was determined to be 47 kilograms
An assay that determines the mass of an evaluant
DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
intracellular electrophysiology recording assay
An electrophysiology assay where the recording location of the electrode is intracellular.
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.
example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation.
This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process.
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.
A data set that is produced as the output of a normalization data transformation.
normalized data set
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.
extracellular electrophysiology recording assay
The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron
An electrophysiology assay where the recording location of the electrode is extracellular.
consume data function
Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
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
There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles.
chromatography detector, defined class/xps
A Bruker autosampler is an autosampler made by Bruker.
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.
The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity).
An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion.
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.
A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry.
Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides.
An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles.
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats.
A pump system optimized for nano flow chromatography.
NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material.
washing system/NMR tube washing system, XPS: device has function washing
The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
An older Varian Broadband NMR spectrometer.
A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness.
An NMR probe that is designed to hold a solid sample.
BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features.
A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range.
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.
The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application.
An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
Any instrument that is used to carry out a chromatography experiment.
Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned).
In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation.
The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement.
A cation exchange column is a chromatography column that is used in cation exchange chromatography.
An NMR probe designed to allow the direct detection of acquisition nuclei.
The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit.
A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution.
Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily.
A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head.
An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
A component of an NMR instrument that controls the activities of the other components.
NMR instrument, TODO: same as or part of acquisition computer?
A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate).
A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup.
An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility.
A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis.
An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century.
A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment.
The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes.
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.
A lubricant used in liquid chromatography that eases sample injector penetration.
removing CD4+ cells from PBMCs using magnetic beads.
a process in which a population of cells with certain characteristics is isolated from a larger population
The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network.
A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe.
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.
Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample.
A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.
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.
An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes.
Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters.
An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism.
A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample.
A container made from solid material and primarily used for holding liquid.
A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle.
Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent.
For preparative LC with injection of sample volumes ranging from L to mL ranges.
Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent.
An NMR probe that is manufactured by JEOL.
An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications.
The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient.
A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
chromatography device, check on definition !
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.
An NMR instrument that is manufactured by tecmag.
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.
A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing.
Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796
An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping
A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity.
An NMR probe that is designed for generating pictures from sample states via NMR imaging.
a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells.
A series of older Bruker NMR magnets, now out of production.
Any device used in a gas chromatography experiment.
A small membrane filter of defined pore size, that filters samples from a syringe.
This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back.
For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step.
A pump system optimized for capillary chromatography.
The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas.
cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs.
a process in which cells with a single nucleus are isolated from a blood sample
A chromatography device where the column cartridge is inserted into and stabilised.
A gas generator that generates nitrogen gas.
The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
reverse transcribed polymerase chain reaction
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
reverse transcription polymerase chain reaction
Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process.
A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven.
An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device.
A pump system optimized for isocratic chromatography.
Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips.
An NMR probe that is designed to hold a liquid sample.
An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
An NMR probe that is manufactured by Bruker.
NMR device, TODO: May need no definition.
An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected.
The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers.
The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area.
An Instrument which is used to carry out a NMR analysis of some sample.
An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design.
The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless.
A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier.
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.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system.
A pump system optimized for gradient chromatography.
A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized.
the sodium and chloride ions in a glass of salt water
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Collective
scattered molecular aggregate
the phosphate concentration should be 0.1M
A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
The predecessor series of the Varian UNITY INOVA spectrometer.
A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently.
A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
Includes the connection to a high-resolution TOF-LC-MS system.
For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector.
An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
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.
The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected.
Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available.
The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data.
An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
An Adapter that enabled the connection of a column to additional devices.
A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC).
An NMR instrument that is manufactured by Bruker.
An NMR magnet that is manufactured by Bruker.
ozone-induced chemiluminescence detector
Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry.
An NMR instrument that is manufactured by JEOL.
A chromatography consumable is a consumable that is used in a chromatography experiment.
A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density).
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.
A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed.
The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration.
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.
Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
A gas generator that generates hydrogen gas.
A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
A gas chromatography device that can auto-inject a small number of samples an inlet.
An NMR instrument that is manufactured by Varian.
The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube.
Bruker Multiple Adjustable Tube Clamp Holder
A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.
Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns.
Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203
An assay that determines protein expression and translation activity using protein extracts collected from a material entity.
high resolution probe with automatic tuning and matching
The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems.
High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
fluorine-induced chemiluminescence detector
A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator.
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.
An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities.
For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples.
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.
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.
Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202
An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement.
The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
A pump system that pump and mix up to four different solvents in parallel.
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.
Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei.
Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943
An assay that studies blood and blood producing organs using a variety of techniques and instruments
MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation.
An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis.
The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure.
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979
An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility.
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.
A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors.
Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems.
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.
An NMR probe designed to allow the indirect detection of acquisition nuclei.
The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element.
A clustered data set is the output of a K means clustering data transformation
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
data set with assigned discovered class labels
clustered data set
A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
data set of features
differential expression analysis data transformation
A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals.
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.
Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133
blood drawn from a human for glucose assay
a material entity derived from a portion of blood collected from an organism
data set of predicted values according to fitted curve
A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
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 data set that is produced as the output of a background correction data transformation.
background corrected data set
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
error corrected data set
class prediction data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
supervised classification data transformation
PERSON: James Malone
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU.
A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies.
obsolete intracellular cytokine staining assay
Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
background correction data transformation
A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.
An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer
error correction data transformation
An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity.
A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating.
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
A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
center value
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
A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set.
reduced dimension data set
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
putting a mouse in the blender. Not: putting a mouse on a scale
A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
Study result is an information content entity that is a specified data output of a study.
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.
creating a mixture of molecules in solution
is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
is an objective to obtain an output material that contains several input materials.
Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
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 first manufactured by 454 Life Science Corporation in 2005, 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.
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
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.
a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector
PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
Methylated DNA immunoprecipitation sequencing assay
animal feeding is a process in which animals are provided with food
In an investigation, this will typically be part of an animal care process
PMID: 271968. DNA sequencing with chain-terminating inhibitors.
A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
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: 18388294. Single-molecule DNA sequencing of a viral genome.
A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length.
A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
An assay that measures the occurrence of death events in one or more organisms over time
A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these.
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.
is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 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. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.
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.
Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT.
A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis.
PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles.
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
a process that realizes an animal care protocol that specifies how animals are kept and maintained
a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences
this should be a child of 'chromosome' if we import that from another source
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.
The administration of a live pathogenic organism to a host.
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/
For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix.
WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes
An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin
chromatin immunoprecipitation sequencing assay
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383
pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role
6 April 2009: from the Vaccine Community
vaccine preparation is a planned process with specified output a vaccine
Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant
The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen.
11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'.
Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891
An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
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
A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
k-nearest neighbors
A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research.
A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site.
Note: 'cloning vector role' is really a function. Should be dealt with globally
Pyrosequencing sheds light on DNA sequencing. PMID:1115661
A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
an enzyme that has a specific target cleavage sites within nucleic acids
5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
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.
a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector.
Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
WEB: http://en.wikipedia.org/wiki/T-test
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.
topologically preserved clustered data set
the output data set generated from a self-organizing map.
A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived.
A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site
Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA.
An assay that determines information about an immune response
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
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
PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J.
A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
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 thisdefinition please notify OBI.
study design independent variable
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
study design dependent variable
A 'blue top' test tube that contains anticoagulant for storing blood specimens'
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable.
Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent.
2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid
In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling
WEB: http://en.wikipedia.org/wiki/Control_variable
study design controlled variable
PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
An assay that measures the amount of antithrombin III in blood.
A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand
A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material
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
Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated
obsolete transcription factor binding site
Diabetic patients use glucometers to determine their glucose levels
A measurement device with the function to measure and record the level/amount of glucose in a blood sample
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
SIINFEKL' is the primary structure of a peptide
The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together
Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro.
cross linking can be used as a probe to link proteins together, to check protein protein interactions
A process in which bonds are created that link one polymer to another
Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
needs more work to see exactly what the data set looks like - HP
PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample.
Is a process in which the tertiary or secondary structure of a polymer is disrupted
informing investigator of subject study arm
A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort
An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard
An objective specification maintains some or all of the qualities of a material over time.
The presentation of a flashing light to a monkey during reward training
a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
Helen Parkinson, Jessica Turner, Dirk Derom
PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration.
DNA that has been produced in an enzymatic amplification process
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.
measuring neural activity in the caudate nucleus assay
An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus
An assay that measures neural activity in the caudate nucleus
to be treated with active ingredient role
Role of a patient in a group treated with an active substance in a clinical trial
A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient
Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder.
For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution
A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber).
the process of using pH buffer adjust a pH meter
A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements.
anticoagulant tube storage of blood specimen
Storage of a blood specimen in a tube with anticoagulant
activated partial thromboplastin time assay
The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660)
An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy.
There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant).
A pill in the form of a small rounded gelatinous container with medicine inside.
A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated
PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
An assay that measures the time between the addition of the thrombin and the clot formation in plasma.
Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material
A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo
A planned process, part of a study design execution, during which the treatment of subjects is ongoing
09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
A dose of medicine or placebo in the form of a small pellet.
The SALK institute is a research organization.
An organization formed with a goal to have its members conduct investigations
obsolete_primary structure of sequence macromolecule
A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds
a quality of a DNA residue that has a methyl group attached to it
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
A person or organization that has a manufacturer role.
A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
An adding a material entity to target with the entity is a pill and the target is the mouth
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
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
The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials
subject agrees they understand informed consent document
A process in which a subject receives an informed consent document and agrees that they have understood it
09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out
A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort
The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays
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; http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
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
fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation
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 statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
An information content entity created to indicate that information about something is not available to the person recording it.
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest.
An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules.
A RNA extraction process in which total cellular and organelle RNA are extracted.
obsolete intracellular material detection by flow cytometry assay
An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
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 database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
a record indicating that the biological sex of an organism is not known.
I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement.
A RNA extraction process in which the desired output material is RNA in the cytoplasm.
The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay.
An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models.
Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
A serum neutralization of viral infectivity assay which is performed in a 96-well plate.
Establishment of HeLa immortal cell line
is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal
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.
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
single-nucleotide-resolution nucleic acid structure mapping assay
An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells.
An assay that quantifies viruses by their hemagglutination activity.
serum neutralization of viral infectivity assay
An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
material obtained through a liver biopsy from a human patient
a specimen that was taken from a live organism
MO_705 premortem
detection of specific nucleic acid polymers with complementary probes
Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays.
An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes.
Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody.
An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors.
Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line
4-20-13 MHB: This class was repositioned as a child of 'establishing cell line', based on the existing definition ("the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro"), and examples and other annotations indicating the intent to describe a process through which a new immortal cell line is established from an existing mortal cell line using genetic modification techniques. The definition above was modified to clarify this perspective.
'establishing immortal cell line through directed genetic modification'
A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line.
PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9.
a labeling in which random primers are used to uniformly label input DNA
need to add Klenow subunit of DNA polymerase I under material entity
Person: Bjoern Peters Person: Chris Stoeckert
PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13.
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
A cytometry assay that monitors a cell population to track how many are killed by other cells.
Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells.
A cell killing assay that measures if and how many target cells are killed within an organism.
secondary structure of sequence macromolecule
A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford.
2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
A RNA extraction process in which the desired output material is RNA in the nucleus.
survival curve
Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
A cytometry assay which measures the degreee to which input cells are replicating.
PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing.
An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity.
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
PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,
Extraction of total RNA from cells with Qiagen mini RNeasy kit.
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe
Extraction of organellar RNA from plant cells using organellar RNA binding protein.
A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
a specimen that was taken from a dead organism
MO_416 postmortem
A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
reporter cell line analyte detection bioassay
CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant.
An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant.
The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'.
WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination
The planned process of providing material entities to be used in an investigation.
5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal.
a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
type of sample used in the PCIRN influenza network
A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium.
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay.
An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody.
real time reverse-transcription polymerase chain reaction assay
An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay.
X-ray crystallography 3D molecular structure determination assay
Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest.
promoter activity detection by reporter gene assay
A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color.
An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene.
A speciemn which derives from nasopharyngeal mucosa after aspiration.
A storage process in temperature that maintenance the frozen status of the stored entities.
2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen.
Person: Alan Ruttenberg, Mathias Brochhausen
MO_481 frozen_storage
Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.
A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
Logical definition should contain all components listed in textual definition at some point.
A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject
may later be refined with more specific list of organisms
Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture.
An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest.
a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
A specimen that has been frozen in order to store it.
Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow.
A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction.
A specimen that has been modified in order to be able to detect it in future experiments
is a material entity bearing the disposition to infect an organism
IEDB
infectious agent
a storage process with input material entity and output freeze dried material for long time storage
can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
A stirrer has a material combination function
A material separation function is a function that decreases the resolution between two or more material entities.
EBI provides training on databases and tools and has a training service provider role
a service provider role which is realized by a servicer provider organization performing some training
A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
the part of the execution of an intervention design study which is varied between two or more subjects in the study
A device with a separation function realized in a planed process
A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule.
is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand.
A person or organization who provides access to a DNA sequencer.
a service provider role which is realized by a servicer provider organization performing access to some material
A measurement datum that is reported on a categorical scale.
e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility
a process that achieves a training objective
A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
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
is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe
PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. Biochimie. 2010 Feb 18.
chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent
The Edinburgh handedness assay is a specific method of determing handedness
An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor.
a function to remove viable organisms from an input material
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis).
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 specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
an intervention design in which the treatment is the administration of a compound
This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
An administering substance in vivo into the mouth of an organism
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.
is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe
A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube.
An assay where a person makes a statement that indicates what handedness he has from a choice of different categories.
A preparation device that uses a vibrating razor blade to cut through tissue.
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?
Immunohistochemical labeling of tissue sections by an autostainer staining system.
A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen.
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.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
An assay in which a measurement is made by observing entities located in a live cell.
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
An assay in which a measurement is made by observing entities located in an organism.
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
a protocol specifying to administer 1 ml of vaccine to a mouse
a directive information entity that describes the dose that will be administered to a target
A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question.
Person: Jessica Turner
JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?
a specimen that is output of a specimen creation process used for an investigation without storage.
a processed material created to have a function and which requires electrical power to execute
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
cell-cell binding detection by flow cytometry assay
Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates.
A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels.
handedness categorical measurement datum
A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally
a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
need to specify paraffin or wax is one of specified input of the process
An assay in which a measurement is made by observing entities located in a container.
DNA sequencing of a sample by a core lab which returns data to the consumer
a service provider role which is realized by a servicer provider organization performing a protocol execution
a specimen that is output of a process that cell culture inoculated into agar for long term storage.
An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation.
The administration of a substance into the intranasal mucosis of an organism
An organism has been injected 1ml of vaccine
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
A study design in which the independent variable is the environmental condition in which the specimen is growing
obsolete_DNA sequencing training service
A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
obsolete_general scalar measurement datum
Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache.
The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
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 microscope that produces an image of an object by targeting it with an electron beam
A score that measures the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
Eagle-i will supply better English definition
A sequencing centre has a service provision objective
An objective which is fulfilled by the provision of some service e.g. a training service
is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe
Staining cells in a tissue slice with a dye.
The directed combination of a material entity with a specimen.
an objective which aims to create a device with a specified function
The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
Right now this may be incomplete. Should also cover e.g. sound, light as well.
PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)"
An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
a storage process with input cell culture and agar and output agar stab for long time storage
need to specify that agar is one of input for this process
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe.
single nucleotide resolution mapping assay using RNAse CL3
A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
single nucleotide resolution mapping assay using CMCT probe
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
A planned process that captures an image of an object.
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe.
single nucleotide resolution mapping assay using Fe-MP probe
obsolete_qualitative binding detection assay
A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context.
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe
single nucleotide resolution mapping assay using ENU probe
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe
single nucleotide resolution mapping assay using RNAse V1
single nucleotide resolution mapping assay using Kethoxal probe
A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes.
A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe
single nucleotide resolution mapping assay using DMS probe
A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
single nucleotide resolution mapping assay using DNAse I
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes.
A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe.
single nucleotide resolution mapping assay using Rhodium probe
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe.
single nucleotide resolution mapping assay using RNA adenosine deaminase I
A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe
single nucleotide resolution mapping assay using Lead probe
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe
single nucleotide resolution mapping assay using RNAse T2
An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene.
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe.
single nucleotide resolution mapping assay using Fe-BABE probe
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe
single nucleotide resolution mapping assay using RNAse U2
Determination of KD value for an antibody binding a protein using a BIACORE assay.
A binding assay where the specified output is a binding constant
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe
single nucleotide resolution mapping assay using NMIA probe
A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe
single nucleotide resolution mapping assay using Terbium probe
A planed process with objective of obtaining quantified values from an image.
A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe
single nucleotide resolution mapping assay using OH-radical probe
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe.
single nucleotide resolution mapping assay using RNAse T1
An image creation process that generate an image from the array.
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
A device which has a function to emit light.
A perturbation device is a device which is designed to perform a perturb function
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe.
single nucleotide resolution mapping assay using Nuclease S1
e.g the function of a bar code reader used to read slide bar codes
a function that allows specific identification of individual speciment from one another.
A specimen fixation function is a function that holds or fastens an entity in a fixed position.
A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe
inline probing RNA structure mapping assay
A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity
A current amplification function is an amplification function that increases the amplitude of a current.
A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity.
a transfer unction where the transfer requires work to move the entity, often against a gradient.
A cell harvester has a cell transfer function.
is a transfer function that displaces cells from one place to another
A device that records the patterns of pulse waves inside blood vessels.
A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed.
A device or system that supports a biologically active environment.
A device that is used to measure the pH (acidity or alkalinity) of a liquid.
An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray.
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 light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons.
A device that moves charged particles through a medium by using an electric field induced by electrodes.
A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
high performance liquid chromatography instrument
A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
A robotic device that is used to excise spots from gels.
A device that is used to apply microwave irradiation to chemical reactions.
A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface.
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.
An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes.
A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
A device or system in which perfusion units are integrated.
A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required.
array manufacturer role
a manufacturer role which is played by the person or organization that manufactured the array
PERSON: Chris Stoeckert, Jie Zheng
MO_695 array_manufacturer
A device that is used to measure ionizing radiation.
A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8
A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION
A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy.
A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy.
A device that creates an appropriate environment for nucleic acid hybridization.
An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
A device that is used to image small laboratory animals (e.g., rats and mice) in vivo.
An image acquisition device that is responsive to an infrared emissive target within a given field of view.
A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
A device that is used to acquire images of laboratory gels.
A device that is used for the separation of proteins.
A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations.
A device that is used to effect the transition of a substance into a glass.
An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects.
A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
A device that is used to freeze dry material.
A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge.
A hardness testing device that is used in light-optical microscopes.
A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
A group of linked computers, working together closely so that in many respects they form a single computer.
A device that is used to sharpen knives used in microtomy.
A device that provides shaking motion for microplates.
A device for automatically analyzing blood coagulation in a clinical laboratory.
laser capture microdissection microscope
A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
A liquid handling device that provides automatic liquid extraction.
A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
A device that is used for the imaging of immunoblots.
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.
electron paramagnetic resonance spectrometer
An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.
A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy.
A microscope that forms images of surfaces using a physical probe that scans the specimen.
A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction.
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.
A device that is used to acquire and image bead array data.
An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
A device that is used for the warming of paraffin embedding medium.
A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents.
J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave
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 for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY.
A device that is used to isolate and collect DNA for subsequent molecular analysis.
A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
A compact fluorometer that can be carried or moved with ease.
An electrophoresis system in which an electric field is applied to a gel matrix
A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it.
A device that is used for the dissection of tissues under magnification.
A device that is used to fabricate glass micropipettes.
A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen.
A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
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.
A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
A device that heats materials in a vacuum.
A device that is used to heat microscope slides.
An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
denaturing high-performance liquid chromatography instrument
A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis.
A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
A measuring instrument that is used to determine the weight or mass of an object.
A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
An device that is used to determine the order of amino acids in protein sequences.
A device that is used to generate X-rays.
A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
spike-in quality control role
a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
MO_937 spike_quality_control
individual organism identifier
a CRID symbol used to distinguish one individual organism from another.
MO_169 Individual
dye swap quality control role
a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes
MO_524 dye_swap_quality_control
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.
binding constant
The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed.
10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class.
3D structure determination of bound molecular complex assay
Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody.
A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration.
Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
An assay with the objective to characterize the disposition of two or more material entities to form a complex.
cell culture expansion
a process that results in the increase of cell numbers
including grow of yeast and bacteria
MO_758 grow
BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process.
gene knock out
a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
MO_771 gene_knock_out
gene knock in
a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
MO_437 gene_knock_in
WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
chromosomal substitution
A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'.
MO_995 chromosomal_substitution
genetically modified material
a material entity, organism or cell, that is the output of a genetic transformation process.
PERSON: Jie Zheng
term is proposed by BP on Oct 25, 2010 dev call
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
transfection
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
induced mutagenesis
A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation.
Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366
MO_564 induced_mutation
The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
A measurement datum that describes the structural orientation of a material entity in 3D space.
PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
age since planting measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call
age since hatching measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted).
This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
age since egg laying measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
assay validation objective
an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
GROUP: Penn Group
age since germination measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
validation by reverse transcription PCR design
a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
MO_986 reverse_transcription_PCR_quality_control
age since eclosion measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
age since sowing measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
age since coitus measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
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
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage.
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
discussed on Nov 15, dev call All subtype will be defined by textual definition now.
age since fertilization measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
Definition of fertilization comes from GO.
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
reverse transcription polymerase chain reaction assay
An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
The time it takes for 50% of a class of stochastic processes to occur.
A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony.
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another.
The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens.
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
Injection of a peptide T cell epitope into a mouse
An immunization in which an individual epitope is administered into a host organism.
3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here.
PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita
An assay that determines the sequence of an RNA molecule.
efficacy of epitope intervention experiment
An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism.
epitope protection from infectious challenge experiment
An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed.
half maximal effective concentration (EC50)
Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed.
half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex.
epitope protection from tumor challenge experiment
An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed.
An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
epitope protection from infectious challenge experiment based on pathogen burden
An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls.
Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus.
An assay that measures the presence or amount of an infectious agent in an evaluant
An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host.
epitope protection experiment based on survival
An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
decreased disease symptoms after treatment
half maximal inhibitory concentration (IC50)
Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope
epitope specific cytokine production by T cells
A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells
An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells.
A study design that assesses the operator performance and relation to data consistency and quality.
cytometric bead array assay measuring epitope specific IP-10 production by T cells
A cytometric bead array assay that detects IP-10 production by T cells.
CXCL10/IP-10 release|cytometric bead array
comparative genome hybridization by array design
A study design that detects genomic copy number variations using microarray technology.
MO_856 comparative_genome_hybridization_design
assay measuring epitope specific interleukin-27 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells.
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
genotyping by high throughput sequencing design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
epitope specific tolerance induction by T cells
A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells.
A DNA microarray used to detect polymorphisms in DNA samples
A study design that compares samples from different cell components.
MO_1019 cell_component_comparison_design
ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells.
epitope specific macrophage inflammatory protein-1 alpha production by T cells
A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
A process of T cell activation resulting from the recognition of a T cell epitope.
assay measuring epitope specific interleukin-10 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells.
cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells
A cytometric bead array assay that detects transforming growth factor-beta production by T cells
A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
epitope specific type IV hypersensitivity by T cells
A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
A study design that tests different normalization procedures.
intracellular material detection assay measuring epitope specific perforin release
A flow cytometry assay that detects epitope specific perforin release by T cells.
cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells
A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells.
assay measuring epitope specific interleukin-22 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells.
assay measuring epitope specific interleukin-8 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells.
epitope specific chemokine (C-C motif) ligand 1 production by T cells
A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells
A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells.
A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin
ELISA measuring epitope specific RANTES production by T cells
An enzyme-linked immunosorbent assay that detects RANTES production by T cells.
cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells
A cytometric bead array assay that detects interleukin-1 beta production by T cells.
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
ELISPOT assay measuring epitope specific interleukin-6 production by T cells
An enzyme-linked immunospot assay that detects interleukin-6 production by T cells
in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response
A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response.
plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor.
dissociation constant KD|surface plasmon resonance (SPR)|nM
assay measuring epitope specific interleukin-5 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells.
ELISA measuring epitope specific transforming growth factor-beta production by T cells
An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells.
assay measuring epitope specific RANTES production by T cells
A T cell epitope specific cytokine production assay that detects RANTES production by T cells.
assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells.
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
transcription profiling by tiling array assay
A transcription profiling by array assay that uses a tiling path array.
ELISA measuring epitope specific interleukin-22 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells.
assay measuring epitope specific interleukin-21 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells.
ELISA measuring epitope specific interleukin-9 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells.
transcription profiling by high throughput sequencing design
A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells
A flow cytometry assay that detects interleukin-6 production by T cells.
cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells
A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells.
cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells.
CCL2/MCP-1 release|cytometric bead array
ELISA measuring epitope specific interleukin-23 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release
A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells.
ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells.
genotyping by high throughput sequencing assay
A genotyping assay that uses a high througput sequencer
An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin
epitope specific T cell tolerance induction
A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
T cell degranulation by intracellular staining
assay measuring epitope specific interleukin-13 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells.
A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
assay measuring interleukin-9 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells.
epitope specific interleukin-3 production by T cells
A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells.
epitope specific lymphotoxin A production by T cells
A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-1 alpha production by T cells
A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications.
A study design that characterizes the association of transcripts and translation machinery.
ELISA measuring epitope specific interleukin-3 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells.
ELISA measuring epitope specific interleukin-1 alpha production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells.
epitope specific interleukin-27 production by T cells
A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response
A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response.
assay measuring epitope specific transforming growth factor-beta production by T cells
A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells.
A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
PERS:Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
DNA methylation profiling by high throughput sequencing assay
A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology
epitope specific transforming growth factor-beta production by T cells
A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells.
assay measuring epitope specific cytotoxic T cell degranulation
A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation.
cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells
A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells.
An RNA sequencing 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
ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells.
cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells
A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells.
epitope specific interleukin-16 production by T cells
A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells.
DNA methylation profiling by array design
A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells.
assay measuring epitope specific interleukin-16 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells.
ELISA measuring epitope specific IP-10 production by T cells
An enzyme-linked immunosorbent assay that detects IP-10 production by T cells.
An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
ELISA measuring epitope specific interleukin-15 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells.
cytometric bead array assay measuring epitope specific interleukin-12 production by T cells
A cytometric bead array assay that detects interleukin-12 production by T cells.
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
ELISA measuring epitope specific lymphotoxin A production by T cells
An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells.
cytometric bead array assay measuring epitope specific interleukin-5 production by T cells
A cytometric bead array assay that detects interleukin-5 production by T cells.
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells.
assay measuring epitope specific interleukin-15 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells.
A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
wild type organism genotype information
C57BL/6J wild type
a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
assay measuring epitope specific interleukin-17 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells.
cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
A cytometric bead array assay that detects interleukin-17 production by T cells.
cytometric bead array assay measuring epitope specific interleukin-10 production by T cells
A cytometric bead array assay that detects interleukin-10 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells
A flow cytometry assay that detects interleukin-5 production by T cells.
cytometric bead array assay measuring epitope specific interleukin-2 production by T cells
A cytometric bead array assay that detects interleukin-2 production by T cells.
cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells
A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells.
ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells.
intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells.
An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
A study design that examines the stability and/or decay of RNA transcripts.
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.
assay measuring epitope specific IP-10 production by T cells
A T cell epitope specific cytokine production assay that detects IP-10 production by T cells.
CXCL10/IP-10 release|biological activity
intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells
A flow cytometry assay that detects interleukin-13 production by T cells.
A study design that assays differences between distinct species.
X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex.
3D structure|x-ray crystallography|angstroms
transcription profiling by RT-PCR design
A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
epitope specific T cell enhancement of B cell mediated immune response
A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells.
epitope specific interleukin-21 production by T cells
A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor.
An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology.
cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells
A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells.
ELISPOT assay measuring epitope specific granzyme B release by T cells
An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells.
A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
in vivo assay measuring T cell epitope specific tolerance induction
An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment.
detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells.
cytometric bead array assay measuring epitope specific interleukin-4 production by T cells
A cytometric bead array assay that detects interleukin-4 production by T cells
assay measuring epitope specific lymphotoxin A production by T cells
A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells.
lymphotoxin A/TNFb release|biological activity
A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
MO_892 development_or_differentiation_design
A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
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
DNA methylation profiling by array assay
A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology
assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells.
epitope specific granulocyte colony stimulating factor production by T cells
A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
An assay that analyses the microRNA component of the transcriptome using a microRNA array.
A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells.
cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells
A flow cytometry assay that detects interleukin-21 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells.
ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells
An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells.
assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells.
ELISA measuring epitope specific interleukin-21 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells.
in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity
An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity.
type IV hypersensitivity (DTH)|in vivo skin test
cytometric bead array assay measuring epitope specific interleukin-13 production by T cells
A cytometric bead array assay that detects interleukin-13 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells.
epitope specific tumor necrosis factor superfamily cytokine production by T cells
A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
allele information
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells
A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells.
ELISPOT assay measuring epitope specific interleukin-17 production by T cells
An enzyme-linked immunospot assay that detects interleukin-17 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells.
post-transcriptional modification design
A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases
ELISA measuring epitope specific interleukin-8 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells.
cytometric bead array assay measuring epitope specific interleukin-6 production by T cells
A cytometric bead array assay that detects interleukin-6 production by T cells.
A transcription profiling assay that uses reverse transcription PCR (RT-PCR).
epitope specific chemokine (C-C motif) ligand 4 production by T cells
A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope.
assay measuring epitope specific interleukin-23 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells.
genetic alteration information
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
epitope specific RANTES production by T cells
A process of RANTES production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells.
cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells.
wild type allele information
an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
MO_605 genotype
intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells.
epitope specific granzyme B production by T cells
A process of granzyme B production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-8 production by T cells
A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope.
A study design in which the response of an organism(s) to injury or damage is studied.
intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells
A flow cytometry assay that detects interleukin-3 production by T cells.
A study design that compares samples from live and dead organisms.
ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells.
cytometric bead array assay measuring epitope specific interferon-gamma production by T cells
A cytometric bead array assay that detects interferon-gamma production by T cells.
assay measuring epitope specific interleukin-18 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells.
epitope specific interleukin-23 production by T cells
A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells.
cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells
A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells.
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells.
epitope specific monocyte chemotactic protein-1 production by T cells
A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope.
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology.
assay measuring epitope specific interleukin-1 alpha production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells.
assay measuring epitope specific interferon-beta production by T cells
A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells.
assay measuring epitope specific interleukin-12 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells.
in vivo assay measuring epitope specific T cell killing
An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC.
comparative genomic hybridization by array assay
An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
epitope specific cytotoxic T cell degranulation
A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells.
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells
A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells.
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
MO_933 binding_site_identification_design
epitope specific interleukin-22 production by T cells
A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope.
assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells.
A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells
A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells.
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
genetic characteristics information
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
MO_66 IndividualGeneticCharacteristics
MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells.
CCL3/MIP-1a release|cytometric bead array
assay measuring epitope specific interleukin-3 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells.
assay measuring epitope specific T cell activation
A T cell epitope dependent biological activity assay that detects T cell activation.
A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.
A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
A study design that compares cells of different type, for example different cell lines.
cytometric bead array assay measuring epitope specific RANTES production by T cells
A cytometric bead array assay that detects RANTES production by T cells.
CCL5/RANTES release|cytometric bead array
cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells
A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells.
assay measuring epitope specific interferon-gamma production by T cells
A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells.
epitope specific interleukin-9 production by T cells
A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope.
assay measuring epitope specific tumor necrosis factor alpha production by T cells
An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production.
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays.
A study design that examines the relationship between the size of the administered dose and the extent of the response.
A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin
epitope specific helper T cell enhancement of T cell mediated immune response
A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope.
epitope specific interferon-beta production by T cells
A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope.
A study design that compares tissues, regions, organs within or between organisms
intracellular material detection measuring epitope specific granzyme B release by T cells
A flow cytometry assay that detects epitope specific granzyme B release by T cells
granzyme B release|intracellular staining
protein binding site identification design
A study design that investigates protein binding sites on nucleic acids.
A study design that assays differences associated with an organism's sex, gender or mating type.
transcription profiling by tiling array design
A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.
A study design that assays events associated with cell development or differentiation.
A study design that identifies forms and abundance of transcripts in the genome.
A study design that identifies locations and members of operons in a genome.
radio immuno assay measuring epitope specific interferon-gamma production by T cells
A radio immuno assay that detects interferon-gamma production by T cells.
DNA methylation profiling by high throughput sequencing design
A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology.
assay measuring epitope specific granzyme B release by T cells
A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells.
intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells.
epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope.
A study design in which all specimens are compared to every other specimen.
A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology.
Person: Chris Stoeckert, Jie Zheng, Dan Berrios
PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
FDR adjusted p-value
Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
assay measuring epitope specific interleukin-2 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells.
epitope specific interleukin-15 production by T cells
A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope.
epitope specific macrophage inflammatory protein-1 gamma production by T cells
A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope.
individual genetic characteristics comparison design
A study design where genotype, haplotype, or other individual genetic characteristics are compared.
MO_527 individual_genetic_characteristics_design
assay measuring epitope specific interleukin-1 beta production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells.
assay measuring epitope specific interleukin-4 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells.
assay measuring epitope specific interleukin-6 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells.
cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells
A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells.
intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells
A flow cytometry assay that detects lymphotoxin A production by T cells.
A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
ELISPOT assay measuring epitope specific interleukin-5 production by T cells
An enzyme-linked immunospot assay that detects interleukin-5 production by T cells.
assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells.
cytometric bead array assay measuring epitope specific interleukin-8 production by T cells
A cytometric bead array assay that detects interleukin-8 production by T cells.
assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
ELISA measuring epitope specific granzyme B release by T cells
An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells.
epitope specific IP-10 production by T cells
A process of IP-10 production by T cells resulting from the recognition of a T cell epitope.
A transcription profiling assay that uses array technology.
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells
A flow cytometry assay that detects interleukin-12 production by T cells.
in vivo assay measuring T cell epitope specific disease exacerbation
An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment.
cell specimen
A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
monospecific T cell recognition assay measuring MHC ligand processing and presentation
A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout.
epitope specific interleukin-17F production by T cells
A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
T cell epitope specific immune intervention
Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
An epitope specific immune intervention in which the induced response targets a T cell epitope
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
in vivo assay measuring T cell epitope specific protection after tumor burden challenge
An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden.
tumor burden after challenge|in vivo assay
lowess group transformation
A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden
An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden.
pathogen burden after challenge|in vivo assay
Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated.
A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner.
lowess transformation
A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.
mass spectrometry assay measuring MHC ligand processing and presentation
A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands
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
Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind.
Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection.
Jason Greenbaum, Randi Vita, Bjoern Peters
IEDB, http://en.wikipedia.org/wiki/Phage_display
lowess global transformation
A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells
A flow cytometry assay that detects transforming growth factor-beta production by T cells.
cell collecting
A planned process that collects cells from culture.
assay measuring T cell epitope specific in vivo activity
A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment.
HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody.
A mixture containing MHC molecules that was purified to remove non-MHC molecular entities.
BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general.
disposition to be bound by an MHC protein complex
Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex.
B cell epitope specific immune intervention
Injecting a mouse with recombinant antibody targeting an anthrax epitope
An epitope specific immune intervention in which the induced response targets a B cell epitope
An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response
mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC
A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC.
ligand presentation|cellular MHC/mass spectrometry
cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells.
binding assay using radioactivity detection
A binding assay that uses radioactivity detection as an indicator of binding.
in vivo assay measuring T cell epitope specific protection based on survival
An in vivo assay measuring T cell epitope specific protection from other challenge using survival.
cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition
A cell bound MHC binding assay that uses a T cell epitope recognition assay.
qualitative binding|cellular MHC/T cell inhibition
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.
in vivo assay measuring epitope specific T cell helper activity
A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function.
intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells
A flow cytometry assay that detects interleukin-22 production by T cells.
assay measuring epitope specific perforin release by T cells
A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells.
atmosphere
A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
binding assay using fluorescence detection
A binding assay that uses fluorescence detection as an indicator of binding.
coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand
A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules.
Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
An assay in which a material's fluorescence is determined.
epitope specific perforin production by T cells
The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope.
Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation
The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex.
The process in which a ligand binds to an MHC molecule to form a stable complex.
6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
dissection
A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
purification
A planned process 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
specimen with pre- or post-mortem status
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
organizational term, used in description of specimen that is created from known pre- or post-mortem status
in vivo assay measuring T cell epitope specific treatment of disease
An efficacy of T cell epitope intervention experiment that detects a decrease in disease.
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
time point
MO_738 timepoint
Edman degradation assay measuring MHC ligand processing and presentation
A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands
mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC
A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC.
ligand presentation|secreted MHC/mass spectrometry
disposition to be a product of antigen processing and presentation
The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER.
A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell.
cytometric bead array assay measuring epitope specific interleukin-17A production by T cells
A cytometric bead array assay that detects interleukin-17A production by T cells.
radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex
A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
qualitative binding|purified MHC/competitive/radioactivity
A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound.
Created following request by Albert Goldfain
Bjoern Peters, coordinated with Albert Goldfain
A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex
A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand.
half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM
radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex
A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM
epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl
fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex
A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand.
qualitative binding|lysate MHC/direct/fluorescence
fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM
ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells
An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells.
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
cytometric bead array assay measuring epitope specific interleukin-17F production by T cells
A cytometric bead array assay that detects interleukin-17F production by T cells.
fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand.
association constant KA|cellular MHC/direct/fluorescence|1/M
The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned.
PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
epitope specific interleukin-17A production by T cells
A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope.
An help desk for an instrument or a software.
A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data.
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
Statistaical analysis service, data visualization service
A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output.
Data analysis service such statistical abalysis or storage service such data backup.
A service that has some information content entity as input and output.
Information content entity was used as specified input and output since it was more appropriate then data item or dataset.
fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex
A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand.
half life|purified MHC/direct/fluorescence|min
cytometric bead array assay measuring epitope specific interleukin-9 production by T cells
A cytometric bead array assay that detects interleukin-9 production by T cells.
A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form.
fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex
A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
qualitative binding|purified MHC/competitive/fluorescence
epitope specific interleukin-7 production by T cells
A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope.
KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex
A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
dissociation constant KD|purified MHC/competitive/fluorescence|nM
A service that offers training for a specific instrument or technique. A course to learn how to use a microscope
A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer.
fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
dissociation constant KD|cellular MHC/competitive/fluorescence|nM
obsolete T cell recognition of eluted MHC ligand assay
Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell.
An assay that identifies an MHC ligand using a T cell response assay as a readout
fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex
A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex.
on rate|purified MHC/direct/fluorescence|nM^-1s^-1
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells.
fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50
A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value.
dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM
radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex
A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation.
dissociation constant KD|lysate MHC/competitive/radioactivity|nM
intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells.
Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference
6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2
Services performing DNA sequencing or Cell Analysis
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex
A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
dissociation constant KD|cellular MHC/competitive/radioactivity|nM
assay measuring binding of a cell-bound-MHC:ligand complex
A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand.
A service that provides acess to a mass spectrometer.
A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service.
Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process.
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells.
assay measuring a binding constant of a MHC:ligand complex
A MHC:ligand binding assay that measures a binding constant.
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
A scalar measurement datum that represents the number of events occuring over a time interval
assay measuring binding of a purified-MHC:ligand complex
A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand.
radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex
A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand.
qualitative binding|lysate MHC/direct/radioactivity
A service that offers liquid nitrogen stroage.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex
A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand.
half life|cellular MHC/direct/radioactivity|min
fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand.
half life|cellular MHC/direct/fluorescence|min
obsolete cell lysate MHC binding constant determination assay
An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant.
fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand.
half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM
intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells
A flow cytometry assay that detects interleukin-17F production by T cells.
A service for cell line creation. A service providing cel line immortalization.
A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer.
radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50
A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value.
dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM
radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex
A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand.
half life|lysate MHC/direct/radioactivity|min
50% dissociation of binding temperature (Tm)
Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated.
A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound.
radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex
A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand.
off rate|lysate MHC/direct/radioactivity|1/s
radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex
A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM
fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex
A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand.
off rate|purified MHC/direct/fluorescence|1/s
assay measuring epitope specific vascular endothelial growth factor production by T cells
A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells.
equilibrium dissociation constant (KD) approximated by IC50
A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
obsolete cell bound MHC binding constant determination assay
An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant.
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.
obsolete cell lysate MHC competitive binding assay using radioactivity detection
competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
cell lysate MHC competitive binding using radioactivity
assigning gene property based on phenotypic assessment
Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result.
obsolete purified MHC binding constant determination assay
An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant.
cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells
A cytometric bead array assay that detects interleukin-22 production by T cells.
ELISA measuring epitope specific vascular endothelial growth factor production by T cells
An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells.
assay measuring binding of a cell-lysate-MHC:ligand complex
A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand.
A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer.
equilibrium dissociation constant (KD) approximated by EC50
A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
Assay Development: Fundamentals and Practices, By Ge Wu, page 74
obsolete cell bound MHC direct binding assay
direct binding assay measuring MHC ligand binding using MHC derived from a cell
The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
phage display binding assay measuring binding of a purified-MHC:ligand complex
A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand.
qualitative binding|purified MHC/direct/phage display
cytometric bead array assay measuring epitope specific interleukin-7 production by T cells
A cytometric bead array assay that detects interleukin-7 production by T cells.
radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex
A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand.
half life|purified MHC/direct/radioactivity|min
assay measuring epitope specific interleukin-7 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells.
A peptide binding to an MHC molecule to form a complex.
The process of material entities forming complexes.
9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells
A flow cytometry assay that detects interleukin-17A production by T cells.
fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex
A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand.
qualitative binding|purified MHC/direct/fluorescence
Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._
A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand.
fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex
A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand.
half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM
Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._
A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material.
fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
qualitative binding|cellular MHC/competitive/fluorescence
X-ray crystallography assay determining the 3D structure of a MHC:ligand complex
A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex.
The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex
A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities.
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition
A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding.
half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM
A database management service, a web hosting service.
A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance.
radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex
A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
qualitative binding|cellular MHC/competitive/radioactivity
assay measuring epitope specific granulocyte colony stimulating factor production by T cells
A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells.
cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells
A cytometric bead array assay that detects interleukin-21 production by T cells.
radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex
A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand.
qualitative binding|cellular MHC/direct/radioactivity
binding off rate measurement datum (koff)
A rate measurement datum of how quickly bound complexes disassociate
fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex
A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand.
50% dissociation temperature|purified MHC/direct/fluorescence|°C
A rate measurement datum of how quickly bound complexes form
fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand.
qualitative binding|cellular MHC/direct/fluorescence
assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production.
TNFSF11/RANKL release|biological activity
radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex
A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand.
qualitative binding|purified MHC/direct/radioactivity
intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells
A flow cytometry assay that detects interleukin-8 production by T cells.
cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells
A cytometric bead array assay that detects interleukin-23 production by T cells.
obsolete purified MHC direct binding assay
direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation
epitope specific vascular endothelial growth factor production by T cells
A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope.
fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex
A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
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
PubMed ID
A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/
PMID
PubMed Identifier
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
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
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
latitude
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
longitude
Specimen Collection Location - Longitude
investigation title
A textual entity that denotes an investigation.
Person:Chris Stoeckert, Jie Zheng
project title
organism identification objective
A biological feature identification objective to identify the organism species in a specimen.
Penn Group
organism species detection objective
An organism detection assay that identifies the organism species in a specimen.
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
country name
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
Website: http://en.wikipedia.org/wiki/Country
investigation identifier
A CRID symbol used to identify an investigation.
Person: Chris Stoeckert, Jie Zhneg
project ID
grant identifier
A CRID symbol used to identify a grant.
grant ID
Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column.
An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material.
Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure.
An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material.
Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye.
A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity.
A mixture of peptide molecules that has been run through an HPLC column to remove 65
A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component
A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell ._
A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy.
antibody binding detection by fluorescence quenching
The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844).
A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope).
grant
A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
Group: OBI
AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50
A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay.
dissociation constant KD|inhibition by antigen (~ IC50)|nM
assay measuring epitope specific Ig-mediated histamine release
A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro.
assay measuring epitope specific immunoglobulin-mediated antigen activation
A B cell epitope dependent biological activity determination assay that detects antigen activation.
assay measuring epitope specific complement-dependent cytotoxicity
A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro .
complement-dependent cytotoxicity|biological activity
assay measuring epitope specific antibody-dependent cellular cytotoxicity
A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro.
antibody-dependent cellular cytotoxicity|biological activity
assay measuring epitope specific immunoglobulin-mediated neutralization
A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen.
assay measuring epitope specific opsonization
A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro .
calorimetry assay measuring binding of a B cell epitope:antibody complex
A calorimetric binding assay that detects the binding of an antigen with an antibody.
electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex
An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex
NMR assay determining the 3D structure of a B cell epitope:antibody complex
A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex.
3D structure|nuclear magnetic resonance (NMR)
cross blocking assay measuring binding of a B cell epitope:antibody complex
A cross-blocking assay that detects the binding of an antigen with an antibody.
RIA measuring binding of a B cell epitope:antibody complex
A radio immuno assay that detects the binding of an antigen with an antibody.
qualitative binding|radio immuno assay (RIA)
immunoblot assay measuring binding of a B cell epitope:antibody complex
An immunoblot assay that detects the binding of an antigen with an antibody.
plasmon resonance assay measuring binding of a B cell epitope:antibody complex
A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody.
qualitative binding|surface plasmon resonance (SPR)
immuno staining assay measuring binding of a B cell epitope:antibody complex
An immuno staining assay that detects the binding of an antigen with an antibody.
immunoprecipitation assay measuring binding of a B cell epitope:antibody complex
An immunoprecipitation assay that detects the binding of an antigen with an antibody.
mass spectrometry assay measuring binding of a B cell epitope:antibody complex
A mass spectrometry assay that detects the binding of an antigen with an antibody.
phage display assay measuring binding of a B cell epitope:antibody complex
A phage display binding assay that detects the binding of an antigen with an antibody.
electron microscopy assay measuring binding of a B cell epitope:antibody complex
An electron microscopy imaging assay that detects the binding of an antigen with an antibody.
ELISA measuring binding of a B cell epitope:antibody complex
An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody.
ELISPOT assay measuring binding of a B cell epitope:antibody complex
An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody.
flow cytometry assay measuring binding of a B cell epitope:antibody complex
A flow cytometry assay that detects the binding of an antigen with an antibody.
intracellular material detection assay measuring epitope specific granzyme A release by T cells
A flow cytometry assay that detects epitope specific granzyme A release by T cells.
granzyme A release|intracellular staining
chromatography assay measuring binding of a B cell epitope:antibody complex
An analytical chromatography assay that detects the binding of an antigen with an antibody.
NMR assay measuring binding of a B cell epitope:antibody complex
A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay.
qualitative binding|nuclear magnetic resonance (NMR)
ELISA measuring epitope specific granulysin release by T cells
An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells.
intracellular material detection assay measuring epitope specific granulysin release by T cells
A flow cytometry assay that detects epitope specific granulysin release by T cells.
granulysin release|intracellular staining
fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand.
off rate|cellular MHC/direct/fluorescence|1/s
fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex
A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand.
on rate|cellular MHC/direct/fluorescence|nM^-1s^-1
fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50
A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value.
dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM
Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. PMID:17513562
A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457
An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay.
Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. PMID:11518275
An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest.
Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. PMID:21918373
An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid.
An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells.
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
ELISA measuring epitope specific interleukin-17A production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells.
epitope specific granulysin production by T cells
A process of granulysin production by T cells resulting from the recognition of a T cell epitope.
Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt
epitope specific granzyme A production by T cells
A process of granzyme A production by T cells resulting from the recognition of a T cell epitope.
Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. PMID:10627486
An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay.
The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. PMID:20300944
A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system.
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702
An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain.
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042
An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence
chromosome organization assay by fluorescence in-situ hybridization
Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449
An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity
methylation-specific polymerase chain reaction assay
Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662
An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
amplification of intermethylated sites assay
Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810
An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265
An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization.
contact representative role
A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178
cytochalasin-induced inhibition of actin polymerization assay
An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041).
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
in vivo assay measuring B cell epitope specific protection from fertility
An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility.
PERSON:Randi Vita, James Overton, Bjoern Peters
in vivo assay measuring B cell epitope specific tolerance induction
An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment.
in vivo assay measuring B cell epitope specific induction of hypersensitivity
An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions.
assay measuring epitope specific immune complex formation
A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro.
in vivo assay measuring B cell epitope specific protection based on survival
An in vivo assay measuring B cell epitope specific protection from other challenge using survival.
in vivo assay measuring B cell epitope specific treatment of disease
An efficacy of B cell epitope intervention experiment that detects a decrease in disease.
assay measuring B cell epitope specific in vivo activity
A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment.
Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format.
A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites.
Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum.
An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies.
antigen inhibition assay measuring binding of a B cell epitope:antibody complex
A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand.
qualitative binding|inhibition by antigen
Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus.
a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR).
assay measuring qualitative binding of a B cell epitope:antibody complex
An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output.
assay measuring epitope specific activation of additional immune response in vitro
A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity.
secondary in vitro activity|biological activity
assay measuring epitope specific antigen inhibition of antibody activity
A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen.
antibody activity inhibition|biological activity
assay measuring biological activity resulting from B cell epitope:antibody binding
A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope.
immunoglobulin mediated histamine release
The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins.
4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile.
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
A B cell epitope binding constant determination assay that measures the dissociation constant KD.
dissociation constant KD|binding assay|nM
assay measuring a binding constant of a B cell epitope:antibody complex
A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant.
in vivo assay measuring B cell epitope specific protection from challenge
An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment.
in vivo assay measuring B cell epitope specific disease exacerbation
An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment.
obsolete B cell epitope direct binding assay
opsonization resulting from antibody binding to epitope
Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl
B cell epitope specific immunoglobulin-mediated neutralization
immunoglobulin-mediated neutralization resulting from antibody binding to epitope
obsolete B cell epitope competitive binding assay
A competitive inhibition of binding assay using a assay
B cell epitope specific complement-dependent cytotoxicity
complement-dependent cytotoxicity resulting from antibody binding to epitope
B cell epitope specific antibody-dependent cellular cytotoxicity
antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope
assay measuring the on rate [kon] of a B cell epitope:antibody complex
A B cell epitope binding constant determination assay that measures the on rate.
assay measuring the association constant [KA] of a B cell epitope:antibody complex
A B cell epitope binding constant determination assay that measures the association constant KA.
association constant KA|binding assay|1/nM
B cell epitope specific immune complex formation
immune complex formation resulting from antibody binding to epitope
3D molecular structure determination assay of an antigen:antibody complex
A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex.
B cell epitope specific hypersensitivity
hypersensitivity resulting from antibody binding to epitope
assay measuring the off rate [koff] of a B cell epitope:antibody complex
A B cell epitope binding constant determination assay that measures the off rate.
viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex
A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody.
qualitative binding| hemagglutination inhibition
B cell epitope specific histamine secretion mediated by immunoglobulin
histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope
quenching assay measuring binding of a B cell epitope:antibody complex
A fluorescence quenching assay that detects the binding of an antigen with an antibody.
RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex
A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody.
dissociation constant KD|radio immuno assay (RIA)|nM
ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex
An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody.
quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody.
surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex
A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody.
association constant KA|surface plasmon resonance (SPR)|1/nM
surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody.
quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex
A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody.
calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex
A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody.
association constant KA|calorimetry|1/nM
calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody.
ELISA measuring the association constant [KA] of a B cell epitope:antibody complex
An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody.
RIA measuring the association constant [KA] of a B cell epitope:antibody complex
A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody.
association constant KA|radio immuno assay (RIA)|1/nM
obsolete B cell epitope specific X-ray crystallography assay
A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms
X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex
A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex.
surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex
A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody.
off rate|surface plasmon resonance (SPR)|1/s
quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex
A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody.
surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex
A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody.
on rate|surface plasmon resonance (SPR)|M^-1s^-1
quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex
A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells
A flow cytometry assay that detects interleukin-1 alpha production by T cells.
ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells
An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells.
cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells
A cytometric bead array assay that detects interleukin-1 alpha production by T cells.
ELISPOT assay measuring epitope specific interferon-beta production by T cells
An enzyme-linked immunospot assay that detects interferon-beta production by T cells.
intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells
A flow cytometry assay that detects interferon-beta production by T cells.
intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells
A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells.
ELISA measuring epitope specific interferon-beta production by T cells
An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells.
ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells
An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells.
cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
selection criterion
rats should be aged between 6 and 8 weeks and weight between 180-250grams
A directive information entity which defines and states a principle of standard by which selection process may take place.
Person: Philippe Rocca-Serra
selection rule
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells.
ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells.
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells.
CCL4/MIP-1b release|cytometric bead array
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells.
intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells.
specimen collector role
An Investigation agent role borne by a person or organization which is realized in a specimen collection process.
intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells
A flow cytometry assay that detects vascular endothelial growth factor production by T cells.
ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells
An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells.
assay measuring epitope specific interleukin-17F production by T cells
An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production.
assay measuring epitope specific interleukin-17A production by T cells
An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production.
assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells.
assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells.
CCL19/MIP-3b release|biological activity
assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells.
CXCL12/SDF-1 release|biological activity
assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells.
assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells.
assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells.
ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells.
cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells.
CCL9/MIP-1g release|cytometric bead array
detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells.
intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells.
ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells.
intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells.
ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells.
cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells
A cytometric bead array assay that detects vascular endothelial growth factor production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells.
intracellular cytokine staining assay measuring epitope specific RANTES production by T cells
A flow cytometry assay that detects RANTES production by T cells.
ELISPOT assay measuring epitope specific RANTES production by T cells
An enzyme-linked immunospot assay that detects RANTES production by T cells.
ELISPOT assay measuring epitope specific lymphotoxin A production by T cells
An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells.
cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells
A cytometric bead array assay that detects lymphotoxin A production by T cells.
lymphotoxin A/TNFb release|cytometric bead array
detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells.
lymphotoxin A/TNFb release|RNA/DNA detection
ELISPOT assay measuring epitope specific IP-10 production by T cells
An enzyme-linked immunospot assay that detects IP-10 production by T cells.
intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells
A flow cytometry assay that detects IP-10 production by T cells.
ELISPOT assay measuring epitope specific interleukin-9 production by T cells
An enzyme-linked immunospot assay that detects interleukin-9 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells
A flow cytometry assay that detects interleukin-9 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells.
ELISPOT assay measuring epitope specific interleukin-8 production by T cells
An enzyme-linked immunospot assay that detects interleukin-8 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells.
ELISPOT assay measuring epitope specific interleukin-3 production by T cells
An enzyme-linked immunospot assay that detects interleukin-3 production by T cells.
ELISA measuring epitope specific interleukin-7 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells.
ELISPOT assay measuring epitope specific interleukin-7 production by T cells
An enzyme-linked immunospot assay that detects interleukin-7 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells
A flow cytometry assay that detects interleukin-7 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells
A flow cytometry assay that detects interleukin-27 production by T cells.
cytometric bead array assay measuring epitope specific interleukin-3 production by T cells
A cytometric bead array assay that detects interleukin-3 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells.
assay measuring epitope specific granzyme A release by T cells
A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells.
assay measuring epitope specific granulysin release by T cells
A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells.
cytometric bead array assay measuring epitope specific interleukin-27 production by T cells
A cytometric bead array assay that detects interleukin-27 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells
A flow cytometry assay that detects interleukin-23 production by T cells.
ELISPOT assay measuring epitope specific interleukin-27 production by T cells
An enzyme-linked immunospot assay that detects interleukin-27 production by T cells.
ELISA measuring epitope specific interleukin-27 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells.
epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope.
Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt
ELISPOT assay measuring epitope specific interleukin-18 production by T cells
An enzyme-linked immunospot assay that detects interleukin-18 production by T cells.
epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope.
epitope specific chemokine (C-C motif) ligand 22 production by T cells
A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope.
epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope.
ELISPOT assay measuring epitope specific interleukin-22 production by T cells
An enzyme-linked immunospot assay that detects interleukin-22 production by T cells.
ELISPOT assay measuring epitope specific interleukin-23 production by T cells
An enzyme-linked immunospot assay that detects interleukin-23 production by T cells.
epitope specific chemokine (C-C motif) ligand 21 production by T cells
A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope.
intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells
A flow cytometry assay that detects interleukin-18 production by T cells.
epitope specific chemokine (C-C motif) ligand 19 production by T cells
A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope.
ELISPOT assay measuring epitope specific interleukin-21 production by T cells
An enzyme-linked immunospot assay that detects interleukin-21 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells.
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells.
CCL1/TCA-3 release|cytometric bead array
ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells.
ELISPOT assay measuring epitope specific interleukin-17F production by T cells
An enzyme-linked immunospot assay that detects interleukin-17F production by T cells.
ELISA measuring epitope specific interleukin-17F production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells.
ELISPOT assay measuring epitope specific interleukin-17A production by T cells
An enzyme-linked immunospot assay that detects interleukin-17A production by T cells.
Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. 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.
A planned process in which new information is inferred from existing information.
cytometric bead array assay measuring epitope specific interleukin-18 production by T cells
A cytometric bead array assay that detects interleukin-18 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells.
ELISA measuring epitope specific interleukin-16 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells.
ELISPOT assay measuring epitope specific interleukin-16 production by T cells
An enzyme-linked immunospot assay that detects interleukin-16 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells
A flow cytometry assay that detects interleukin-16 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells
A flow cytometry assay that detects interleukin-1 beta production by T cells.
ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells
An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells.
detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells.
ELISPOT assay measuring epitope specific interleukin-12 production by T cells
An enzyme-linked immunospot assay that detects interleukin-12 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells
A flow cytometry assay that detects interleukin-15 production by T cells.
ELISPOT assay measuring epitope specific interleukin-15 production by T cells
An enzyme-linked immunospot assay that detects interleukin-15 production by T cells.
chromatin interaction analysis by paired-end tag sequencing assay
Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262]
An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide.
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'.
RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay
Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659]
An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs).
cross-linking immunoprecipitation high-throughput sequencing assay
Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288]
An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein.
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.
methylation-sensitive restriction enzyme sequencing assay
Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]
An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA.
reduced representation bisulfite sequencing assay
Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174]
A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome.
Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030].
A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing.
whole-genome shotgun bisulfite sequencing
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.
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 cultured cell that has been passaged or derives from a cell that has been passaged in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants.
MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion).
OBI developer calls, March 4 2013 and March 11 2013
Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells).
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
A BeadChip made for an analyte assay that generates information about DNA methylation.
A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously.
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
number of errors
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2
a data item that is the number of times that a given process failed, as an integer
PRS, AGB
random access memory size
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads"
random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation
a cultured cell population comprised of a single type of immune system cell
MHB 3-5-13: created as a (temporary) organizational class to organize IEDB immune cultured cell population types. These were all previously labled as 'cell cultures' - and relabeld here as 'cultured cell populations' since a CLO alignment outcome was to use the term 'cell culture' to refer to cultured cells + media. Consult with BP as to whether this organizational class is useful and if so, how to define it. Also check whether the intent was to represent cell populations rather than cell cultures.
cultured immune cell population
A material entity comprised of cultured cells and the media in which they are being propagated or stored.
OBI-CLO Alignment Working Group (Spring 2013)
A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored.
random access memory
Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location
RAM
http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02
establishing primary cell culture
Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages. Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488 When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium.
an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture
PERSON: Matthew Brush
Cells are originally plated at a certain concentration referred to as seeding density. Upon a first passage this primary culture becomes a secondary cell culture that can be propagated to become a stable and homogneous cell line. This class covers establishment of primary cultures from any native cell - 'in vivo' cells isolated from some multicellular organism, or 'in environment' unicellular organisms isolated from some natural environment.
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
target material in specimen specification
Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome.
A plan specification which specifies the type of material that will be assayed in an investigation.
Bioinformatics Resource Center contact person
A person who is the contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact Name
specimen-based scope of investigation specification
Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic.
A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
specimen repository organization
An organization that provides a service to store and distribute specimens
email address of Bioinformatics Resource Center contact person
An email address of the person who is contact representative of a Bioinformatics Resource Center
Bioinformatics Resource Center Contact's email
sequencing facility contact person
A person who is the contact representative at the sequencing facility
specimen provider principal investigator
A person who is a principal investigator and provides the specimen
Sample Provider Principal Investigator (PI) Name
email address of specimen collector
An email address of the person collecting the specimen
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
email address of sequencing facility contact person
An email address of the contact representative at the sequencing facility
specimen collector
investigation assay specification
Some examples of Project Method are Sequence, Array, Mass Spectrometry
A plan specification which indicates the assay type used to obtain data.
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
comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting
target capture specification
Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey
A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen.
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
sample preparation for sequencing assay
A sample preparation for assay that preparation of nucleic acids for a sequencing assay
email address of specimen provider principal investigator
An email address of the principal investigator providing the specimens for the investigation
sequencing service
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
A cultured cell population that is derived through one or more passages in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
An immortal cell line derived from a transformed cell that was part of a malignant tumor.
a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture
An information content entity that expresses an assertion that is intended to be tested.
In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored.
primary cell culture
A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored.
A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored.
cell line culture
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
computation run time
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4
computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency.
computation run time datum
PRS,AGB
multiplex ligation-mediated amplification
A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation.
Multiplex ligation-dependent probe amplification
web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/
Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067]
An assay which quantifies the timing of DNA replication as a function of genome position using array technology.
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.
RNA-binding protein immunoprecipitation array profiling assay
Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495]
An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs).
Carbon-copy chromosome conformation capture assay
van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094]
An assay that measures the organization of chromosomes at the genome-wide scale.
DNA replication timing by sequencing assay
Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139_�_144. [PMID:19966280]
An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing.
RNA-binding protein immunoprecipitation tiling array profiling assay
An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs).
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.
protein sequencing by tandem mass spectrometry assay
Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305]
A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation.
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
chromatin immunoprecipitation with exonuclease sequencing assay
Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]
A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site
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)
selection process
A value specification that specifies the mass of some thing.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
A planned process in which predicted values for some thing are compared to measured values for that thing.
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error.
A predicted value where the prediction specifies the mass of some thing.
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
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "The genome coverage increased from 81.16% to 93.91%"
A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%.
A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. PMID: 22510764
N50
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
weighted median item size
adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html"
contig N50
N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
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 planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
scaffold N50
N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information
forward PCR primer
SP6 promoter, forward primer (SP6 TTTAGGTGACACTATAG)
A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm.
5' primer
forward primer
sense primer
adapted from http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p
sequence annotation provider
A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence.
sequence assembly name
A textual entity that is used to denote a sequence assembly.
sequence annotation reporting role
A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence.
reverse PCR primer
5' end of luciferase, reverse primer (LucNrev CCTTATGCAGTTGCTCTCC)
A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm.
3' primer
antisense primer
reverse primer
adapted from "http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p"
flash freezing
A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C.
WEB: http://en.wikipedia.org/wiki/Flash_freezing
freezing
A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities.
An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed
competitive binding reference ligand role
The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion.
A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target.
assay using chromatin immunoprecipitation
An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation
A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision.
Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/
The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/
A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed.
multiplexed nucleotide library sequencing
A planned process which consists in running a set of samples as a pool on a sequencing instrument, while retaining the ability to associate individual results to each of the individual input samples through the use of a ligated oligonucleotide (the "multiplex identifier sequence"). This oligonucleotide is introduced during the sequence library preparation, and is unique to and specific for all library fragments derived from each sample in a sample pool.
taxonomic diversity assessment by targeted gene survey
An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity.
PCR program
a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program.
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
target subfragment specification
http://www.ncbi.nlm.nih.gov/pubmed/23335919 "performing a profiling of microbial phylogenetic composition using massively-parallel pyrotag sequencing targeting the V9 hypervariable region (used as target subfragment) of the 18S ribosomal RNA (rRNA) gene (used as target gene)
is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey
target subfragment
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.
a study design that has a decision analysis objective specification as part
sequence library data demultiplexing
is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to separate all reads belonging to a given single sample following the sequencing of a multiplexed library
multiplexing sequence identifier
We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. in http://www.ncbi.nlm.nih.gov/pubmed/22574170
A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library
operational taxonomic unit matrix
Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism.
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
multiplexed sequencing library
http://www.ncbi.nlm.nih.gov/pubmed/24997861 Nat Methods. 2014 Aug;11(8):834-40. doi: 10.1038/nmeth.3022. Epub 2014 Jul 6. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run.
DNA-barcoded sequencing library
An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb.
Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/
An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb.
Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/
An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface.
Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/
An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb.
Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/
hydrogen/deuterium exchange footprinting assay
Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface.
A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure.
An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.
An assay that counts and/or measures characteristics of cells.
An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules.
A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other.
Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival.
An assay in which the effect of a targeted process (the intervention) on an organism is tested.
The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay.
disease exacerbation in vivo intervention experiment
Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide.
An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host.
Should have data about disease severity as readout; could just use disease for now
protection from challenge in vivo intervention experiment
Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide.
An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host.
tolerance induction intervention experiment
Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide.
An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response.
should have tolerance induction as intervention
Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals.
An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested.
Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray.
An analyte assay where binding of the analyte to immobilized matrix is measured.
Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques.
An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section.
assay measuring the association constant [KA] of a MHC:ligand complex
A MHC binding constant determination assay measuring equilibrium association constant (KA).
association constant KA|binding assay|1/M
assay measuring the dissociation constant [KD] of a MHC:ligand complex
A MHC binding constant determination assay measuring equilibrium dissociation constant (KD).
radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex
A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
dissociation constant KD|purified MHC/direct/radioactivity|nM
assay measuring the half life of a MHC:ligand complex
A MHC binding constant determination assay measuring half life of binding.
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex
A MHC binding constant determination assay measuring half maximal effective concentration (EC50).
half maximal effective concentration (EC50)|binding assay|nM
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex
A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50).
half maximal inhibitory concentration (IC50)|binding assay|nM
assay measuring the off rate measurement [koff] of a MHC:ligand complex
A MHC binding constant determination assay measuring binding off rate measurement data item (koff).
assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex
A MHC binding constant determination assay measuring binding on rate (kon).
chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex
An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody.
association constant KA|chromatography|1/nM
chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody.
dissociation constant KD|chromatography|nM
hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex
A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody.
qualitative binding|hydrogen/deuterium exchange footprinting assay
immunohistochemistry assay measuring binding of a B cell epitope:antibody complex
A immunohistochemistry assay that detects the binding of an antigen with an antibody.
qualitative binding|immunohistochemistry
3D molecular structure determination assay of a T cell epitope:MHC:TCR complex
A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex.
Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897
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 IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380
A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
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 Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.
Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301]
A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.
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 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.
Illumina Infinium Human Methylation 450K BeadChip
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.
Illumina Infinium Human Methylation 27K BeadChip
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.
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.
Mouse 385K Whole Genome CGH Tiling Array
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 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.
Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array
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.
Nimblegen Human 3x720K Whole Genome CGH Tiling Array
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.
Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0
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.
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 human 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 removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511.
DNA methylation profiling by ChIP-chip assay
An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies.
A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS).
histone modification identification by ChIP-chip assay
An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques.
histone modification identification by ChIP-Seq assay
An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques.
transcription factor binding site identification by ChIP-chip assay
A transcription factor binding site assay that utilizes ChIP-chip technology.
transcription factor binding site identification by ChIP-Seq assay
A transcription factor binding site assay that utilizes ChIP-seq technology.
An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation.
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.
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.
A genotyping by array assay that uses tiling array technology.
DNA sequence variation detection by tiling array
A genotyping by array assay that uses SNP array technology.
DNA sequence variation detection by snp array
parallel analysis of RNA structure assay
A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes
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.
A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein.
array based nucleic acid structure mapping assay
An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray.
micrococcal nuclease digestion followed by tiling array assay
An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays
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.
assay for transposase-accessible chromatin using sequencing
Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766.
An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion.
chromatin isolation by RNA purification sequencing assay
Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111.
A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing.
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
carbon-copy chromosome conformation capture assay followed by sequencing assay
Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049.
A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture.
Carbon-copy chromosome conformation capture assay followed by sequencing
individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay
Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141
A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes.
individual-nucleotide resolution cross-linking and immunoprecipitation
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 device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached
Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL).
A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added.
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.
3D molecular structure determination assay of a MHC:ligand complex
A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex.
in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden
An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden.
in vivo assay measuring B cell epitope specific protection after tumor burden challenge
An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden.
microarray assay measuring binding of a B cell epitope:antibody complex
A microarray assay that detects the binding of an antigen with an antibody.
NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay.
dissociation constant KD|nuclear magnetic resonance (NMR)|nM
assay measuring biological activity resulting from T cell epitope:MHC:TCR binding
A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope.
assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells
A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells.
assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells
A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells.
assay measuring epitope specific oncostatin M production by T cells
A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells.
oncostatin M release|biological activity
assay measuring a binding constant of a T cell epitope:MHC:TCR complex
A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant.
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells.
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells
A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells.
in vitro assay measuring epitope specific T cell killing
An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC.
cytometric bead array assay measuring epitope specific granzyme A release by T cells
A cytometric bead array assay that detects epitope specific granzyme A release by T cells.
granzyme A release|cytometric bead array
detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells
A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells.
cytometric bead array assay measuring epitope specific granzyme B release by T cells
A cytometric bead array assay that detects epitope specific granzyme B release by T cells.
granzyme B release|cytometric bead array
detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells
A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells
cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells
A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells.
cytometric bead array assay measuring epitope specific oncostatin M production by T cells
A cytometric bead array assay that detects oncostatin M production by T cells.
oncostatin M release|cytometric bead array
ELISPOT assay measuring epitope specific perforin release by T cells
An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells.
in vivo assay measuring epitope specific proliferation of T cells
A T cell epitope specific proliferation assay that is performed in vivo.
in vitro assay measuring epitope specific proliferation of T cells
A T cell epitope specific proliferation assay that is performed on cells in vitro.
assay measuring qualitative binding of a MHC:ligand complex
An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output.
in vivo assay measuring T cell epitope specific protection from challenge
An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment.
assay measuring T cell epitope specific suppression in vitro
T cell epitope dependent biological activity assay that detects suppression of an in vitro response.
An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
specimens derived from shared ancestor
Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy.
A collection of specimens derived from one common specimen via one or more material processing process(es).
specimen family
Duke Biobank, OBIB, OBI
specimen set collection process
Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy.
A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
OBIB, OBI
specimens collected in one encounter
Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy.
A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
specimen set
human specimen set
A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
specimens collected longitudinally
A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity.
Bjoern Peters, OBI
An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest.
enhancer activity detection by reporter gene assay
PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules"
A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest.
transcription cofactor activity region identification by ChIP-Seq assay
PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue"
A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase.
chromatin modifier binding site identification by ChIP-Seq assay
transcript expression location detection by hybridization chain reaction assay
PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells"
An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers.
transcript expression location detection by fluorescent HCR.
A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected.
containing a specimen function
A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
Biobank
COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
A container with the function of containing a specimen.
A container with an environmental control function.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA.
For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/
Jason Hilton, Chris Stoeckert
ENCODE
rapid amplification of cDNA ends
5' rapid amplification of cDNA ends
A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 5' end of the mRNA.
5' RACE
3' rapid amplification of cDNA ends
A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 3' end of the mRNA.
3' RACE
5' RNA ligase mediated rapid amplification of cDNA ends
A 5' rapid amplification pf cDNA ends that uses RNA ligase to add an RNA adapter oligonucleotide to intact 5' mRNA ends, allowing the amplification of cDNA only from full-length, capped mRNA.
5' RLM RACE
MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants.
A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing.
specimen family creation
Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum.
A material processing that has as its input a specimen and as its output a collection of specimens.
For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Mathias Brochhausen, Chris Stoeckert, Jie Zheng
OBI, OBIB
carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells
A CFSE assay that detects T cell epitope specific proliferation in vitro.
assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
A T cell epitope binding constant determination assay that measures the dissociation constant KD.
assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex
A T cell epitope binding constant determination assay that measures the on rate.
assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex
A T cell epitope binding constant determination assay that measures the off rate.
assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex
A T cell epitope binding constant determination assay that measures the association constant KA.
small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex
A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex
3D structure|small-angle scattering assay
bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex
A bio-layer interferometry assay that measures the on rate of an antigen with an antibody.
on rate|bio-layer interferometry assay|M^-1s^-1
bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex
A bio-layer interferometry assay that measures the off rate of an antigen with an antibody.
off rate|bio-layer interferometry assay|1/s
bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex
A bio-layer interferometry assay that detects the binding of an antigen with an antibody.
qualitative binding|bio-layer interferometry assay
bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody.
dissociation constant KD|bio-layer interferometry assay|nM
carboxyfluorescein succinimidyl ester staining assay
Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division.
An assay using carboxyfluorescein succinimidyl ester staining.
Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds.
A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor.
small-angle scattering 3D molecular structure determination assay
Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein
A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined.
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
digital object identifier
The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073
A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.
Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/
https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/
enhanced cross-linking immunoprecipitation high-throughput sequencing assay
An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments.
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.
Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining reflective of the level of expression of those surface receptors.
A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry.
high performance liquid chromotography assay
On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml.
An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution.
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).
Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy.
An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells.
A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators).
killer cell immunoglobulin-like receptor typing assay
DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself.
A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined.
Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both_ according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size_ were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.
A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined.
IHC slide staining
A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues.
Chris Stoeckert, Ned Haubein
H&E slide staining
A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink.
H&E-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of H&E slide staining.
IHC-stained fixed tissue slide specimen
A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
immunohistochemistry slide specimen
single cell specimen
A cell specimen that contains only one cell.
Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
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.
A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann
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.
pulse stable isotope labeling by amino acids in cell culture
An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability.
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells
A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells.
CCL20/MIP-3a release|cytometric bead array
assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells
A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells.
CCL20/MIP-3a release|biological activity
A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace.
RNA Integrity Number calculation
RNA Integrity Number value specification
A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact).
A value specification that specifies the temperature of some thing.
temperature value specification
A value specification that specifies the volume of some thing.
volume value specification
An assay to determine the temperature of an evaluant.
An assay to determine the volume of an evaluant.
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.
Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens
An analyte assay that measures the presence or amount of antibodies to a specified antigen.
An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens.
HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36)
An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens.
An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens.
An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens.
An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens.
An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens.
venereal disease research laboratory test
An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood.
An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope.
An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens.
An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids.
An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids.
A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states.
systematic evolution of ligands by exponential enrichment assay
A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._
An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions.
An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis
A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together.
An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied.
A protein localization assay that determines the specific location of a protein in a living tissue sample.
A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy.
subcellular protein immunohistochemistry assay
An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins.
A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples.
A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules.
An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies.
A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane.
A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane.
An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed
An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen.
An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance).
Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues.
An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations.
A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations.
A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels.
An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell.
The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation.
The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques.
The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels.
An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface.
An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique.
Can be used on any cell, not just neurons.
An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time.
An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.
An organization that delivers messages, packages, and mail.
courier organization
A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item.
courier tracking number
An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories.
A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right.
A device that is the part of a microtome used to slice specimens to a desired thickness.
Sakura Low profile Accu-Edge microtome blade
A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering.
A length measurement datum that is the result of an assay measuring the thickness of a tissue section.
tissue section thickness
molecular analysis facility organization
An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs.
An organization that provides molecular analysis service.
cannot be assessed, not applicable, unknown
An information content entity that provides an explanation why a data item is not provided.
A reason for lack of data item that is the negative output of a determination if assay will provide reliable results.
determination if assay will provide reliable results
A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay.
AJCC 7th edition GX: cannot be assessed.
A cannot be assessed determination for histologic tumor grade.
AJCC 7th edition pTX: cannot be assessed.
A cannot be assessed determination for pathologic primary tumor staging.
AJCC 7th edition pNX: cannot be assessed.
A cannot be assessed determination of pathologic staging of lymph nodes.
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
A clinical history in which there is a diagnosis of cancer.
A clinical history in which there was no diagnosis of cancer.
A clinical history in which it is not known whether there was a diagnosis of cancer.
A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer.
A clinical history in which there is a diagnosis of cancer in a blood relative.
A clinical history in which there is a diagnosis of cancer in the female sibling of a parent.
A clinical history in which there is a diagnosis of cancer in a male sibling.
A clinical history in which there is a diagnosis of cancer in a person's female child.
A clinical history in which there is a diagnosis of cancer in a male parent.
A clinical history in which there is a diagnosis of cancer in a female parent.
A clinical history in which there is a diagnosis of cancer in a female sibling.
A clinical history in which there is a diagnosis of cancer in a person's male child.
A clinical history in which there is a diagnosis of cancer in a male sibling of a parent.
A clinical history in which there is a diagnosis of cancer in a female parent of a parent.
A clinical history in which there is a diagnosis of cancer in a male parent of a parent.
A clinical history in which there is a diagnosis of cancer in a male child of a sibling.
A clinical history in which there is a diagnosis of cancer in a female child of a sibling.
A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease.
A diagnosis of infectious disease caused by the hepatitis B virus.
A diagnosis of infectious disease caused by the hepatitis C virus.
A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2).
A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays.
A clinical history in which there has been second hand exposure to tobacco smoking.
exposure to second hand smoke in household during childhood
An exposure to second hand smoke that occurred in the (patient's) household when the person was a child.
exposure to second hand smoke in current household
An exposure to second hand smoke in person's current household.
A clinical history in which a female has had a pregnancy.
A measurement datum of the total number of pregnancies a woman has had.
A measurement datum of the total number of live births a female has had.
An age measurement datum performed on a female when her first biological child was born.
A clinical history in which a woman has had gynecologic surgery in the past.
A gynecologic surgery history in which a woman has had a hysterectomy.
A gynecologic surgery history in which a woman has had a unilateral oophorectomy.
neither hysterectomy nor oophorectomy history
A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy.
An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy.
hormonal birth control former use history
A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user.
hormonal birth control current use history
A hormonal birth control use history that indicates an individual is currently a hormonal birth control user.
A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user.
A clinical history in which an individual has had hormonal replacement therapy in the past.
delivery form for hormonal replacement therapy
A processed material used for delivery of hormones in hormone replacement therapy.
pill delivery form for hormonal replacement therapy
A delivery form for hormonal replacement therapy that is a pill for oral administration.
patch delivery form for hormonal replacement therapy
A delivery form for hormonal replacement therapy that is a patch for transdermal administration.
cream delivery form for hormonal replacement therapy
A delivery form for hormonal replacement therapy that is a cream for transdermal administration.
An information content entity that indicates the state of a female's cessation of menstruation.
A menopausal status that is neither pre- nor post-menopausal.
A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement.
A menopausal status indicating that it has been 6-12 months since last menstrual period.
A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy.
exposure to environmental and workplace carcinogens history
An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment.
An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic.
An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos.
An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust.
An exposure to environmental and workplace carcinogens history where the carcinogen is chromium.
An exposure to environmental and workplace carcinogens history where the carcinogen is silica.
indicator of whether an inclusion criterion was met
An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process.
indicator of whether all inclusion criteria were met
An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process.
An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process.
chemotherapy treatment exclusion criterion
An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
chemotherapy treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years.
An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
radiation treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years.
An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0
An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process.
history of metastatic cancer exclusion criterion
An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process.
intravenous drug use exclusion criterion
Donor eligibility based on history of intravenous drug abuse in the last 5 years.
An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of blood borne infection exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of intravenous drugs exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process.
exposure to blood borne infectious disease exclusion criterion
Donor eligibility based on whether the donor has been exposed to HIV/AIDS.
An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process.
An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry.
A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated.
An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei.
A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR.
A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes.
An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques.
A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site.
methidiumpropyl-EDTA-iron(II) footprinting assay
A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA.
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
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.
A study design in which proteins in a sample are detected, quantified or otherwise analysed.
An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library.
An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes.
footprinting assay measuring binding of a B cell epitope:antibody complex
A footprinting assay that detects the binding of an antigen with an antibody.
hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex
A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody.
qualitative binding|hydroxyl-radical footprinting assay
ELISA measuring epitope specific interferon-alpha production by T cells
An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells.
assay measuring epitope specific interferon-alpha production by T cells
A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells.
health status inclusion criterion
‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension'
An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
MIABIS2.0
clinically relevant lifestyle inclusion criterion
'smoking behavior’
An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process.
clinically relevant exposure inclusion criterion
'exposure to cigarette smoke’, ‘exposure to lead through drinking water'
An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process.
gravidity inclusion criterion
'pregnant’, ‘not pregnant'
An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process.
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
chromosome conformation capture-on-chip assay
A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest.
circularized chromosome conformation capture assay
A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples.
inclusion based on age, sex, and living region (rural area or specified city).
An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
defined population inclusion criterion
BCL format
A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell.
Stephen A. Fisher, Junhyong Kim, Dan Berrios
A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids.
SIRV RNA spike-in
A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes.
SRS identifier
An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database.
Stephen Fisher, Dan Berrios
SRA sample accession number
age since culture seeding measurement datum
An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish).
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).
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 algorithm
An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer
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.
date process started
A data item that is the date when a process was initiated.
Chris Stoeckert, Daniel Berrios, Stephen A. Fisher
dbGaP study identifier
A central registered identifier symbol that denotes a specific study in dbGaP.
dbGaP accession number
material amplification role
A worker role played by the person who runs the enzymatic amplifying process.
material sequencing library preparation role
A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced.
number of PCR cycles during library construction
A data item that is the number of PCR cycles used during the construction of a sequencing library.
library construction PCR cycles
number of rounds of amplification
A data item that is the number of times an amplification reaction happened.
reference genome role
A reference substance role that is played by a reference genome when used during sequence alignment.
reference genome-transcriptome alignment algorithm
An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome.
sequence read length measurement datum
A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence.
read length, read length measurement datum
sequencing library input quantity measurement datum
A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer.
Stephen A. Fisher, Junhyong Kim
library input amount
single-end library
A cDNA library that is a collection of short tags from only one end of DNA fragments.
specimen harvest quantity
A scalar measurement datum that indicates the amount of specimen collected.
harvest quantity
spike-in dilution factor
A data item that indicates the dilution of spike-in added to a specimen.
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.
transcript analysis by single-end sequencing assay
A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions.
transcript analysis by single-end sequencing
verse algorithm
An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads.
http://kim.bio.upenn.edu/software/verse.shtml or http://biorxiv.org/content/early/2016/05/14/053306
A material separation device also commerically known as Isoraft, that is used to isolate single cells.
A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser.
An organism detection assay that uses a differential medium to achieve its objective.
EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm
A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material
A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment
case role in case-control study
A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design.
John Judkins, Bjoern Peters
control role in case-control study
A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design.
A specimen that is derived from amniotic fluid.
A specimen that is derived from cerbrospinal fluid.
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
A specimen that is derived from pericardial fluid.
A specimen that is derived from synovial fluid.
A specimen that is derived from vireous humor.
A specimen that is derived from bone marrow.
A specimen that is derived from placenta.
A specimen that is derived from peritoneal fluid.
A specimen that is derived from pleural fluid.
A specimen that is derived from prostate gland.
A specimen that is derived from skeletal muscle.
A specimen that is derived from renal medulla.
A specimen that is derived from adrenal gland.
A specimen that is derived from urinary bladder.
A specimen that is derived from tibial artery.
A specimen that is derived from pancreas.
A specimen that is derived from stomach.
A specimen that is derived from pituitary gland.
A specimen that is derived from adipose tissue.
A specimen that is derived from cortex of kidney.
A specimen that is derived from esophagus mucosa.
A specimen that is derived from esophagus muscularis mucosa.
A specimen that is derived from cerebral cortex.
A specimen that is derived from thyroid gland.
A specimen that is derived from cerebellum.
A specimen that is derived from tibial nerve.
A specimen that is derived from coronary artery.
A specimen that is derived from the atrium auricular region.
A specimen that is derived from the esophagogastric junction.
A specimen that is derived from minor salivary gland.
A specimen that is derived from omentum.
A specimen that is derived from female gonad.
A specimen that is derived from sigmoid colon.
A specimen that is derived from suprapubic skin.
age group inclusion criterion
"18-33 years old"
An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process.
minimum age value specification
A value specifcation that specifies the youngest age when specifying an age range.
maximum age value specification
A value specifcation that specifies the oldest age when specifying an age range.
use of medication inclusion criterion
"received at least 2 days of vancomycin"
An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process.
hospital patient inclusion criterion
"included hospital patients"
An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process.
family status inclusion criterion
"included married and unmarried patients", "included divorced individuals"
An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process.
sex inclusion criterion
"included males and females", "included male patients"
An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
country of residence inclusion criteria
"include US residents"
An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process.
ethnicity inclusion criterion
"include only Hispanic individuals"
An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
A histological assay that is intended to check for the presence or level of a specific disease.
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.
The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables.
The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective.
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 extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified.
Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869
A RNA extraction process in which only RNAs lacking a polyA tail are retained
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 sequence data feature count tabulation.
The results of a DNA methylation profiling assay
The results of a differential expression analysis.
A data transformation in which subsequences of a molecular sequence are cut (removed).
The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device).
digital acquisition and digital generation card
A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task.
A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples.
A machine learning process that infers a function describing the structure of "unlabeled" data (i.e. data that has not been classified or categorized).
molecular interaction identification design
A study design that investigates the features of interaction between molecules.
A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules.
genetic interaction identification design
A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone.
functional association identification design
A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other.
direct interaction identification design
A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another.
enzymatic reaction identification design
A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme.
A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule.
chromosome conformation capture sequencing assay
A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing.
A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR.
A specimen that is stored on a swab as the output of a collecting specimen with swab process.
A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
Sequence data in which an identifier subsequence has been used to categorize each reads by source.
Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source.
A specimen that is collected with a swab from the surface of an areola of a breast.
A specimen that is collected with a swab from the surface of a breast.
A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth.
A specimen that is collected with a swab from the surface of a nasopharynx.
A specimen that is collected with a swab from the inside surface of a mouth.
A specimen that is collected with a swab from the surface of a oropharynx.
A specimen that is collected with a swab from the surface of a rectum.
A specimen that is collected with a swab from the surface of a tongue.
A specimen that is collected with a swab from the surface of a vagina.
A specimen that is collected with a swab from the surface of a feces.
A specimen that is collected with a swab from the surface of an environmenal material.
The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases.
A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up.
A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design.
A study design for which material and information is collected from subjects that have already developed a particular disease.
genealogical record
A family tree is a type of genealogical record.
A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption.
national registry
The Social Security Administration's Death Master File is a national registry in the United States.
An information content entity that contains information about a nationwide group of individuals.
national biomedical registry
The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry.
A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes.
Site-directed mutagenesis was used to prepare mutants of the Hypoxia-inducible factor-1 (HIF-1) alpha subunit to investigate the role of certain amino acids in hypoxia. (PMID:12393189)
An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer.
Error-prone PCR was used to introduce amino acid mutations to the cAMP receptor protein (CRP) of E. coli to investigate strain engineering to improve osmotolerance for industrial requirements. (PMID:22179860)
An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR.
"In an attempt to define the mechanism of insulin-regulated glucose transporter 4 (Glut4) translocation, we have developed an in vitro reconstitution assay... insulin-induced Glut4 translocation can be reconstituted in vitro to a limited extent by using isolated membranes." (PMID:10611313)
An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together.
in vitro transcription reconstitution assay
An in vitro reconstituted mouse transcription system helped identify an NF-Y interacting promoter as essential for high-level expression from the R2 promoter. (PMID:11502214)
A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components.
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.).
A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants.
A genetic transformation which reduces the expression of a specific gene or genes in an organism.
A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease.
Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation.
An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
"Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid Acyrthosiphon pisum. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed Ap-crt genes encoding a calreticulin and the gut specific Ap-cath-L gene encoding a cathepsin-L." (PMID:17903251)
A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts.
An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA.
Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system.
A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.
Single-cell RNA sequencing (scRNA-seq) assays provide the expression profiles of individual cells.
An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin.
The cDNAs were sequenced on the PacBio Sequel platform.
A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation
The cDNAs were sequenced on the PacBio Sequel II platform.
A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation.
in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells
An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells.
disease exacerbation after adoptive transfer|in vivo assay
in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells
An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells.
decreased disease after adoptive transfer|in vivo assay
in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells
An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells.
in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells
An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells.
protection from challenge after adoptive transfer|in vivo assay
in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells
An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells.
in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden
An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden.
pathogen burden after challenge after adoptive transfer|in vivo assay
in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden
An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden.
in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival
An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival.
survival from other challenge after adoptive transfer|in vivo assay
in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival
An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival.
in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden
An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden.
tumor burden after challenge after adoptive transfer|in vivo assay
in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden
An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden.
in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells
An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells.
tolerance after adoptive transfer|in vivo assay
in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells
An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells.
Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs
An assay that uses a Giemsa stain to characterize cells.
A specimen composed of an individual organism to be studied in an investigation.
An organism detection assay that detects microorganisms in a blood specimen.
A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.
Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland.
A biopsy which uses an imaging procedure to guide a needle biopsy.
A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle.
A needle biopsy guided by real-time computed tomography (CT) scan images.
Computed Tomography-Guided Needle Biopsy
An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid.
A needle biopsy guided by ultrasound visualization.
A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin.
A biopsy that uses a hollow needle to extract cells.
A fine needle aspiration biopsy is commonly performed in order to test for cancer.
A biopsy that uses a thin needle to extract cells.
Chris Stoeckert, Helena Ellis, Jie Zheng
A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed.
A biopsy that uses a hollow tube to collect a core of tissue.
Surgical biopsy may be required to collect hard-to-reach tissue.
A biopsy involving a surgical incision into an organism to access the biopsy material.
The makeup of fat in the abdominal wall can be investigated by fat biopsy.
A biopsy involving the collection of a small part of the abdominal wall fat pad.
A mouse tail biopsy was performed to collect material for DNA extraction.
A biopsy involving the collection of the tip of a mamallian tail.
A bone marrow biopsy removes bone with the marrow inside to look at under a microscope
A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected.
A three or four millimeter punch is used in s skinpunch biopsy proceedure.
A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool.
cytometric bead array assay measuring epitope specific interleukin-15 production by T cells
A cytometric bead array assay that detects interleukin-15 production by T cells.
cytometric bead array assay measuring epitope specific interleukin-16 production by T cells
A cytometric bead array assay that detects interleukin-16 production by T cells.
in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells
An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells.
hypersensitivity after adoptive transfer|in vivo assay
in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells
An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells.
type IV hypersensitivity (DTH) after adoptive transfer|in vivo skin test
in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells
A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells.
proliferation after adoptive transfer|in vivo assay
assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells
A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells.
antibody help after adoptive transfer|in vivo assay
assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells
A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells.
T cell help after adoptive transfer|in vivo assay
in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells
An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells.
cytotoxicity after adoptive transfer|in vivo assay
ELISA measuring epitope specific perforin release by T cells
An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells.
Selenite broth is an enrichment culture medium used to selectively isolate Salmonella species.
A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest.
A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included.
An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.
in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells
An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells.
in vivo response after adoptive transfer|in vivo assay
in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells
An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells.
in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells
An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells.
Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source.
A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material.
“Inhibition of MERS-CoV-spike-mediated pseudovirus entry by the HKU4 S1 domain “ (from https://doi.org/10.1073/pnas.1405889111); “protease treatment did not enhance pseudotype entry in the absence of host receptor “; “bat-derived cell lines derived from other species were infected with VSV-reporter particles pseudotyped with chimeric spikes and luciferase was measured as readout for cell entry” (from https://doi.org/10.1038/s41564-020-0688-y) ; “teicoplanin could inhibit the entry of HIV-1-2019-nCoV-S pseudoviruses with the IC50 value of 1.66 uM” (from https://doi.org/10.1101/2020.02.05.935387)
An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest.
Figure 1c in https://doi.org/10.1038/s41564-020-0688-y or Materials & Method in https://www.pnas.org/content/111/34/12516
A container with a narrow neck that is made of glass.
A glass bottle that coated with material designed to control insects.
short interspersed nuclear elements polymerase chain reaction
A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs).
A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction.
An electrophoresis that separates and characterize proteins based on reaction with antibodies.
An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions.
A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product.
An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR.
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 specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito.
A specimen of the blood ingested by an arthropod.
The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human.
An assay that uses polymerase chain reaction technique to amplify DNA.
restriction fragment length polymorphism assay
An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences.
restriction fragment length polymorphism
restriction fragment length polymorphism analysis
An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA.
An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population.
insecticide resistance by monitoring known mutations assay
An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes.
insecticide resistance by detecting enzyme activity assay
An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes.
An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism.
insecticide resistance by detecting alpha esterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase.
insecticide resistance by detecting beta esterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase.
insecticide resistance by detecting acetylcholinesterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase.
insecticide resistance by detecting glutathione S-transferase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST).
insecticide resistance by detecting carboxylic ester hydrolase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate.
insecticide resistance by detecting mixed-function oxidase assay
An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present.
An insecticide resistance bioassay without the use of any synergist.
topical application insecticide resistance bioassay
An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect.
direct insecticide resistance diagnostic assay
A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population.
insecticide resistance dose response assay
A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance.
insecticide resistance time response assay
A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide.
Centre for Disease Control and Prevention bottle bioassay
A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations.
A direct insecticide resistance diagnostic assay uses WHO cone kit.
A direct insecticide resistance diagnostic assay uses WHO paper kit.
A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide.
insecticide resistance dose response by bottle assay
An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides.
insecticide resistance dose response by survival of larvae assay
An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide.
insecticide resistance dose response by WHO paper kit assay
An insecticide resistance dose response assay using WHO paper kit.
insecticide resistance time response by bottle assay
An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist.
insecticide resistance time response by WHO paper kit assay
An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist.
insecticide resistance by amplification refractory mutation system assay
An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations.
Amplification Refractory Mutation System
insecticide resistance by primer introduced restriction analysis PCR assay
An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes.
Primer Introduced Restriction Analysis PCR
polymerase chain reaction-primer-introduced restriction analysis
insecticide resistance by nested polymerase chain reaction assay
An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique.
insecticide resistance by ligase detection reaction assay
An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix.
insecticide resistance by ligase detection reaction-fluorescent microsphere assay
An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction.
ligase detection reaction-fluorescent microsphere assay
insecticide resistance by PCR amplification of specific alleles assay
An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles.
allele-specific amplification and amplification refractory mutation system
insecticide resistance by fluorogenic PCR assay
An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation.
insecticide resistance by PCR-RFLP assay
An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay.
insecticide resistance by short interspersed elements PCR assay
An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs).
An organism detection assay that detects pathogens.
A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip.
pathogen detection by Rapid Analyte Measurement Platform assay
A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances.
pathogen detection by loop-mediated isothermal amplification assay
A pathogen detection assay that is based on loop-mediated isothermal amplification.
An assay that analyzes the specimen taken from blood meal fed organism, such as insect.
blood meal by counter current immunoelectrophoresis assay
A blood meal assay that uses a counter current immunoelectrophoresis technique.
DNA based blood meal finger printing assay
A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect.
An organism detection assay that is based on the size of organism.
organism detection by cross mating assay
An organism detection assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced.
organism detection by cytological chromosome examination assay
An organism detection assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species.
organism detection by isoenzyme electrophoresis assay
An organism detection assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species.
organism detection by morphological examination assay
An organism detection assay that is based on examination of morphology and the use of specific taxonomic keys to determine the species of the specimen.
An organism detection assay that is based on PCR.
organism detection by specific DNA hybridization assay
An organism detection assay that is based on DNA hybrdization.
organism detection by salinity tolerance assay
An organism detection assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species.
molecular label role
A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743.
molecular tracer role
molecular label
A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744.
molecular tracer
A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue.
A biopsy performed with a needle augmented with a vacuum device.
A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
passage process
A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number.
passage history record
A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process.
John Judkins
Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION
A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.
Nineteen libraries were constructed and sequenced on nineteen different R9.4 FlowCells using the GridION X5 sequencer
A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually.
Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome.
A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.
Precision nuclear run-on and sequencing to detect Pol II initiation sites
cDNA library lacks the non-coding and regulatory elements found in genomic DNA
A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription.
Dan Berrios
modified from Wikipedia
ordinal value specification
A categorical value specification in which the available categories were created with an explicit order.
https://en.wikipedia.org/wiki/Ordinal_data provides references for follow-up, but more than one OBI developer has objected to "...whose levels have natural, ordered categories and the distances between those categories is not known..." Separate from that, an OBI mechanism for asserting the order of ordinal values specification levels with OWL has not been determined yet.
Mark Andrew Miller, ORCID:0000-0001-9076-6066
Bjoern Peters in https://github.com/obi-ontology/obi/issues/862
ribosomal RNA-depleted RNA sequencing assay
An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection.
An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome.
An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism.
snATAC-seq can be used to dissect heterogeneity and delineate gene regulatory sequences in complex tissues, and uncover both the cell types and the regulatory elements in each cell type without prior knowledge.
An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei.
An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.
An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles.
microbiome protein expression profiling assay
A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome.
An analyte assay to study presence, concentration, or amount of cytokines.
A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.
A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.
karyotype information
A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell.
EFO_0004426 karyotype
VEuPathDB
partial karyotype information
A karyotype information that is about the structural variation of partial genome rather than whole genome.
full karyotype information
A karyotype information that is about the structural variation of the whole genome.
presence or over-threshold value specification
An ordinal value specification that indicates that either a) an analyte or mesaurand is present in an evaluant, or b) that the amount of analyte/measurand detected is over some predetermined threshold.
LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 32
single-value binding of antibody with reporter to antigen assay
Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2.
An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest
LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA)
LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47
platelet-poor plasma specimen
A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter.
PERSON: Matthew Diller
platelet-poor plasma preparation process
A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm.
A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest.
A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest.
A specimen that is collected with a suctioning tube from the trachea.
A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity.
A specimen that is collected with a suctioning tube from the nasal cavity.
nasal wash specimen|nasopharyngeal aspirate
lower respiratory tract aspirate specimen
A specimen that is collected with a suctioning tube from the lower respiratory tract.
A specimen that is derived from the upper respiratory tract
A specimen that is derived from the lower respiratory tract.
A specimen that is derived from the anterior nasal wall
aspiration specimen collection
Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue.
Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection.
PPE is equipment worn by a worker to minimize exposure to specific hazards.
A device which is a wearable garment designed to protect the wearer's body from injury or infection.
A systematic review on the efficacy of face coverings against respiratory viruses analyzed 19 randomized trials and concluded that use of face masks and respirators appeared to be protective in both health care and community settings
A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles.
Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask
A non-medical mask may contain fabrics that are not regulated for use in surgical masks or respirators, or may not be designed to form a seal around the nose and mouth.
A face mask not manufactured according to medical equipment standards.
The finding of a much higher rate of infection in the cloth mask arm could be interpreted as harm caused by cloth masks, efficacy of medical masks, or most likely a combination of both.
A face mask manufactured according to a recognized medical equipment standard.
A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles.
A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials.
A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff.
Examples consist of a short-sleeve V-necked shirt and drawstring pants or a short-sleeve calf-length dress, a tie-back or bouffant-style cap, a mask, a surgical gown, latex gloves, and supportive closed-toe shoes.
A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap.
A patient gown intended to be reused after being laundered.
A patient gown intended for a single period of continuous use and then disposed of.
A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional.
A garment which is worn over other clothing and covers mainly the front of the body.
A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures.
A personal protective device which is a glove.
A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing.
A personal protective clothing item which is an overcoat worn by medical or laboratory professionals.
A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients.
A personal protective glove which is made out of nitrile rubber.
A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements.
A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants.
A footwear cover which is designed for a single period of continuous use and then disposed of.
A footwear cover which is designed for repeated use.
A N95 respirator which has been approved by the FDA as a surgical mask.
A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination.
A protective sleeve can be designed to provide protection from heat, welding spatter or hot metal, chemicals, sharp objects, paint or other liquids.
A personal protective clothing item which is a protective cover worn over the arm.
A personal protective clothing item which is an apron.
A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp.
A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography.
An absorbent pad and its accompanying container are designed to provide safe storage and transport to various degrees for diagnostic and clinical samples, infectious and hazardous materials, chemicals, pharmaceuticals and environmental samples.
A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter.
A swab stick allows a worker to collect samples without touching the inside of the bag
A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material.
A device which is a cotton pad mounted on one or both ends of a stick.
A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string
A specimen collection swab stick that is pre-moistened with liquid prior to sampling.
Surface sampling procedures involved the use of polyester wipes, swabs, contact slides (two types), and adhesive tapes; a gelatin filter was used to sample the air.
A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces.
A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter.
A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body.
An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity.
A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound.
A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
A compound study group consisting of geographically proximate households that share a common water source.
A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system.
A light source that provides visible light for use in a distant area using a delivery system.
A light source that light is produced from solar energy.
adult arthropod specimen collection process
A live arthropod specimen collection process in which the arthropods are in the adult stage.
animal-biting arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal.
animal-biting outdoor arthropod specimen collection by aspiration
An animal-biting arthropod specimen collection by aspiration that occurs outside a building.
aquatic arthropod specimen collection process
An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment.
arthropod resting in animal house specimen collection by aspiration
An arthropod specimen collection by aspiration that catches specimens resting inside an animal house.
arthropod resting outdoors on artificial support specimen collection by aspiration
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture.
arthropod resting outdoors on natural support specimen collection by aspiration
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant.
arthropod resting outdoors specimen collection by aspiration
An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity.
arthropod specimen collection by aspiration
A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container.
A specimen collection process that has the objective of collecting arthropods as specimens.
human-biting arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human.
human-biting indoor arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building.
human-biting outdoor arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building.
knockdown arthropod specimen collection by pyrethrum spray
A knockdown arthropod specimen collection process in which the pesticide is pyrethrum.
knockdown arthropod specimen collection process
An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized.
live arthropod specimen collection process
An arthropod specimen collection process meant to collect live specimens.
An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected.
An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal.
An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container.
A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods.
An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current.
Centers for Disease Control and Prevention light trap
A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery.
This trap is also designed to be lightweight and operate in environments in which electricity may be scarce.
A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan.
A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods.
An arthropod trap that is designed to collect gravid female arthropods or their eggs.
An arthropod trap that uses light as an attractant.
A light trap designed to be placed inside a building.
A light trap designed to be placed outside a building.
An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods.
A gravid trap consisting of an arthropod attractant and adhesive surface.
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant.
Onderstepoort Veterinary Institute light-suction trap
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter.
An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building.
An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females.
An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity.
An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity.
An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host).
An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap.
An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected.
An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive.
A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design
fluorescence imaging-based apoptosis assay
A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis.
fluorescence imaging-based cell proliferation assay
A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells.
fluroescence imaging-based cell count assay
fluroescence imaging-based cell cycle state assay
A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states.
fluorescence imaging-based cell viability assay
A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability.
fluorescence imaging-based drug synergy assay
A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects.
fluorescence imaging-based cell morphology assay
A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology.
fluorescence imaging multiplex cytological profiling
A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters.
A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc.
fluorescence imaging-based protein phosphorylation state assay
A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states.
mass spectrometry-based protein state assay
A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states.
targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay
A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations.
P100 phosphoprotein quantification assay
reverse phase protein array profiling assay
A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications.
reverse phase lysate array profiling assay
A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides.
sequential window acquisition of all theoretical mass spectra protein profiling assay
A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins.
fluorescence imaging-based reporter gene assay
A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression.
global chromatin profiling by mass spectrometry assay
A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin.
A type of assay that identifies compounds that inhibit the activity of kinases.
A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions.
A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP.
A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence.
A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity.
microwestern meso-scale quantitative western blot assay
A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose.
positive/negative ion switching metabolite profiling assay
A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples.
positive/negative ion switching metabolomic assay
A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation.
multiplex bead-based protein state immunoassay
A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states.
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea.
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube.
When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being analyzed is the input protein sequence start site.
The position of the first amino acid in a protein sequence being analyzed (input protein sequence).
When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence being analyzed is the input protein sequence stop site.
The position of the last amino acid in a protein sequence being analyzed (input protein sequence).
When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site.
The position of the first nucleotide in a gene sequence being analyzed (input gene sequence).
When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence being analyzed is the input gene sequence stop site.
The position of the last nucelotide in a gene sequence being analyzed (input gene sequence).
When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being used for comparison is the reference protein sequence start site.
The position of the first amino acid in a reference protein sequence (sequence being used for comparison).
When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence used for comparison is the reference protein sequence stop site.
The position of the last amino acid in a reference protein sequence (sequence being used for comparison).
When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence used for comparison is the reference gene sequence start site.
The position of the first nucleotide in a reference gene sequence (sequence being used for comparison).
When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence used for comparison is the reference gene sequence stop site.
The position of the last nucelotide in a reference sequence (sequence being used for comparison).
A length measurement datum between a point at sea or ground level and some point above it.
Adapted from https://www.merriam-webster.com/dictionary/altitude
PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA.
A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest.
An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity.
Alexander D. Bartnik, ORCID:0000-0001-9676-7377
An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity.
positron emission tomography imaging assay
An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity.
Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration.
A time measurement datum that is the count of collection cycles over which a specimen collection process occurs.
A person or organization that provides material supplies to other people or organizations.
T cell receptor repertoire sequencing assay
A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample.
B cell receptor repertoire sequencing assay
A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample.
prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR
A data item that is the frequency of detection of a specified pathogenic organism in collected specimens.
prevalence of blood meal specimens from a host organism
prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal.
A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens.
presence of blood from host organism in blood meal specimen
presence of blood meal host organism indicated by boolean values of yes or no.
A data item that indicates whether blood in a blood meal specimen came from a specified host organism.
An organism that is the source of a blood meal.
A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal.
A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism.
Will deprecate this term in VEuPathDB ontology once in OBI.
A role of a material entity realized in drawing an arthropod in the direction of the material.
arthropod collection process with automated identification
An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected.
gravid female arthropod specimen collection process
An arthropod specimen collection process that has the objective of collecting gravid female arthropods.
resting flight-capable arthropod specimen collection process
An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity.
daytime arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs in the daytime.
arthropod resting in human house specimen collection by aspiration
An arthropod specimen collection by aspiration that catches specimens resting inside a human house.
landing arthropod specimen collection process
An arthropod specimen collection process that occurs while the arthropods land on a surface.
flying adult arthropod collection process by passive interception
An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap.
device for collection of resting adult arthropods
A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity.
A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net.
arthropod trap containing small non-human animal bait
An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller.
trap containing small non-human animal bait
An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage.
American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389
An analyte assay that measures the abundance of iron
An analyte assay that measures the abundance of ionized calcium
An analyte assay that measures the abundance of transferrin
An analyte assay that measures the abundance of uric acid
An analyte assay that measures the abundance of globulin
A cytometry assay that measures the abundance and/or characteristics of myelocytes
A cytometry assay that measures the abundance and/or characteristics of metamyelocytes
A cytometry assay that measures the proportion of red blood cells
A cytometry assay that measures the abundance and/or characteristics of promyelocytes
A cytometry assay that measures the abundance and/or characteristics of basophils
A cytometry assay that measures the abundance and/or characteristics of neutrophils
A cytometry assay that measures the abundance and/or characteristics of eosinophils
A cytometry assay that measures the abundance and/or characteristics of lymphocytes
A cytometry assay that measures the abundance and/or characteristics of monocytes
A cytometry assay that measures the abundance and/or characteristics of reticulocytes
A cytometry assay that measures the abundance and/or characteristics of macrophages
A cytometry assay that measures the abundance and/or characteristics of platelets
An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR.
Chris Stoeckert https://orcid.org/0000-0002-5714-991X
A processed material that consists of oligonucleotides that bear a primer role.
A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores.
genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci.
A genotyping assay that uses polymerase chain reaction.
Chris Stoeckert, ORCID:0000-0002-5714-991X
cleavage under targets and release using nuclease assay
A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing.
A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing.
Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale.
A physical examination of an organism that has the objective to determine the severity of coma in a patient.
An assay that detects Plasmodium gametocytes in a specimen.
An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood.
An assay that detects parasite in a specimen.
An organism detection assay that detects microorganisms in a feces specimen.
An assay that has a blood specimen as evaulant.
A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood.
A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites.
An assay that has a urine specimen as evaluant.
parasite species identification by PCR assay
A parasite detection by PCR assay that identifies the species of parasite.
A parasite detection assay that uses PCR.
Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658]
An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die.
A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin.
A device that consists of a network of mesh and is designed to capture adult arthropods.
Centers for Disease Control and Prevention gravid trap
The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658]
A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan.
An arthropod specimen collection process in which the arthropods are in the embryo stage.
An arthropod specimen collection process in which the arthropods are in the larval stage.
An arthropod specimen collection process in which the arthropods are in the pupal stage.
A blood specimen that is located in a vacutainer.
A blood specimen that is located on a filter paper.
A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads.
Administering substance in vivo where an antibiotic substance is administered to a living organism.
A data item that is about resistance to an insecticide.
A data item that is the specified output of an organism detection assay.
A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection.
Easting and northing coordinates are commonly measured in meters from a horizontal datum.
A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection.
Organization that undertakes a clinical study at some point in time.
A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial.
A protocol that specifies processes to fulfill a specimen collection objective.
A symbol that denotes a participant under investigation.
A temperature measurement datum that is about an axilla.
organismal body temperature measurement datum
A temperature measurement datum that is about an organism.
A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized.
An age since birth measurement datum at the time of subject enrollment.
An age since birth measurement datum at the time of a clinical visit.
A data item that is about a collection of insects.
A scalar measurement datum that is the result of measuring temperature.
organismal body temperature measurement assay
An assay that detects body temperature of an organism.
A time measurement datum that specifies when some material was extracted from an input material.
Chris Stoeckert, ORCID: 0000-0002-5714-991X
A time measurement datum that is the result of measuring the duration of an extraction process.
specimen collection time post disease onset
A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host.
A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts.
A postal address used as a directive to deliver something to a laboratory.
Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033)
A population where the collection of individuals is located and maintained in a laboratory, research, or production facility.
A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength.
An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength.
bulk assay for transposase-accessible chromatin using sequencing
An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells.
An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells.
multiplexed fluorescent antibody imaging assay
An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells.
A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section.
A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels.
fluorescence in-situ hybridization assay
An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences.
decoding amplified targeted transcripts with fluorescence in situ hybridization assay
A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types.
A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry.
liquid chromatography mass spectrometry assay
A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance.
lightsheet fluorescence microscopy assay
A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera.
matrix assisted laser desorption ionization imaging mass spectrometry assay
A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses.
A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry.
nanospray desorption electrospray ionization assay
A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray.
nanodroplet processing in one pot for trace samples assay
A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression.
A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components.
single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing
An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation.
single-cell combinatorial indexing RNA sequencing assay
A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation.
sequential fluorescence in-situ hybridization assay
A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved.
An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing.
single-nucleus chromatin accessibility and mRNA expression sequencing assay
A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs.
A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing.
gas chromatography mass spectrometry assay
A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds.
An analyte assay that uses aptamers to detect protein analytes in serum.
Rohloff JC, et al. Nucleic acid ligands with protein-like side chains: modified aptamers and their uses as diagnostic and therapeutic agents. Mol Ther Nucleic Acids. 2014;3:e201.
A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR.
An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex.
Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526
A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run.
antigen detection by cytometric bead array assay
A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest.
antibody detection by cytometric bead array assay
A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest.
3D molecular structure determination assay
An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex.
electron-microscopy 3D molecular structure determination assay
A 3D molecular structure determination assay that uses electron microscopy imaging.
A complex of molecular entitites which is the result of an antibody binding to an antigen.
A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex.
A complex of molecular entities which is the result of a MHC molecule binding with a ligand.
A 3D structure determination assay that determines the 3-dimensional configuration of a cell.
3D neural cell structure determination assay
A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell.
A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron.
mosaicism with repeat frameshift genetic sparse labeling
A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons.
A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST).
The representation of the morphology (3D structure) of a neuron can be a summary of various measurements relating to the dimensions of the neuron in question.
An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope.
An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope.
129/Sv male mice were injected with ENU and mated to C57BL/6 females. Their first-generation (G1) male progeny were again crossed to C57BL/6 females, and then backcrossed to one of their second-generation (G2) daughters to yield a third-generation (G3). PMID:18802465
A form of random mutagenesis that produces a mutation by introducing the organism to a chemical mutagen.
Equivalent to FlyBase "chemical" (FBcv:0000525) in the origin of mutation branch and Dd mutagenesis meth0d term chemical mutagenesis (DDMUMET:0000014).
Susan Bello ORCID:orcid.org/0000-0003-4606-0597
Groups of (101 x C3H)F1 hybrid male mice 11 weeks old were exposed to two different doses of 137Cs gamma rays. PMID:7035547
A form of random mutagenesis that produces a random mutation by exposing the organism to radiation.
Equivalent to FlyBase "irradiation" (FBcv:0000503) in the origin of mutation branch.
Exons 20 and 21 were targeted for deletion because they encode the signature and Walker B motifs of the first ATP-binding domain, elements that are known to be critical for ABCA1 function. PMID:15550377
An induced mutation in which a specific gene(s) or part of a gene(s) is altered.
We have generated a WMS mouse model with S236X mutation in ADAMTS10 which is similar to the R237X mutation identifiedin WMS patients using CRISPR-Cas9. PMID:30060141
A directed mutagenesis in which guide RNAs and an endonuclease (cas9, TALEN) are used to introduce a mutation at a specific location in a gene.
Equivalent to FlyBase term "site specific cleavage" (FBcv:0003007) in the origin of mutation branch.
Briefly, to create Adar1 M249A/M249A mice, guide RNA targeting 5’-ACCTTCTGAGCCTCTTGACA-3’ was synthesized by using Gene Art Precisiong RNA Synthesis Kit (ThermoFisherScientific). Pronuclear-stage mouse embryos (CLEA Japan Inc., Tokyo, Japan) were electroporated to introduce Cas9 mRNA, the guide RNA and a single-stranded donor... PMID:33983932
An endonuclease mediated mutagenesis in which guide RNAs and cas are used to introduce a mutation at a specific location in the genome.
Equivalent (narrow match) to FlyBase term "CRISPR/Cas9" (FBcv:0003008, narrow match as the OBI term covers all forms of cas) in the origin of mutation branch and Dd mutagenesis method term "CRISPR/Cas9" (DDMUMET:0000025).
We designed transcription activator-like effector nucleases (TALENs) and a single-stranded oligo (ssOligo) donor template to edit the endogenous Actb locus within the mouse genome. PMID:30012594
An endonuclease mediated mutagenesis in which guide RNAs and transcription activator-like effector nucleases (TALENs) are used to introduce a mutation at a specific location in the genome.
Equivalent to FlyBase term "TALEN" (FBcv:0003009) in the origin of mutation branch.
ZFN constructs targeting the third exon of the mouse Apoc2 gene were designed and synthetized by Sigma Aldrich... PMID:26574515
An endonuclease mediated mutagenesis in which synthetic zinc-finger proteins designed to target specific DNA sequences are used to introduce a mutation at a specific location in the genome.
Equivalent to FlyBase term "ZFN" (FBcv:0003239) in the origin of mutation branch.
Transgenic mice were then generated by pronuclear injection of either the mixed MoPrP-PS1 and MoPrP-APP or the bicistronic MoPrP–APP/IRES/PS1 expression cassettes into single cell embryos derived from F2 hybrids of C57BL/6J and C3H/HeJ mice... PMID:11337275
A form of random mutagenesis that produces a mutation by introducing a construct into the genome of an organism in a random or semi-random fashion.
Constructs lacking a promoter and including a B3-galactosidase gene, or a reporter gene encoding a protein with both B3-galactosidase and neomycin phosphotransferase activity, were designed so that activation of the reporter gene depends on its insertion within an active transcription unit. PMID:1653172
A transgenic mutagenesis that produces a mutation by introducing a construct designed to capture the expression of an endogenous gene by creating a spliced fusion transcript when inserted into the genome of an organism.
We generated several lines of enhancer trap mice carrying an enhancer detector cassette expressing Cre recombinase under the transcriptional control of the minimal promoter (129 base pairs) of the mouse Thy-1.2 gene. PMID:22492032
A transgenic mutagenesis that produces a mutation by introducing a construct designed to monitor transcriptionally active regions when inserted into the genome of an organism by inserting a reporter gene that requires cis-acting DNA sequences in the genome to activate reporter gene expression.
To disrupt the mdr1a gene a 1.6 kb NheI genomic fragment containing exons 6 and 7 was replaced by a hygromycin phosphotransferase cassette in a targeting vector. PMID:7910522
A directed mutation in which a construct is used to introduce a mutation into a specific genome location through homologous recombination.
Equivalent to FlyBase term "gene targeting by homologous recombination" (FBcv:0000710) in the origin of mutation branch.
gene targeting by homologous recombination
In order to achieve SB transposon-mediated mutagenesis in mice, we employed the gene trap scheme using a novel transposon vector, and we have generated a large number of mutant mice, approximately 30% of which displayed the phenotype. PMID:16880528
A random mutagenesis in which expression of a transposase causes the mobilization of an artificial or modified transposable element with the insertion of the element into the genome creating a mutation.
Equivalent to FlyBase "transposable element activity" (FBcv:0000483) in the origin of mutation branch.
A binding datum that is expressed as a categorical value.
A binding datum that is expressed using numbers.
A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50).
A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50).
assay measuring quantitative binding of a MHC:ligand complex
An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output.
assay measuring quantitative binding of an antigen:antibody complex
An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output.
assay measuring quantitative binding of an epitope:MHC:TCR complex
An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output.
An albumin assay that measures the concentration of albumin in a specimen.
A basophil assay that measures the percentage of basophils in a specimen.
A calcium cation assay that measures the concentration of calcium cations in a specimen.
A chloride assay that measures the concentration of chloride in a specimen.
A cholesterol assay that measures the concentration of cholesterol in a specimen.
A creatinine assay that measures the concentration of creatinine in a specimen.
An eosinophil assay that measures the percentage of eosinophils in a specimen.
A globulin assay that measures the concentration of globulin in a specimen.
A hemoglobin assay that measures the amount of hemoglobin in a specimen.
high-density lipoprotein cholesterol concentration assay
A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen.
An iron assay that measures the concentration of iron cation in a specimen.
low-density lipoprotein cholesterol concentration assay
A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen.
A lymphocyte assay that measures the percentage of lymphocytes in a specimen.
A metamyelocyte assay that measures the number of metamyelocytes in a specimen.
A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen.
A methemoglobin assay that measures the percentage of methemoglobin in a specimen.
A monocyte assay that measures the percentage of monocytes in a specimen.
A myelocyte assay that measures the number of myelocytes in a specimen.
A neutrophil assay that measures the percentage of neutrophils in a specimen.
A phosphate ion assay that measures the concentration of phosphate ions in a specimen.
A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen.
A reticulocyte assay that measures the percentage of reticulocytes in a specimen.
A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen.
thyroid stimulating hormone concentration assay
A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen.
A triglyceride assay that measures the concentration of triglycerides in a specimen.
3,3',5'-triiodothyronine concentration assay
A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen.
A fibrinogen assay that measures the concentration of fibrinogen in a specimen.
A thyroxine assay that measures the concentration of free thyroxine in a specimen.
A thyroxine assay that measures the concentration of total thyroxine in a specimen.
A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen.
A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen.
A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen.
A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes.
mean cell hemoglobin concentration assay
A hemoglobin assay that measures the concentration of hemoglobin in a specimen.
A platelet assay that measures the average volume of platelets in a specimen.
A neutrophil assay that measures the number of immature neutrophils in a specimen.
An neutrophil assay that measures the percentage of immature neutrophils in a specimen.
An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen.
An erythrocyte assay that measures the average volume of erythrocytes in a specimen.
A cytometry assay that measures the abundance and/or characteristics of erythrocytes.
A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes.
An analyte assay that measures the abundance of adiponectin
An adiponectin assay that measures the concentration of adiponectin in a specimen.
An analyte assay that measures the abundance of creatine
A creatine assay that measures the concentration of creatine in a specimen.
An analyte assay that measures the abundance of estradiol
An estradiol assay that measures the concentration of estradiol in a specimen.
An analyte assay that measures the abundance of leptin
An leptin assay that measures the concentration of leptin in a specimen.
An analyte assay that measures the abundance of lipoprotein
high-density lipoprotein concentration assay
A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen.
low-density lipoprotein concentration assay
A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen.
very-low-density lipoprotein concentration assay
A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen.
An analyte assay that measures the abundance of luteinizing hormone
A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen.
An analyte assay that measures the abundance of nitrite
A nitrite assay that measures the concentration of nitrite in a specimen.
An analyte assay that measures the abundance of phospholipid
A phospholipid assay that measures the concentration of phospholipids in a specimen.
An analyte assay that measures the abundance of progesterone
A progesterone assay that measures the concentration of progesterone in a specimen.
An analyte assay that measures the abundance of testosterone
A testosterone assay that measures the concentration of testosterone in a specimen.
An analyte assay that measures the abundance of bile salt
A bile salt assay that measures the concentration of bile salt in a specimen.
An analyte assay that measures the abundance of fatty acid
A fatty acid assay that measures the concentration of free fatty acids in a specimen.
An analyte assay that measures the abundance of insulin
A insulin assay that measures the concentration of insulin in a specimen.
An analyte assay that measures the abundance of follicle stimulating hormone
follicle stimulating hormone concentration assay
A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen.
A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen.
A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen.
A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies.
A proteomics profiling assay that detects proteins in a blood plasma specimen.
A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers.
A blood harvesting process in which white blood cells are separated from a blood specimen.
An assay that has a cerebrospinal fluid specimen as evaluant.
An assay that has an endotracheal aspirate specimen as evaluant.
An assay that has an induced sputum specimen as evaluant.
An assay that has a lung specimen as evaluant.
An assay that has a milk specimen as evaluant.
An assay that has a feces specimen as evaluant.
An assay that has an umbilical cord blood specimen as evaluant.
An assay that has a saliva specimen as evaluant.
An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen.
endotracheal tube aspirate microbiology assay
An organism detection assay that detects microorganisms in an endotracheal aspirate specimen.
An organism detection assay that detects microorganisms in an induced sputum specimen.
A data item that is the specified output of a blood assay.
An organism detection datum that is the specified output of a blood microbiology assay.
A data item that is the specified output of a feces assay.
An organism detection datum that is the specified output of a feces microbiology assay.
A data item that is the specified output of a urine assay.
An organism detection datum that is the specified output of a urine microbiology assay.
A data item that is the specified output of a induced sputum assay.
biomedical laboratory organization
An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences.
Christian Stoeckert ORCID:0000-0002-5714-991X
An organism detection datum that is the specified output of an induced sputum microbiology assay.
A data item that is the specified output of a cerebrospinal fluid assay.
An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay.
An organism detection datum that is the specified output of an endotracheal aspirate assay.
endotracheal tube aspirate microbiology datum
An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay.
An organism detection datum that is the specified output of a lung microbiology assay.
nasopharyngeal or oropharyngeal swab microbiology datum
An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay.
An organism detection datum that is the specified output of a pleural fluid microbiology assay.
A data item that is the specified output of an umbilical cord blood assay.
An organism detection datum that is the specified output of an umbilical cord blood microbiology assay.
A blood microbiology datum that is about bacteria.
A blood microbiology datum that is about a virus.
A blood microbiology datum that is about eukaryota.
A feces microbiology datum that is about bacteria.
A feces microbiology datum that is about eukaryota.
A feces microbiology datum that is about a virus.
A urine microbiology datum that is about eukaryota.
An induced sputum microbiology datum that is about bacteria.
An induced sputum microbiology datum that is about eukaryota.
An induced sputum microbiology datum that is about a virus.
bacteria in endotracheal tube aspirate datum
An endotracheal tube aspirate microbiology datum that is about bacteria.
A lung microbiology datum that is about bacteria.
A lung microbiology datum that is about eukaryota.
A lung microbiology datum that is about a virus.
bacteria in nasopharyngeal or oropharyngeal swab datum
A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria.
eukaryota in nasopharyngeal or oropharyngeal swab datum
A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota.
virus in nasopharyngeal or oropharyngeal swab datum
A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus.
A pleural fluid microbiology datum that is about bacteria.
A pleural fluid microbiology datum that is about eukaryota.
A pleural fluid microbiology datum that is about a virus.
An umbilical cord blood microbiology datum that is about eukaryota.
An organism detection assay that detects microorganisms in a lung specimen.
An organism detection assay that detects microorganisms in a pleural fluid specimen.
An organism detection assay that detects microorganisms in an umbilical cord blood specimen.
nasopharyngeal or oropharyngeal swab microbiology assay
An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen.
An organism detection assay that detects microorganisms in a urine specimen.
multiplex real time polymerase chain reaction assay
A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle.
multiplexed real time polymerase chain reaction assay
multiplex real time reverse-transcription polymerase chain reaction assay
A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle.
multiplexed real time reverse-transcription polymerase chain reaction assay
A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host.
Testing the effectiveness of drugs or antibodies against parasite transmission.
An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them.
A study design that is executed primarily on a computer.
cytometric bead array assay measuring epitope specific granulysin release by T cells
A cytometric bead array assay that detects epitope specific granulysin release by T cells.
granulysin release|cytometric bead array
cytometric bead array assay measuring epitope specific perforin release by T cells
A cytometric bead array assay that detects epitope specific perforin release by T cells.
modified acid-fast stain microscopy assay
A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating.
A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex.
antibodies from lymphocyte secretions assay
PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes.
An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells.
antibodies from lymphocyte supernatant assay
tyramide signal amplification sequencing assay
A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm.
DNA adenine methyltransferase identification assay
An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed.
A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site.
nucleolus-associated domain sequencing assay
A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains.
A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts.
A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step.
single cell combinatorial indexing Hi-C assay
A Hi-C assay performed on massively multiplexed single-cell samples.
A Hi-C assay performed on isolated nuclei.
A Hi-C assay performed on a single cell.
A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells.
A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer.
transposase-mediated analysis of chromatin looping assay
A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions.
split-pool recognition of interactions and tag extension assay
A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed.
DNA split-pool recognition of interactions and tag extension assay
A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA.
RNA-DNA split-pool recognition of interactions and tag extension assay
A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions.
A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions.
A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed.
assay measuring epitope specific amphiregulin production by T cells
A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells.
amphiregulin release|biological activity
ELISA measuring epitope specific amphiregulin production by T cells
An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells.
perforin release during T cell degranulation
The release of perforin during cytotoxic T cell degranulation.
granzyme A release during T cell degranulation
The release of granzyme A during cytotoxic T cell degranulation.
granzyme B release during T cell degranulation
The release of granzyme B during cytotoxic T cell degranulation.
granulysin release during T cell degranulation
The release of granulysin during cytotoxic T cell degranulation.
A blood microbiology assay that detects a microorganism in a venous blood specimen.
high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex
Next-generation high-density peptide microarrays measuring antibody responses to overlapping peptides: PMID:25922409.
A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay.
antibody binding|High throughput multiplexed assay
high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex
Adaptive Biotech multiplexed TCR sequencing assays: PMID:32793919.
A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay.
T cell binding|High throughput multiplexed assay
high throughput multiplexed assay measuring binding of a MHC:ligand complex
Peptide microarray with fluorescence detection for millions of MHC binding measurements: PMID: 33705522.
A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay.
MHC binding|High throughput multiplexed assay
high throughput multiplexed assay measuring MHC ligand processing and presentation
Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands witth a false discovery rate: PMID: 29789417.
A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay.
ligand presentation|High throughput multiplexed assay
The output produced by a digital imaging technique, such as microscopy, MRI, or CT.
A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced.
https://orcid.org/0000-0001-9625-1899 "William D. Duncan"
https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik"
https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl"
https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie"
https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith"
The DICOM file produced by an MRI machine when a multiple sclerosis patient undergoes a brain scan.
An image data set whose information content originates from some MR imaging assay and is about some MRI participant.
magnetic resonance imaging participant
The subject being scanned in an MRI study, and bearor of data derived from that study.
magnetic resonance imaging evaluant role
An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role.
The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain.
An image data set that encodes measurement values produced by some instrument before undergoing a data transformation.
https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg"
magnetic resonance pulse sequence protocol
The NMR/MRI machine protocol about the radiofrequency pulse sequence.
The production of JPEG file by a digital camera.
An image data set that is the output of an image data set analysis.
reconstructed magnetic resonance image data set
The product of a mathematical transformation of raw "k-space" data produced by an MRI machine into a form that represents the anatomical structure of the brain.
An image data set that is the direct output of a raw magnetic resonance image data set reconstruction or a transformation of another MR image data set.
An image data set that is the direct output of an magnetic resonance imaging assay and whose values encode spatial frequencies produced by the NMR or MRI instrument.
The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item.
raw magnetic resonance image data set reconstruction
A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined.
A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set.
A data item that is the specified output of a milk assay.
organism diagnostic process
A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output.
diagnosis of an organism
A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these.
Using a radioactivity detection assay as part of a tritiated thymidine incorporation assay to determine the degree to which cells are replicating by detecting radioactivity of tritiated thymidine, where radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating.
An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B.
Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf
A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit.
epitope specific XCL1 release by T cells
A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope.
assay measuring epitope specific lymphotactin production by T cells
A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells.
lymphotactin release|biological activity
ELISA measuring epitope specific lymphotactin production by T cells
An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells.
remote patient assessment
A telephone or video remote patient assessment conducted between a physician and patient.
An organism diagnostic process which involves a remote assessment of a patient by a clinician.
telehealth patient assessment
A specimen that is derived from placental blood.
A blood microbiology assay that detects microorganisms in a placental blood specimen.
An organism detection datum that is the specified output of a placental blood microbiology assay.
A placental blood microbiology datum that is about eukaryota.
A material component separation process where a synaptic terminal is isolated from a neuron by mild homogenization of nervous tissue under isotonic conditions and subsequent fractionation using differential and density gradient centrifugation.
Michelle Giglio
Suvarna Nadendla
synaptosome preparation process
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option.
A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing.
Agilent-026655 Whole Mouse Genome Microarray 4x44K v2
A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays.
Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray
A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays.
Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray
A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays.
A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database.
A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database.
A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile.
A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db.
A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response.
Affymetrix Human Transcriptome Array 2.0
A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome.
A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™.
Applied Biosystems GeneChip PrimeView Human Gene Expression Array
A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events.
A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways.
A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways.
Illumina HumanHT-12 V4.0 expression beadchip
An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants.
An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content.
https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/arraykits/whole-genome-gene-expression/WGGEX_Direct_Hybridization_Assay_Guide_11322355_A.pdf, https://www.illumina.com/documents/products/datasheets/datasheet_gene_exp_analysis.pdf
A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome.
A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome.
administering substance in vivo to cause disease
An administration of substance in vivo with the intention to induce disease in the organism.
administering substance in vivo to reduce or prevent disease
An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism.
peripheral blood mononuclear cell specimen
A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system.
A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm.
The Mother and Child Health and Education Trust
A data item that is the specified output of an antigen specific antibodies assay.
antigen specific antibodies in blood assay
An antigen specific antibodies assay that has a blood specimen as evaluant.
antigen specific antibodies in milk assay
An antigen specific antibodies assay that has a milk specimen as evaluant.
antigen specific antibodies in blood assay datum
An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay.
antigen specific antibodies in milk assay datum
An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay.
An assay in which the level of catalytic activity of an enzyme is determined.
An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample.
alanine aminotransferase activity level assay
An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample.
alkaline phosphatase activity level assay
An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample.
An enzymatic activity level assay that measures the activity of amylase in a sample.
aspartate aminotransferase activity level assay
An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample.
An enzymatic activity level assay that measures the activity of cholinesterase in a sample.
An enzymatic activity level assay that measures the activity of creatine kinase in a sample.
gamma-glutamyltransferase activity level assay
An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample.
glutamate dehydrogenase activity level assay
An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample.
isocitrate dehydrogenase activity level assay
An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample.
lactate dehydrogenase activity level assay
An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample.
sorbitol dehydrogenase activity level assay
An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample.
An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample.
N-acetyl-beta-glucosaminidase activity level assay
An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample.
An enzymatic activity level assay that measures the activity of ribonuclease in a sample.
An enzymatic activity level assay that measures the activity of galactosidase in a sample.
An arthropod trap that is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor.
The administration of a malignant cell to a host.
The administration of a challenge to a live host.
epitope protection from infectious challenge experiment based on survival
An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls.
epitope protection from tumor challenge experiment based on burden
An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls.
epitope protection from tumor challenge experiment based on survival
An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls.
in vivo assay measuring T cell epitope specific protection from pathogen challenge
An in vivo assay measuring T cell epitope specific protection from pathogen challenge.
protection from pathogen challenge|in vivo assay
in vivo assay measuring T cell epitope specific protection from tumor challenge
An in vivo assay measuring T cell epitope specific protection from tumor challenge.
protection from tumor challenge|in vivo assay
in vivo assay measuring T cell epitope specific protection from other challenge
An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor.
protection from other challenge|in vivo assay
in vivo assay measuring T cell epitope specific survival after tumor challenge
An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival.
survival from tumor challenge|in vivo assay
in vivo assay measuring T cell epitope specific survival after pathogen challenge
An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival.
survival from pathogen challenge|in vivo assay
in vivo assay measuring B cell epitope specific protection from pathogen challenge
An in vivo assay measuring B cell epitope specific protection from pathogen challenge.
in vivo assay measuring B cell epitope specific protection from tumor challenge
An in vivo assay measuring B cell epitope specific protection from tumor challenge.
in vivo assay measuring B cell epitope specific protection from other challenge
An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor.
in vivo assay measuring B cell epitope specific survival after pathogen challenge
An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival.
in vivo assay measuring B cell epitope specific survival after tumor challenge
An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival.
in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells
An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells.
protection from pathogen challenge after adoptive transfer|in vivo assay
in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival
An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival.
survival after pathogen challenge after adoptive transfer|in vivo assay
in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells
An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells.
protection from tumor challenge after adoptive transfer|in vivo assay
in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival
An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival.
survival after tumor challenge after adoptive transfer|in vivo assay
in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells
An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells.
protection from other challenge after adoptive transfer|in vivo assay
in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells
An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells.
in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival
An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival.
in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells
An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells.
in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival
An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival.
in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells
An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells.
An organism detection assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall.
Gram-positive bacteria retain the violet stain whereas gram-negative bacteria do not.
A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent.
A specimen that is derived from a portion of lymph collected from an organism.
A specimen that is derived from part of a digestive tract.
assay measuring epitope specific interleukin-25 production by T cells
A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells.
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells
A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells
A flow cytometry assay that detects interleukin-25 production by T cells.
ELISA measuring epitope specific interleukin-25 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells.
cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells.
An assay kit that is manufactured by InBios International to use ELISA to test for IgM antibodies for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716, with a protein microarray that has a 96-well plate and the 56-kDa type-specific antigen.
An assay kit that is manufactured by Abbott to test for IgM antibodies for Dengue with a two-plate protein microarray. One plate contains stabilized Dengue viruses 1 through 4, and the other plate contains anti-human IgM antibody.
An assay kit that is manufactured by Abbott to detect the NS1 Dengue viral protein with a protein microarray and an anti-NS1 monoclonal antibody.
A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus in blood, using analytical chromatography.
SD Bioline Chikungunya IgM capture ELISA kit
An assay kit that is manufactured by Abbott to detect human IgM antibodies for Chikungunya with a protein microarray and ELISA.
An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA.
An assay that detects a type of organism and/or the quantity of individuals of a type of organism.
This term is a generalized version of the term previously known as 'organism identification assay', to include classification other than species and to include quantities as outputs.
A physical examination of an individual's ability to perform functional activities.
An observational assessment of the loss of facial muscle tissue due to inactivity or disease.
An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease.
A functional assessment of an individual's ability to cough forcefully.
A functional assessment of an individual's ability to understandably repeat spoken sentences.
A functional assessment of an individual's ability to touch index fingers together in front of the sternum without oscillation for a specified duration of time
A functional assessment of an individual's ability to touch their own nose and then touch an examiners finger in front of them and then touch their own nose once more.
A functional assessment of an individual's ability to accurately touch a moving target with their finger and then touch their own chin a number of times in a row.
A functional assessment of an individual's ability to alternate the forearm between pronation and suppination as quickly as possible during a specified duration of time
A functional assessment of an individual's ability to touch their finger-tip to thumb as many times as possible during a specified duration of time.
A functional assessment of an individual's ability to slide their heel back and forth along their contralateral tibia from the patella to the ankle with the contralateral leg extended.
A functional assessment of an individual's ability to tap their heel to the midpoint of the contralateral shin a number of times.
An observational assesment of an individual's muscle tissue loss due to inactivity or disease.
A functional assessment of an individual's ability to perform muscle movement to overcome gravity or physical resistence.
A functional assessment of an individual's ability to sense vibration.
A functional assessment of an individual's ability to sense the position of a finger or toe that has been manipulated by minimal random movements.
A functional assessment of an individual's muscle contraction when a muscle is triggered by a signal from a muscle spindle in response to a stimulus applied to a specific trigger point on the body.
The functional assessment of an individual's ability to maintain balance, posture or upright stability.
A limits of stability assessment designed to assess an individual's ability to maintain unsupported posture while sitting over a given time period.
A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet 20 cm apart.
stance feet apart assessment, with eyes closed
A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with their eyes closed.
A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together.
stance feet together assessment, with eyes closed
A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together and eyes closed.
A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet in tandem placement.
A limits of stability assessment designed to assess an individual's ability to maintain a stable stance on one foot.
A limits of stability assessment designed to assess an individual's ability to maintain balance while walking in a straight line placing steps in tandem.
A limits of stability assessment designed to assess an individual's manner or pattern of walking.
A functional assessment of an individual's lower cranial nerve function via proxy of facial muscle performance.
A functional assessment of an individual's ability to articulate spoken words.
A functional assessment of an individual's ability to coordinate limb movement.
A limb coordination assessment designed to assess an individual's ability to coordinate upper limb movement.
A limb coordination assessment designed to assess an individual's ability to coordinate lower limb movement.
A functional assesment of an individual's nerve performance. Specifically the nerves connecting the sensory and motor structures with the central nervous system.
A functional assessment of an individual's ability to maintain upright body posture.
deep tendon reflex assessment of the knee joint
A deep tendon reflex assessment of an individual's reaction to stimulus applied to a knee joint.
A physical examination of an individual through visual assesment.
deep tendon reflex assessment of the ankle joint
A deep tendon reflex assessment of an individual's reaction to stimulus applied to an ankle joint.
deep tendon reflex assessment of the tendon of biceps brachii
A deep tendon reflex assessment of an individual's reaction to stimulus applied to a tendon of biceps brachii.
deep tendon reflex assessment of the brachioradialis
A deep tendon reflex assessment of an individual's reaction to stimulus applied to a brachioradialis.
A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.
A mass spectrometry assay that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules).
Discussed on the OBI developer call 2022-03-07: 'tandem mass spectrometry' OBI:0200198 is under 'data transformation' but is actually defined like an assay. Moving OBI:0200198 from 'data transformation' to 'assay' is a major logical change, so the OBI development team supports obsoleting 'tandem mass spectrometry' OBI:0200198 and replacing it with ‘tandem mass spectrometry assay’ OBI:0003540.
Hector Guzman-Orozco, ORCID:0000-0003-3430-8997
ELISA measuring Orientia tsutsugamushi IgM antibody
An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi.
microarray assay measuring Dengue IgM antibody
A microarray assay that detects the IgM antibody that binds Dengue.
analytical chromatography measuring Chikungunya IgM antibody
Analytical chromatography that detects the IgM antibody that binds Chikungunya.
ELISA measuring Chikungunya IgM antibody
An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Chikungunya.
microarray ELISA measuring Chikungunya IgM antibody
An enzyme-linked immunosorbent assay that uses a microarray as the solid support and detects the IgM antibody that binds Chikungunya.
A preparative chromatography in which material components are separated in a liquid solution.
A value specification that specifies the largest concentration/amount of a substance that can be quantified in an analyte assay.
A value specification that specifies the smallest concentration/amount of a substance that can be detected in an analyte assay.
A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap.
A resting arthropod trap that consists of a container composed primarily of clay.
A chromosome conformation capture assay in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation. Immunopreciptation with an antibody that targets a transcription factor or histone modification allows for selection and enrichment of specific genomic regions for investigation of long-range chromosomal interactions.
An organism detection assay that detects microorganisms in a skin of body specimen.
An organism detection datum that is the specified output of a skin of body microbiology assay.
An organism detection assay that detects microorganisms in a bone marrow specimen.
An organism detection datum that is the specified output of a bone marrow microbiology assay.
An organism detection assay that detects microorganisms in a nasal aspirate specimen.
An organism detection datum that is the specified output of a nasal aspirate microbiology assay.
cell proliferation assay using carboxyfluorescein succinimidyl ester staining
A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division.
A cytometry assay which measures the number of living cells in a population.
cell viability assay using Annexin V staining
A cell viability assay that uses Annexin V staining to detect apoptotic cells.
carboxyfluorescein succinimidyl ester staining
Staining using carboxyfluorescein succinimidyl ester.
Annexin V staining
Staining using Annexin V to detect apoptotic cells.
The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc.
adapted from WEB: http://www.dictionary.net/injection
Epstein Barr virus transformed B cell
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
chimera
An organism which contains cells or tissues with a different genotype
PERSON: Helen Parkinson
Tissue, organ, system, sperm, blood or body location (arm).
An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
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
a cell derived from a multicellular organism that has the potential to replicate indefinitely
the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme
A material entity which is derived from a protein
phosphate buffered saline solution
PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes.
Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic).
PERSON: Tina Boussard
PBS buffer
WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A material entity that represents generations of a primary culture.
xenograft
Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world
A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species.
xenotransplant
WEB: http://en.wikipedia.org/wiki/Xenograft
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934
cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use)
A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged.
2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.'
primary cultured cell population
consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture.
A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592.
He, Tong-Chuan, et al. Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512. - To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene. Note that common usage in the literature is often of the form a human colorectal cancer cell line, as seen above. But such references to studies in a line refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture).
cultured clonal cell population
cell cut Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557
A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical.
screening library
PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application change biomaterial to material in definition
7/13/09: Need to clarify if this meets reagent role definition
synthetic peptide
the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme
a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment
changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi).
PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application
original term: protein fragment split into synthetic polypeptide and fragment derived from protein DS: Is this synthetic an oxymoron to the biomaterial?
organ section
A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
GROUP: CEBS
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
A scattered aggregate of glucose molecules in a liquid
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Ryan Brinkman
data analysis
data processing
Branch editors
geometric mean calculation
A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations).
PERSON: Mathias Brochhausen
A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations).
logistic-log curve fitting
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve.
A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n).
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
logit-log curve fitting
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively.
A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points.
The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model.
log-log curve fitting
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution.
A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points.
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446
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
biexponential transformation
This type of transformation is typically used in flow cytometry.
A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation.
Joseph Spliden
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
box-cox transformation
A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
hyperlog transformation
A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation.
ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42."
loess scale group transformation one-channel
Loess scale group normalization applied to data from two one-channel expression microarray assays.
A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar.
OTHER: Editor's adjustment based on MGED Ontology term
logical transformation
A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation.
loess scale group transformation two-channel
Loess scale group normalization applied to data from a two-channel expression microarray assay.
A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar.
OTHER: Adjusted from MGED Ontology
loess global transformation one-channel
Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
OTHER: Editor's generalization based on MGED Ontology term
split-scale transformation
A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t.
loess global transformation two-channel
Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
sine transformation
sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc.
A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html.
WEB: http://mathworld.wolfram.com/Sine.html
cosine transformation
cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc.
A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html.
WEB: http://mathworld.wolfram.com/Cosine.html
loess group transformation one-channel
A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
loess group transformation two-channel
A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
homogeneous polynomial transformation
a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables.
A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree.
WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html
linlog transformation
This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782.
A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
PMID: 16646782
variance stabilizing transformation
This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536.
A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper.
variance stabilising transformation
PMID: 12169536
loess global transformation
A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
loess group transformation
A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
loess scale group transformation
A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
total intensity transformation single
This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
total intensity transformation paired
This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays.
A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
quantile transformation
This 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 quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
PERSON: Elisabetta Manduchi
mean centering
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered.
A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input.
mean centring
median centering
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered.
A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input.
median centring
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.
K-fold cross validation method
K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used
leave one out cross validation method
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure
Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method
jackknifing
jackknifing method
boostrapping
Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved.
Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient
Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points
Benjamini and Hochberg false discovery rate correction method
Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
2011-03-31: [PRS]. specified input and output of dt which were missing
pareto scaling
A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable.
modular decomposition
Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins.
editor
k-means clustering
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
WEB: http://en.wikipedia.org/wiki/K-means
hierarchical clustering
A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
average linkage hierarchical clustering
An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.
complete linkage hierarchical clustering
an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.
single linkage hierarchical clustering
A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.
Benjamini and Yekutieli false discovery rate correction method
The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
dimensionality reduction
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
principal components analysis dimensionality reduction
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
pca data reduction
probabilistic algorithm
A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data.
expectation maximization
EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function.
global modularity calculation
A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network.
PERSON: Richard Scheuermann
dye swap merge
A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
moving average
The moving average is often used to handle data from tiling arrays.
A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
replicate analysis
Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data.
A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
PERSON:Elisabetta Manduchi
b cell epitope prediction
A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope.
mhc binding prediction
An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule.
t cell epitope prediction
A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope.
data imputation
Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm.
ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60.
continuum mass spectrum
A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion.
PERSON: Tina Hernandez-Boussard
continuum mass spectrum analysis
characteristic path length calculation
Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices
centroid mass spectrum
A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data.
Person:Tina Hernandez-Boussard
centroid mass spectrum analysis
Holm-Bonferroni family-wise error rate correction method
t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179
a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition Also added restriction to specify the output to be a FWER adjusted p-value The 'editor preferred term' should be removed
WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method
edge weighting
Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network.
was classified under algorithm class which is not acceptable super-class TO BE DEALT WITH STILL BY RICHARD. JAMES
loess transformation
A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
curve fitting data transformation
A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints.
WEB: http://en.wikipedia.org/wiki/Curve_fitting
family wise error rate correction method
A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt
FWER correction
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
submatrix extraction
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set.
A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.)
Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix.
WEB: http://en.wikipedia.org/wiki/Submatrix
row submatrix extraction
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set.
A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows.
column submatrix extraction
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set.
A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns.
gating
Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry.
Josef Spidlen
PERSON: Josef Spidlen
PERSON: Ryan Brinkman
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.
PERSON: Monnie McGee
arithmetic mean calculation
An arithmetic mean calculation 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.
From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
network analysis
A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network.
sequence analysis objective
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time.
longitudinal data analysis
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
mass spectrometry analysis
A data transformation which has the objective of spectrum analysis.
spread calculation data transformation
A spread calculation is a data transformation that has objective spread calculation.
Kaplan Meier
a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored)
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
multiple testing procedure
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
multiple testing correction method
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
Westfall and Young family wise error rate correction
Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing
PRS: 2011-03-31: set specified input and specified output to the data transformation
Westfall and Young FWER correction
polynomial transformation
a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables
A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
WEB: http://mathworld.wolfram.com/Polynomial.html
logarithmic transformation
A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
WEB: http://en.wikipedia.org/wiki/Logarithm
exponential transformation
An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function.
WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function
WEB: http://en.wikipedia.org/wiki/Exponential_function
Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix.
Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero.
non-negative matrix factorization
soft independent modeling of class analogy analysis
Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes.
SIMCA
WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies
discriminant function analysis
Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
WEB: http://www.statsoft.com/textbook/stdiscan.html
canonical variate analysis
canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form.
CVA
WEB: http://en.wikipedia.org/wiki/Canonical_analysis
linear discriminant functional analysis
Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective.
regression analysis method
Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
multiple linear regression analysis
multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
principal component regression
The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html
partial least square regression analysis
Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data.
PLS-RA
ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263.
discriminant analysis
Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
partial least square discriminant analysis
PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information.
PLS-DA
WEB: http://www.camo.com/rt/Resources/pls-da.html
eh transformation
An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization.
b transformation
A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization.
s transformation
An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization.
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
data visualization
similarity calculation
A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are.
euclidean distance calculation
An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered.
pearson correlation coefficient calculation
A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered.
WEB: http://en.wikipedia.org/wiki/Correlation
loess fitting
A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda).
ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101.
mode calculation
A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
quantile calculation
A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details.
WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html
median calculation
A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
variance calculation
A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment.
From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
standard deviation calculation
A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean.
From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
interquartile-range calculation
The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data.
skewness calculation
A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment
WEB: http://www.riskglossary.com/link/skewness.htm
From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
kurtosis calculation
A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html
WEB: http://davidmlane.com/hyperstat/A53638.html
data combination
A data transformation in which individual input data elements and values are merged together into a output set of data elements and values.
network graph construction
A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph.
weighted network graph construction
A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph.
directed network graph construction
A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph.
node quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network.
node degree calculation
A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node.
quantitative node degree calculation
A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node.
node in-degree calculation
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node.
node out-degree calculation
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node.
node shortest path identification
A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network.
edge quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network.
edge betweenness calculation
An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge.
network subgraph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network.
subgraph degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph.
quantitative subgraph degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph.
feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation
This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review)
mathematical feature
The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1.
log base
subgraph in-degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph.
subgraph out-degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph.
intra subgraph connectivity calculation
A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph.
subgraph modularity calculation
A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity.
network graph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole.
unit-variance scaling
A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable.
autoscaling
MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2.
An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation.
The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1).
exponential base
The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
polynomial degree
The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space.
number of variables
agglomerative hierarchical clustering
An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining.
divisive hierarchical clustering
A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain.
data partitioning
Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets.
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
generalized family wise error rate correction method
A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer.
gFWER correction
quantile number of false positives correction method
A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'
QNFP
tail probability for the proportion of false positives correction method
A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1.
TPPFP correction method
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20
false discovery rate correction method
The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt
FDR correction method
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
proportion of expected false positives correction method
A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses.
PEFP correction method
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
quantile proportion of false positives correction method
A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate).
QPFP correction method
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
normalization data transformation
A normalization data transformation is a data transformation that has objective normalization.
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
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.
class discovery data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
unsupervised classification data transformation
Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests.
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
center calculation data transformation
A center calculation data transformation is a data transformation that has objective of center calculation.
data vector reduction data transformation
A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k.
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
descriptive statistical calculation data transformation
A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
scaling data transformation
A scaling data transformation is a data transformation that has objective scaling.
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 visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.
A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type.
A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type.
A data transformation which has the objective of performing survival analysis.
Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system.
WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model
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.
Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules.
Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds.
The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.
A statistical hypothesis test in which the means of several groups are all equal.
PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs.
Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
obsolete_collection (of entities of organismal origin)
PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings]
a collection is a bfo:aggregate object, that is a set of material object of the same kind
pool of specimens
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
chemical solution
PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
liquid chemical solution
A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
a role which inheres in some molecular entity realized during the process of buffering
buffer role
PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
solvent role
PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
solute role
PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay.
An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis
PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene?
An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions
polymerase chain reaction-single strand conformation polymorphism assay
PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93.
liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates
PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4.
adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates.
Is a polymer which has lost secondary or tertiary structure
denatured polymer
Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172
decapitated organism is an organism which has had it's head removed
OBI Biomaterial
decapitated organism
PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..."
an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means.
validated information
PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6.
An information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions.
2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference
curated information
A person enrolled in a randomized clinical trial bears a randomized group participant role
a role that borne by an organism and realized by some group randomization process
randomized group participant role
Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922
A methylated polymer which has artificially acquired one or more methyl groups
methylated polymer
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
an organism that is the output of a genetic transformation process
genetically modified organism
A data item that was generated on the basis of a calculation or logical reasoning
BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted.
predicted data item
a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value
mean-centered data
The OBI manuscript is (much) edited imformation
A document which is the output of a document editing process
edited document
Salt molecules that have been mixed into water
A material entity that has been going through a process of being put into solution
dissolved material entity
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
OBI-Branch: adapted from wikipedia and wordnet
filtration
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 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: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
A planned process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays, X-rays, charged particles or neutrons) or non-ionizing radiation (such as UV light or microwaves)
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
planned irradiation
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
PRS:22102008: need to import catalyst from CHEBI 35223
polymerization
The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483
trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity
trypsination
PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202.
An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity
enzymatic ligation
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
storage
PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock.
BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process.
adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
cell lysis
PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376.
electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process.
electrocution
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion
PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax)
cervical dislocation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms.
asphyxiation
In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment. J Neurooncol. 1994;22(3):209-20. PMID: 7760097
intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death
lethal injection
intentional overdosing
decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..)
decapitation
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
group randomization
PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63.
a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!)
PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23.
immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum.
immobilization
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
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
elution
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
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190
a process by which an event or an entity is described before it actually happens or is being discovered and identified.
prediction
PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results
validation
PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13.
a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA
electroporation
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
digital curation
A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells.
A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus.
The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection.
An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal.
An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis.
Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point.
An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes.
An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes.
A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others.
BioSorter 1000 at TSRI Flow Cytometry Core Facility
A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter.
BioSorter 2000 at TSRI Flow Cytometry Core Facility
A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter.
BioSorter 250 at TSRI Flow Cytometry Core Facility
A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter.
BioSorter 500 at TSRI Flow Cytometry Core Facility
A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length.
A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells.
Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting.
Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells.
A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells.
A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting.
a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels.
A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement.
CyFlow Space at TSRI Flow Cytometry Core Facility
A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research.
CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations
A flow cytometer analyser which is manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters.
A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites.
A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle.
A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid.
FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc.
A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer.
Rhodamine 101 dye laser used to irradiate cells in a flow cytometer.
A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification.
The FACS Calibur is one of the most popular cytometers in use for research.
http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11
A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications.
A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications.
A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications.
FACSAria at TSRI Flow Cytometry Core Facility
A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters.
FACSvantage at TSRI Flow Cytometry Core Facility
The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells.
A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications.
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.
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
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.
helium-neon gas laser used to erradiate cells in a flow cytometer.
A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas.
A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement.
A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement.
A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement.
The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement.
A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer.
A helium neon laser can by used to irradiate cells in a flow cytometer.
A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm.
The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer.
It has both components, an Image cytometer and a flow cytometer.
The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells.
Influx Cell Sorter at TSRI Flow Cytometry Core Facility
A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells.
interrogation_point
Interrogation point in BD FACS Calibur
Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point.
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11
An ion laser is a gas laser which uses an ionized gas as its lasing medium.
jet_in_air_flow_chamber
Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter
A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air.
A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however.
A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy.
A laser is the most common way to irradiate a cell in a flow cytometer.
A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer.
light amplification by the stimulated emission of radiation
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH
A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale.
A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm.
LSR2 at TSRI Flow Cytometry Core Facility
A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use.
The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette.
A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation
A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications.
Gold vapor laser, Helium-cadmium metal-vapor laser
A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer.
A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer.
MoFlo at TSRI Flow Cytometry Core Facility
A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium.
multi-well plate
96 well plate, 48 multiwell plate
A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
FG this is synonymous with microtiter plate
A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer.
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
A device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles.
DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one.
particle delivery vessel
FC 500 particle delivery vessel
Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube.
FG: this should be delted - particle delivery is a role that an object can play
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer.
A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect.
quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar
Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell.
think this is natural thing, not a device HP/JF
piezo electric crystal
Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications.
measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future.
Built in preamplifier in a Hamamatsu H9656 PMT
A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing.
CVF-Q-10 flow chamber, CV-Q-10 flow chamber
A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells.
Reflection at TSRI Flow Cytometry Core Facility
A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells.
A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer.
Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid.
A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm.
Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command
A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser.
A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk.
The SomaScope is an instrument to quantify somatic cells in milk.
http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10
A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest.
Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates.
http://www.answers.com/topic/syringe, 2007-05-11
Linear amplifier, log amplifier, microwave amplifier
A voltage amplifier is a device that amplifies the voltage signal.
Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished.
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip
BioRobotics Microgrid II TAS, Affymetrix GMS 417
A device which deposits biological material onto a substrate in a defined pattern.
A device with a rapidly rotating container that applies centrifugal force to its contents
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
An instrument used to heat and/or maintain material at a set temperature.
A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay
A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
A device that is used for automated liquid transfer and handling.
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation.
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function.
Automated Multiplex Oligonucleotide Synthesizer
An instrument used to chemically synthesize oligonucleotides.
A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions.
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
An instrument which removes liquid by the application of negative pressure, i.e. vacuum.
A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
A device that is used to wash Affymetrix-type arrays.
VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature).
A device that is able to chemically join two or more molecules.
AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly.
The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining.
An image_cytometer is an instrument for image-based study or measurement of cells.
A cytometer is an instrument for counting and/or measuring characteristics of cells.
CHEF gel box, slab gel box, capillary electrophoresis
A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
was power_pack, maps to SEP electrical_power_supply
laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample.
A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations.
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.
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.
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.
A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal.
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period.
An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample).
A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound.
A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal.
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
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
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
A processed material which has the function to define a bounded habitat which is amenable to keeping animals.
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
The definition needs to be extended to other things than simply patients
Clinical Research Glossary Version 4.0 CDICS glossary group
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice.
balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i'
http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
A reference experiment design type is where all samples are compared to a common reference.
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
Greco-Latin square design is a study design which relates to Latin square design
only 2 articles in pubmed ->probably irrelevant
no example found in pubmed->not in use in the community
factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared.
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
Groups of assays that are related as part of a time series.
stopping rule
PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy.
a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen
compliance rule
a compliance rule is a rule which ensures a compliance process occurs
standard compliance rule
a standard compliance rule is a compliance rule which defines conformity to a representation standard
ethical standard compliance rule
an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur
eligibility criterion
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion criterion
PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
inclusion condition
inclusion rule
exclusion rule
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
exclusion criterion
adding substance to cell culture
adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient
is process in which a material substance is added to a cell culture
renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms
An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
obsolete performing a clinical assessment
A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition.
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
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
killing
Terminal sacrifice of animals by cervical dislocation at the end of an investigation.
A protocol application in which an organism is intentionally put to death
difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing.
death status type
euthanisia
life termination
sacrifice
CEBS, Biomaterial_branch
administering substance in vivo
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
Different routes and means of administration should go as children underneath this
Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
acquisition
Downloading a 3D structure from the PDB. Purchasing antibodies from sigma.
the planned process of gaining possession of a continuant.
5/31/2012 - OBI workshop: This process is not implying ownership of the material / information.
Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule'
This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition
exposure of material to environment
Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input.
Alan says there will be problmes, e.g. with selection by survival
material acquisition
Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI.
An acquisition in which possession of a material entity is gained.
The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation
This excludes processes that create or change materials, such as material transformations.
Bjoern Peters, Alan Ruttenberg, Helen Parkinson
acclimatization
placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment.
environmental material collection
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
relabel the term and add axiom connecting to EnVO:'environmental material' discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/
Bjoern Peters, Alan Ruttenberg
the researcher is very interested in the location
environmental material collection process
information acquisition
Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC
An acquisition in which possession of information is gained.
This excludes processes that create or change information, such as assays and data transformations.
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
group assignment
Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
group assignment is a process which has an organism as specified input and during which a role is assigned
OBI Plan
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
Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present
An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached
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
non-specific labeling
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies.
The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial
definition blessed by Allyson, Bjoern, Jay & Randi
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement.
cell fixation
http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus
a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time
should include capturing what qualities are being preserved
we could generalize this for other input materials
excision
Cutting out the portion of a gel which contains a DNA fragment
the use physical means to remove a portion of a substance from the rest
Alan Ruttenberg, Kevin Clancy
www.crohnsresource.com/glossary.jsp (via google define:resection)
non specific enzymatic cleavage
The use of agarase to digest an agar gel
an enzymatic cleavage that uses an enzyme without a strong affinity for specific cleavage sites in the input material
PERSON:Kevin Clancy
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
the detection of phycoerytherin by means of flow cytometry
An assay that detects a specified substance
The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection
An assay that measures the mass of a material at two or more time points
artificially induced cell membrane lysis
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent.
a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate
---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined.
artificially induced reverse transcription
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
isolation of cell culture supernatant
Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube.
a protocol which results in the separation of supernatant material from a cell culture
This does not apply to the case where the cells are lysed
experimental disease induction
the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome.
a protocol application to induce a specific disease in an organism
could be defined class
Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell.
A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest.
artificially induced DNA repair
the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands
a protocol application to repair damaged DNA molecules
---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi
cell permeabilization
Electroporation of HeLa cells to allow transfection with pUC19.
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
need to add output cell has_quality permeable
definition blessed by Jay, Alan, Randi
precipitation
The use of ethanol to precipitate DNA molecules from a solution containing DNA
a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate)
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
artificially induced methylation
the use of enzymes to add methyl groups to DNA molecules
A planned process of adding methyl groups to polymers
making cDNA from nucleotides using RNA as a template
the construction of a biomaterial from simpler biomaterials
This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription
synthesize
synthesis
concentrate
Evaporation of the solution containing DNA to increase the concentration of the DNA molecules
a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material
recombinant plasmid cloning
The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35.
the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial
genetic transformation
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
the introduction. alteration or integration of genetic material into a cell or organism
genetic modification
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
The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein.
An assay that determines the 3-dimensional configuration of an input material.
preparative chromatography
The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides.
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
PERSON:Kevin Clancy; Bjoern Peters
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
E coli expressing the gene for M avium p35 were cultured in order to produce p35.
The process of creating a copy of some biological entity in cell culture
vector mediated amplification
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
specific enzymatic cleavage
The use of a protease to digest a protein into peptides
an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material
gradient separation
the use of a sucrose gradient to isolate mitochondria
a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
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
electrophoresis
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers.
selection by survival
The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected
the use of environmental conditions to select for the organism or cells that have a certain trait
DNA cleavage, restriction analysis
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence
restriction enzyme assay
DNA restriction enzyme digestion
protease cleavage
the use of trypsin to cleave pepsin into peptide fragments
protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments).
enzymatic digestion
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
DNA transduction
The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein
a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism
DNA transfection
The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest
a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell
vector mediated expression
Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity.
vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector
needs defined relationship to cell culture
recombinant vector cloning
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
specific labeling
The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells
a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
requested by Helen Parkinson for MO
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
cell culture supernatant
solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615
Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell.
cell pellet
Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension
phage display library
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
display library
WEB: http://www.immuneepitope.org/home.do
cell lysate
The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
a cell lysate is a material entity which is output of a cell lysis process
PRS:22-02-2008: is a material which has output_role during lysis protocol-application. old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process
PERSON: Susanna Sansone
lysate
peptide construct
Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617
a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion
transgenic organism
HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162
a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it
PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application
whole mount tissue
A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
whole mount sample
PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
assay bead
Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules.
DS: Probably better modeled as a role.
bead
A material entity with the disposition to be bound by an adaptive immune receptor.
epitope
An occurrence of disease is a process involving pathologic changes within an organism
a process in which an infectious agent comes into physical contact with a host organism.
host exposure to infectious agent
administration in vivo with infectious agent
is an administration of an infectious agent to a host organism
Is an occurrence of a disease caused by an infection
occurrence of infectious disease
disposition to cause an allergic reaction
The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease.
an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen)
allergic reaction
The process of an allergic disease occurring in an organism.
occurrence of allergy
ELISPOT assay measuring epitope specific interleukin-2 production by T cells
An enzyme-linked immunospot assay that detects interleukin-2 production by T cells.
epitope binding by adaptive immune receptor
is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding.
Process of administering an object playing the role of immunogen to a living organism
Immunization in vivo
A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience.
adaptive immune effector function
a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent
living with infected household contact
a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely
living in endemic area
a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent
pathogen release in laboratory accident
Process of administering an object playing the role of immunogen to a cell culture
Immunization in vitro
the detrimental process in which an infectious agent colonizes or replicates in a host environment
infection process
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
adaptive immune receptor
a material entity bearing the immunogen role
immunogen
environmental exposure to infectious agent
Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent
A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses.
An organism in which an immune response process occurs.
In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation.
host of immune response
A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication.
293-T cell line
A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)).
C1R cell line
is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
experimental infection of cell culture
A cell line derived from mouse (C57BL/6N) lymphoma cells.
EL-4 cell line
A cell line derived from human cervical cancer cells.
HeLa cell line
A cell line derived from mouse dendritic cells.
JAWS II cell line
A material entity that has the antigen role.
antigen
Jurkat cell line
The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia)
JY cell line
assay measuring binding of a T cell epitope:MHC:TCR complex
A T cell epitope assay that measures the binding of T cell receptor to an epitope.
A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface.
RMA cell line
A human T-B lymphoblastoid hybrid cell line
T2 cell line
is a disease caused by an infectious agent
infectious disease
A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
lymph node cell specimen
A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role.
MHB 3-27-13: Following CLO alignment efforts, propose to update definition to read: "A cultured cell population comprised of cells that are able to grow attached to a solid substrate provided by tissue culture flasks or plates". The current definition seems to describe a more specific type of adherent culture of immunological origin as needed by IEDB. MHB 3-5-13: Need to review axiom on this class in light of clarification that it refers to a cell line sample, and not an entire line. Not every population of adhernet cells is the output of an isolation process.
cultured adherent cell populaiton
A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types).
cultured PBMC cell population
disposition to be bound by an adaptive immune receptor
Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor.
The process of removing an organ from its source organism
organ harvesting
A T cell population characterized by expressing the CD3 molecule on its surface.
cultured CD3+ T cell population
A T cell population characterized by not expressing the CD3 molecule on its surface.
cultured CD3- T cell population
is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect
allergy
A T cell population characterized by not expressing the CD4 molecule on its surface.
cultured CD4- T cell population
A T cell population characterized by not expressing the CD8 molecule on its surface.
cultured CD8- T cell population
A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface.
cultured CD4-/CD8- T cell population
A disease characterized by abnormal and uncontrolled cell division
cancer
Is a disease characterized by an immune response of an organism against parts of itself
autoimmune disease
placeholder to be imported from disease ontology
epitope specific IL-2 release by T cells
A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope.
a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule.
MHC:epitope complex binding to TCR
ELISPOT assay measuring epitope specific interferon-gamma production by T cells
An enzyme-linked immunospot assay that detects interferon-gamma production by T cells.
a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity
exposure resulting in immune reactivity
A role of a material entity that is realized when the material elicits an immune response targeting itself in whole or in part.
immunogen role
is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host.
03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO.
host of immune response role
The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex.
effector T cell function
a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface.
APC
should add a reference to the antigen processing and presentation process.
antigen presentation function
The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell.
restricting MHC role
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
donor role
A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity.
03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence.
immune epitope carrier role
Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response.
adjuvant role
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
disposition to infect an organism
Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope).
The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope.
immunization
A material separation where blood is taken from an organism.
blood harvesting
A cell line derived from mouse fibroblasts.
L cell line
cultured antigen presenting cell population
A culture of PBMCs. A culture of Hela cells.
a cell culture including cells that have an antigen presentation function
A cell culture including cells that have an effector T cell function
A mixture of peptides that is being added into a cell culture.
A material entity that is added to another material entity in an “adding a material entity into a target” process.
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
A cell culture into which a mixture of peptides is being added.
A material entity that receives the addition of another material entity in an “adding a material entity into a target” process.
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
environmental proximity to infectious agent
Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result
contact to pathogen carrying biological vector
a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result
A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
splenocyte specimen
A cell line derived from mouse mastocytoma.
P815 cell line
An antigen role that is realized as part of an assay, where immune recognition of the material with the assay antigen role is being detected as part of the assay.
assay antigen role
abnormal, harmful processes caused by or associated with a disease
pathologic process
assay measuring qualitative binding of a T cell epitope:MHC:TCR complex
An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output.
assay measuring MHC ligand processing and presentation
A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them.
assay measuring binding of a MHC:ligand complex
A MHC ligand assay that detects the binding of a ligand to an MHC molecule.
assay measuring binding of a B cell epitope:antibody complex
A B cell epitope assay that measures the binding of an antibody receptor to an epitope.
An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, or characterizes the structrue of the complex resulting from such a binding event.
assay measuring epitope specific cytokine production by T cells
A T cell epitope assay that detects cytokine production by T cells.
assay measuring epitope specific T cell killing
A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC.
assay measuring epitope specific proliferation of T cells
A T cell epitope dependent biological activity assay that detects T cell proliferation.
A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor.
This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009.
51 chromium assay measuring epitope specific T cell killing
A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC.
ELISA measuring epitope specific interferon-gamma production by T cells
An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells.
ELISA measuring epitope specific interleukin-2 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells.
ELISA measuring epitope specific interleukin-4 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells.
ELISA measuring epitope specific interleukin-5 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells.
ELISA measuring epitope specific tumor necrosis factor alpha production by T cells
An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells.
ELISA measuring epitope specific interleukin-10 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells.
ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells.
ELISA measuring epitope specific interleukin-6 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells.
ELISA measuring epitope specific interleukin-13 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells.
ELISA measuring epitope specific interleukin-12 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells.
ELISA measuring epitope specific interleukin-1 beta production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells.
ELISA measuring epitope specific interleukin-17 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells.
ELISA measuring epitope specific interleukin-18 production by T cells
An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells.
ELISPOT assay measuring epitope specific interleukin-4 production by T cells
An enzyme-linked immunospot assay that detects interleukin-4 production by T cells.
ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells
An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells
ELISPOT assay measuring epitope specific interleukin-10 production by T cells
An enzyme-linked immunospot assay that detects interleukin-10 production by T cells.
ELISPOT assay measuring epitope specific interleukin-13 production by T cells
An enzyme-linked immunospot assay that detects interleukin-13 production by T cells.
intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells
A flow cytometry assay that detects interferon-gamma production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells
A flow cytometry assay that detects interleukin-2 production by T cells.
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells
A flow cytometry assay that detects tumor necrosis factor alpha production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells
A flow cytometry assay that detects interleukin-4 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells
A flow cytometry assay that detects interleukin-10 production by T cells.
intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells
A flow cytometry assay that detects interleukin-17 production by T cells.
MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex
A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor.
3H-thymidine assay measuring epitope specific proliferation of T cells
A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro.
BrdU assay measuring epitope specific proliferation of T cells
A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro.
A biological process where T cells proliferate resulting from the recognition of a T cell epitope.
epitope specific T cell proliferation
epitope specific GM-CSF release by T cells
A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope.
epitope specific IFN-g release by T cells
A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope.
epitope specific IL-10 release by T cells
A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope.
epitope specific IL-12 release by T cells
A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope.
epitope specific IL-13 release by T cells
A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope.
epitope specific IL-17 release by T cells
A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope.
epitope specific IL-18 release by T cells
A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope.
epitope specific IL-1b release by T cells
A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope.
epitope specific IL-4 release by T cells
A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope.
A material entity bearing the disposition to cause an allergic reaction
epitope specific IL-5 release by T cells
A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope.
epitope specific IL-6 release by T cells
A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope.
A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell.
epitope specific killing by T cells
A biological process where T cells produce TNF resulting from the recognition of a T cell epitope.
epitope specific TNF release by T cells
An IFN-g ELISPOT is an assay detecting ifn-gamma production
An assay that determines information about the production of the cytokine interferon gamma
The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. The content of that report on the IEDB website is here: http://iedb.org/refId/1013357
A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB)
Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/
A specimen that has been fixed in formalin and embedded in paraffin.
formalin-fixed paraffin-embeded specimen
A specimen that is derived from some uterine cervix
A specimen that is derived from some urethra
A specimen that is derived from some cervical mucus
A specimen that is derived from some throat
A specimen that is derived from some eye
A specimen that is derived from some respiratory system
A specimen that is derived from some upper respiratory tract
A specimen that is derived from some nasopharynx
A specimen that is derived from some semen
A specimen that is derived from some bodily fluid
A specimen that is derived from some chorionic villus
A specimen that is derived from some meconium
A specimen that is derived from some umbilical cord blood
A specimen that is derived from some arterial blood
A specimen that is derived from some venous blood
A specimen that is derived from some capillary blood
A specimen that is derived from some erythrocytes
A specimen that is derived from some reticulocytes
A specimen that is derived from some leukocytes
An analyte assay that measures the abundance of carbon dioxide
An analyte assay that measures the abundance of sodium(1+)
An analyte assay that measures the abundance of creatinine
An analyte assay that measures the abundance of potassium(1+)
A cytometry assay that measures the count of basophils
A cytometry assay that measures the count of neutrophils
A cytometry assay that measures the count of eosinophils
A cytometry assay that measures the count of lymphocytes
A cytometry assay that measures the count of monocytes
An analyte assay that measures the abundance of chloride
A cytometry assay that measures the count of erythrocytes
A cytometry assay that measures the count of platelets
A cytometry assay that measures the count of leukocytes
An analyte assay that measures the abundance of hemoglobin
An analyte assay that measures the abundance of phosphate ion
An analyte assay that measures the abundance of alanine aminotransferase
An analyte assay that measures the abundance of alkaline phosphatase (human)
An analyte assay that measures the abundance of bilirubin IXalpha
aspartate aminotransferase (human) assay
An analyte assay that measures the abundance of aspartate aminotransferase (human)
An analyte assay that measures the abundance of glucose
An analyte assay that measures the abundance of magnesium cation
An analyte assay that measures the abundance of albumin
An analyte assay that measures the abundance of protein
An analyte assay that measures the abundance of calcium cation
An analyte assay that measures the abundance of creatine kinase
A cytometry assay that measures the count of nucleate erythrocytes
segmented neutrophil of bone marrow count assay
A cytometry assay that measures the count of segmented neutrophil of bone marrows
An assay that measures lactate dehydrogenase complex
An analyte assay that measures the abundance of triglyceride
high-density lipoprotein cholesterol assay
An analyte assay that measures the abundance of high-density lipoprotein cholesterol
An analyte assay that measures the abundance of cholesterol
low-density lipoprotein cholesterol assay
An analyte assay that measures the abundance of low-density lipoprotein cholesterol
An analyte assay that measures the abundance of thyroid stimulating hormone
An analyte assay that measures the abundance of prostate-specific antigen
An analyte assay that measures the abundance of thyroxine
An analyte assay that measures the abundance of elemental oxygen
An analyte assay that measures the abundance of folic acids
A cytometry assay that measures the count of reticulocytes
An analyte assay that measures the abundance of methemoglobin
cytosolic creatine kinase complex, MB-type assay
An assay that measures cytosolic creatine kinase complex, MB-type
An analyte assay that measures the abundance of hydrogencarbonate
An analyte assay that measures the abundance of vancomycin
An analyte assay that measures the abundance of tobramycin
An analyte assay that measures the abundance of 3,3',5'-triiodothyronine
An analyte assay that measures the abundance of C-reactive protein
A cytometry assay that measures the count of megakaryocytes
A cytometry assay that measures the count of mesothelial cells
A cytometry assay that measures the count of macrophages
An analyte assay that measures the abundance of 3-hydroxybutyric acid
panel5 venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order
An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order
An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order
An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order
automated differential venous blood basophil count assay
A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order
automated differential venous blood neutrophil count assay
A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order
automated differential venous blood eosinophil count assay
A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order
automated differential venous blood lymphocyte count assay
A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order
automated differential venous blood monocyte count assay
A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order
An analyte assay that measures the abundance of chloride in venous blood
CBC with automated differential venous blood RBC count assay
A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order
CBC with automated differential venous blood platelet count assay
A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order
CBC with automated differential venous blood WBC count assay
A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order
CBC with automated differential venous blood hematocrit assay
A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order
CBC with automated differential venous blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order
An analyte assay that measures the abundance of phosphate in venous blood
liver injury venous blood alanine aminotransferase assay
An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order
liver injury venous blood human alkaline phosphatase assay
An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order
liver injury venous blood bilirubin assay
An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order
liver injury venous blood human aspartate aminotransferase assay
An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order
An analyte assay that measures the abundance of glucose in venous blood
An analyte assay that measures the abundance of magnesium in venous blood
A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order
A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order
A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order
A cytometry assay that measures the count of platelets in venous blood as part of a CBC order
An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order
corrected venous blood leukocyte count assay
A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order
liver evaluation venous blood bilirubin assay
An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order
liver evaluation venous blood globulin assay
An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order
liver evaluation venous blood albumin assay
An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order
liver evaluation venous blood human aspartate aminotransferase assay
An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order
liver evaluation venous blood alanine aminotransferase assay
An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order
liver evaluation venous blood human alkaline phosphatase assay
An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order
liver evaluation venous blood protein assay
An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order
basic metabolic panel venous blood chloride assay
An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order
basic metabolic panel venous blood potassium assay
An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order
basic metabolic panel venous blood sodium assay
An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order
basic metabolic panel venous blood creatinine assay
An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order
basic metabolic panel venous blood glucose assay
An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order
basic metabolic panel venous blood calcium assay
An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order
basic metabolic panel venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order
An analyte assay that measures the abundance of creatine kinase in venous blood
An analyte assay that measures the abundance of calcium in venous blood
An assay that measures ferritin in venous blood
An analyte assay that measures the abundance of calcium in venous blood as part of a total order
An analyte assay that measures the abundance of iron in venous blood
CBC with manual differential venous blood band neutrophil count assay
A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order
CBC with manual differential venous blood WBC count assay
A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order
CBC with manual differential venous blood eosinophil count assay
A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order
CBC with manual differential venous blood lymphocyte count assay
A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order
CBC with manual differential venous blood nucleated RBC count assay
A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order
CBC with manual differential venous blood monocyte count assay
A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order
CBC with manual differential venous blood segmented neutrophil count assay
A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order
CBC with manual differential venous blood basophil count assay
A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order
An analyte assay that measures the abundance of albumin in venous blood
cardiac enzymes venous blood creatine kinase assay
An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order
An analyte assay that measures the abundance of haptoglobin in venous blood
venous blood lactate dehydrogenase assay
An assay that measures lactate dehydrogenase in venous blood
An analyte assay that measures the abundance of prealbunin in venous blood
lipid panel venous blood triglyceride assay
An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order
lipid panel venous blood high density lipoprotein assay
An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order
lipid panel venous blood cholesterol assay
An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order
lipid panel venous blood low density lipoprotein assay
An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order
An assay that measures hemoglobin A1c in venous blood
An analyte assay that measures the abundance of uric acid in venous blood
An analyte assay that measures the abundance of protein in venous blood as part of a total order
venous blood thyroid stimulating hormone assay
An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood
venous blood prostate specific antigen assay
An analyte assay that measures the abundance of prostate specific antigen in venous blood
An assay that measures volume in urine as part of a 24 hour total order
An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order
An analyte assay that measures the abundance of glucose in arterial blood
CBC with manual differential venous blood cell count assay
A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order
hemoglobin oxygen saturation arterial blood oxygen assay
An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order
hemoglobin oxygen saturation arterial blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order
inpatient profile venous blood sodium assay
An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order
inpatient profile venous blood creatinine assay
An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order
inpatient profile venous blood potassium assay
An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order
inpatient profile venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order
An analyte assay that measures the abundance of folic acid in venous blood
count venous blood reticulocyte count assay
A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order
An analyte assay that measures the abundance of potassium in venous blood
An analyte assay that measures the abundance of carbon dioxide in venous blood
An analyte assay that measures the abundance of transferrin in venous blood
An analyte assay that measures the abundance of sodium in venous blood
An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order
random electrolytes urine potassium assay
An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order
An analyte assay that measures the abundance of creatinine in urine
An assay that measures osmolality in urine
An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order
cooximitery arterial blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order
cooximitery arterial blood methemoglobin assay
An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order
An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order
An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order
Biosite cardiac panel arterial blood creatine kinase MB assay
An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order
An assay that measures fibrinogen in venous blood
comprehensive metabolic panel venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood calcium assay
An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood potassium assay
An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood sodium assay
An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood glucose assay
An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood albumin assay
An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood human alkaline phosphatase assay
An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood bilirubin assay
An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood chloride assay
An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood human aspartate aminotransferase assay
An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood protein assay
An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood creatinine assay
An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order
comprehensive metabolic panel venous blood alanine aminotransferase assay
An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order
An assay that measures LDH in venous blood
An assay that measures creatine kinase MB in venous blood
An assay that measures lactic acid in venous blood
A cytometry assay that measures the proportion of red blood cells in venous blood
An analyte assay that measures the abundance of creatinine in venous blood
An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order
ionized venous blood ionized calcium assay
An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order
blood gas venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order
blood gas venous blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order
An analyte assay that measures the abundance of creatinine in arterial blood
An analyte assay that measures the abundance of tacrolimus in venous blood
An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order
An analyte assay that measures the abundance of mycophenolic acid in venous blood
non-vented blood gas arterial blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order
non-vented blood gas arterial blood oxygen assay
An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order
non-vented blood gas arterial blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order
An assay that measures IgG in venous blood as part of a quantitative order
An assay that measures IgM in venous blood as part of a quantitative order
An assay that measures IgA in venous blood as part of a quantitative order
An analyte assay that measures the abundance of sodium in arterial blood
An analyte assay that measures the abundance of potassium in arterial blood
An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order
vented blood gas arterial blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order
vented blood gas arterial blood oxygen assay
An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order
vented blood gas arterial blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order
A cytometry assay that measures the proportion of red blood cells in arterial blood
An analyte assay that measures the abundance of chloride in arterial blood
An analyte assay that measures the abundance of hemoglobin in arterial blood
GEM premier blood gas venous blood hematocrit assay
A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood ionized calcium assay
An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood potassium assay
An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood oxygen assay
An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood glucose assay
An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood sodium assay
An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood lactic acid assay
An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order
GEM premier blood gas venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order
An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order
An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order
CBC with manual differential venous blood metamyelocyte count assay
A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order
An assay that measures lactic acid in arterial blood
An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood
An analyte assay that measures the abundance of digoxin in venous blood
An analyte assay that measures the abundance of protein in urine
An analyte assay that measures the abundance of tobramycin in venous blood
CBC with manual differential venous blood myelocyte count assay
A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order
SPEP protein electrophoresis venous blood beta-globin assay
An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order
SPEP protein electrophoresis venous blood albumin assay
An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order
SPEP protein electrophoresis venous blood protein assay
An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order
An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order
hepatic panel venous blood protein assay
An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order
hepatic panel venous blood bilirubin assay
An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order
hepatic panel venous blood alanine aminotransferase assay
An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order
hepatic panel venous blood human aspartate aminotransferase assay
An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order
hepatic panel venous blood albumin assay
An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order
hepatic panel venous blood human alkaline phosphatase assay
An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order
estimated venous blood glomerular filtration assay
An assay that measures glomerular filtration in venous blood as part of a estimated order
An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order
An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order
An analyte assay that measures the abundance of amikacin in venous blood as part of a random order
An analyte assay that measures the abundance of ammonia in venous blood
An analyte assay that measures the abundance of GGT in venous blood
An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order
An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order
An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order
An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order
chem11 venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order
An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order
An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order
An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order
An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order
An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order
An assay that measures IgE in venous blood as part of a total order
chem16 venous blood human aspartate aminotransferase assay
An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order
An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order
An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order
chem16 venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order
An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order
An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order
An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order
An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order
An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order
chem16 venous blood human alkaline phosphatase assay
An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order
An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order
An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order
An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order
chem16 venous blood alanine aminotransferase assay
An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order
An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order
An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order
POC chem8 arterial blood ionized calcium assay
An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order
POC chem8 arterial blood potassium assay
An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order
An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order
POC chem8 arterial blood creatinine assay
An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order
POC chem8 arterial blood hematocrit assay
A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order
An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order
An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order
An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order
An analyte assay that measures the abundance of PTH in venous blood as part of a intact order
An analyte assay that measures the abundance of PSA in venous blood as part of a total order
An analyte assay that measures the abundance of T3 in venous blood as part of a total order
An analyte assay that measures the abundance of protein in urine as part of a 24 hour order
An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order
An analyte assay that measures the abundance of triglyceride in venous blood
tube 4 count cerebrospinal fluid cell count assay
A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order
An analyte assay that measures the abundance of protein in cerebrospinal fluid
An analyte assay that measures the abundance of glucose in cerebrospinal fluid
tube 1 count cerebrospinal fluid cell count assay
A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order
venous blood dehydroepiandrosterone assay
An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood
An analyte assay that measures the abundance of cortisol in venous blood
An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order
An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood glucose assay
An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood lactic acid assay
An assay that measures lactic acid in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood chloride assay
An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood hematocrit assay
A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood calcium assay
An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood temperature assay
An assay that measures temperature in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order
ABL90 panel arterial blood potassium assay
An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order
CBC with manual differential venous blood promyelocyte count assay
A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order
An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order
ABL90 panel venous blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order
ABL90 panel venous blood ionized calcium assay
An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order
ABL90 panel venous blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order
ABL90 panel venous blood hematocrit assay
A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order
An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order
An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order
ABL90 panel venous blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order
ABL90 panel venous blood lactic acid assay
An assay that measures lactic acid in venous blood as part of a ABL90 panel order
An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order
An analyte assay that measures the abundance of T4 in venous blood
An analyte assay that measures the abundance of T4 in venous blood as part of a free order
ABL90 panel venous blood potassium assay
An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order
An analyte assay that measures the abundance of sodium in urine
An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order
An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order
bone profile venous blood human alkaline phosphatase assay
An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order
An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order
bone profile venous blood phosphate assay
An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order
ABG/electrolytes arterial blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order
ABG/electrolytes arterial blood oxygen assay
An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order
ABG/electrolytes arterial blood ionized calcium assay
An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order
CBC with automated differential venous blood nucleated RBC count assay
A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order
ABL90 panel venous blood methemoglobin assay
An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order
ABL90 panel arterial blood methemoglobin assay
An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order
An analyte assay that measures the abundance of valproic acid in venous blood
high sensitivity cardiac/neonatal venous blood c-reactive protein assay
An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order
An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order
GEM4000 ANLCOOX arterial blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood oxygen assay
An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood hematocrit assay
A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood temperature assay
An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood potassium assay
An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood glucose assay
An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood ionized calcium assay
An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order
GEM4000 ANLCOOX arterial blood sodium assay
An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order
An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order
An analyte assay that measures the abundance of hemoglobin in venous blood
CBC with manual differential venous blood megakaryocyte count assay
A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order
non-cardiac venous blood c-reactive protein assay
An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order
An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order
An analyte assay that measures the abundance of parathyroid hormone in venous blood
An analyte assay that measures the abundance of protein in bodily fluid as part of a total order
An analyte assay that measures the abundance of glucose in bodily fluid
A cytometry assay that measures the count of cells in bodily fluid as part of a count order
manual differential bodily fluid segmented neutrophil count assay
A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order
manual differential bodily fluid mesothelial cell count assay
A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order
manual differential bodily fluid monocyte count assay
A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order
manual differential bodily fluid lymphocyte count assay
A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order
manual differential bodily fluid macrophage count assay
A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order
manual differential bodily fluid basophil count assay
A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order
manual differential bodily fluid eosinophil count assay
A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order
liver function venous blood bilirubin assay
An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order
liver function venous blood alanine aminotransferase assay
An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order
liver function venous blood human aspartate aminotransferase assay
An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order
liver function venous blood albumin assay
An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order
liver function venous blood protein assay
An analyte assay that measures the abundance of protein in venous blood as part of a liver function order
liver function venous blood human alkaline phosphatase assay
An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order
vitamin B12 and Folate venous blood folic acid assay
An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order
A cytometry assay that measures the count of cells in bodily fluid
A cytometry assay that measures the count of reticulocytes in venous blood
An analyte assay that measures the abundance of cholesterol in bodily fluid
TSH reflex Free T4 venous blood thyroid stimulating hormone assay
An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order
An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order
An analyte assay that measures the abundance of T3 in venous blood as part of a free order
An analyte assay that measures the abundance of albumin in bodily fluid
An analyte assay that measures the abundance of triglyceride in bodily fluid
hemoglobin and hematocrit venous blood hematocrit assay
A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order
hemoglobin and hematocrit venous blood hemoglobin assay
An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order
An analyte assay that measures the abundance of ionized calcium in venous blood
An assay that measures temperature in venous blood
An analyte assay that measures the abundance of bicarbonate in venous blood
An analyte assay that measures the abundance of oxygen in venous blood
An assay that measures osmolality in venous blood
liver fibrosis (chronic viral hepatitis) venous blood platelet count assay
A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order
An analyte assay that measures the abundance of T3 in venous blood
CBC with manual differential venous blood neutrophil count assay
A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order
creatinine clearance urine creatinine assay
An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order
venous blood beta hydroxybutryic acid assay
An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood
A cytometry assay that measures the count of megakaryocytes in venous blood
A cytometry assay that measures the count of nucleated RBCs in venous blood
A cytometry assay that measures the count of WBCs in venous blood
automated count venous blood reticulocyte count assay
A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order
An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order
An analyte assay that measures the abundance of Ceruloplasmin in venous blood
An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order
An assay that measures lactic acid in arterial blood as part of a GEM4 order
An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order
An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order
An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order
An assay that measures temperature in arterial blood as part of a GEM4 order
An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order
An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order
A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order
GEM4 arterial blood ionized calcium assay
An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order
GEM4 arterial blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order
liver fibrosis (NAFLD) venous blood platelet count assay
A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order
venous blood beta hydroxybutric acid assay
An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood
CBC with manual differential venous blood plasma cell count assay
A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order
An analyte assay that measures the abundance of erythropoietin in venous blood
An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order
blood gas arterial blood bicarbonate assay
An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order
blood gas arterial blood carbon dioxide assay
An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order
An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order
cerebrospinal fluid lymphocyte count assay
A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid
cerebrospinal fluid segmented neutrophil count assay
A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid
cerebrospinal fluid mesothelial cell count assay
A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid
cerebrospinal fluid macrophage count assay
A cytometry assay that measures the count of macrophages in cerebrospinal fluid
cerebrospinal fluid basophil count assay
A cytometry assay that measures the count of basophils in cerebrospinal fluid
cerebrospinal fluid monocyte count assay
A cytometry assay that measures the count of monocytes in cerebrospinal fluid
cerebrospinal fluid eosinophil count assay
A cytometry assay that measures the count of eosinophils in cerebrospinal fluid
An analyte assay that measures the abundance of beta-2-microglobulin in venous blood
lipid panel reflex direct venous blood low density lipoprotein assay
An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order
lipid panel reflex direct venous blood triglyceride assay
An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order
lipid panel reflex direct venous blood cholesterol assay
An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order
lipid panel reflex direct venous blood high density lipoprotein assay
An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order
Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones.
A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced.
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died.
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.
The totality of all processes through which a given disease instance is realized.
replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role'
The representation of a conclusion of a diagnostic process.
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
fixed tissue specimen
A processed specimen that is the output of a fixation process.
fixed tissue slide specimen
A fixed tissue specimen that is placed in a slide.
health care provider role
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class.
A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality 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 spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A physical quality of the thermal energy of a system.
A quality in which events occur in sequence.
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
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.
A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled.
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity.
A quality which inheres in a continuant.
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
A scalar optical quality which obtains by the magnitude of the light emitted by the bearer.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A mating type that indicates whether the F plasmid has integrated into the chromosome.
A biological sex quality inhering in a population of multiple sexes.
A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial.
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating.
A S. pombe mating type determined by the gene configuration on the mat1 locus.
A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids.
A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus.
A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus.
A bacterial mating type indicating the presence of F plasmid in a bacterial cell.
A bacterial mating type indicating the absence of F plasmid in a bacterial cell.
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes.
A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.
A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father.
A monadic quality of continuant that exists at the cellular level of organisation.
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
A physical quality inhering in a bearer by virtue of the bearer's motion characteristic.
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity.
frontal
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate.
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity.
A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
A biological sex quality inhering in an individual or a population that undergo sexual reproduction.
A physical quality inhering in a bearer by virtue of the bearer's participation in movement.
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 that inheres in an entire population or part of a population.
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent.
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
A quality inhering in a bearer by virtue of its constitution.
A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
A trypsin that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof.
A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof.
double-stranded RNA-specific adenosine deaminase
A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human EPO gene or a 1:1 ortholog thereof.
glial cell line-derived neurotrophic factor
A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof.
A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof.
A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human PTH gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TF gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TTR gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof.
Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction.
A protein that is a translation product of the Aspergillus oryzae RIB40 rntA gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Aspergillus oryzae RIB40 nucS gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof.
A protein with ribonuclease activity that is a constituent of cobra venom.
A protein with ribonuclease activity that is purified from chicken liver.
cytosolic creatine kinase complex, MB-type
A cytosolic creatine kinase complex that is a heterodimer of a B-type subunit and an M-type subunit.
A protein that contains a single ATP:guanido phosphotransferase N-terminal domain (Pfam:PF02807) followed by a single ATP:guanido phosphotransferase C-terminal catalytic domain (Pfam:PF00217).
protein-glutamine gamma-glutamyltransferase
A dengue virus genome polyprotein proteolytic cleavage product that is the N-terminal most non-structural protein within the dengue virus genome polyprotein. Example: UniProtKB:P29990, 776-1127, Asn-905/Asn-982, MOD:00160.
A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof.
A protein-containing complex that is composed of four subunits of L-lactate dehydrogenase, cytoplasmic.
A protein that is a translation product of any of the following alkaline phosphatase genes in human: ALPG (encoding the germinal form; GCAP), ALPP (encoding the placental form; PLAP), ALPI (encoding the intestinal form; IAP), and ALPL (encoding the tissue non-specific form; TNAP).
A protein that is a translation product of any of the following genes in human: GOT1/GOT2.
A hemoglobin complex that is composed of at least one beta-N-1-deoxy fructosyl hemoglobin subunit, in which the glycan is attached to the N-terminal valine (after initiator methionine removal) of one or both beta subunits.
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.
A DNA site where a transcription factor binds.
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually 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 quality of a nucleotide polymer that has no terminal nucleotide residues.
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
A region of sequence that is involved in the control of a biological process.
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
A spatiotemporal region encompassing some part of the life cycle of an organism.
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
A fluid that is composed of blood plasma and erythrocytes.
The upper ventral region of the torso of an organism.
A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
The inner portion of the kidney consisting of the renal pyramids.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
A gonad of a male animal. A gonad produces and releases sperm.
Anatomical group that has its parts adjacent to one another.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
The portion of the hindlimb that contains both the stylopod and zeugopod.
The gonad of a female organism which contains germ cells.
The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
Functional system which consists of structures involved in respiration.
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
A filament, mostly protein, that grows from follicles found in the dermis[WP].
The terminal portion of the intestinal tube, terminating with the anus.
Transudate contained in the pleural cavity.
Excretion that is the output of a kidney.
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
Muscle tissue that consists primarily of skeletal muscle fibers.
A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
Transudate contained in the peritoneal cavity.
The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
The part of the forelimb extending from the shoulder to the autopod[cjm].
The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted].
A joint that connects the hindlimb autopod and zeugopod skeletons.
A tube extending from the mouth to the anus.
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
A muscular organ in the floor of the mouth.
The section of the pharynx that lies above the soft palate.
The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.
A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.
The mucous membrane that lines the nasal cavity[MP].
One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP].
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species.
Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion.
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
Organism substance that is composed of sperm cells suspended in seminal fluid.
Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple.
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
Respiration organ that develops as an outpocketing of the esophagus.
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
The organ covering the body that consists of the dermis and epidermis.
The organ that functions to filter blood and to store red corpuscles and platelets.
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
The portion of the small intestine that extends from the jejunum to the colon.
A serous membrane that lines the peritoneal cavity[VHOG,modified].
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
The soft tissue that fills the cavities of bones.
The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants.
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
Transudate contained in the pericardial cavity.[FMA].
An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail.
A mucosa that is part of a esophagus [Automatically generated definition].
A cerebral hemisphere that is in the left side of a brain.
A cerebral hemisphere that is in the right side of a brain.
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
A fold of peritoneum originating at the stomach and supporting the viscera.
A muscularis mucosa that is part of a esophagus.
A mucosa that is part of a nasopharynx [Automatically generated definition].
A mucosa that is part of a oropharynx [Automatically generated definition].
The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A portion of organism substance that secreted_by a respiratory system.
A small conical pouch projections located on the upper anterior portion of each atrium of the heart.
One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot.
The junction between the esophagus and the stomach epithelium.
A tendon that attaches_to a biceps brachii.
Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon.
Brachioradialis is a muscle of the forearm that acts to flex the forearm at the elbow. It is also capable of both pronation and supination, depending on the position of the forearm. It is attached to the distal styloid process of the radius by way of the brachioradialis tendon, and to the lateral supracondylar ridge of the humerus.
Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
Area of skin in the hypoastric region of the abdomen.
Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule.
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the dimension in which events occur in sequence.
A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response.
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
obsolete_core
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
obsolete_other
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Transformation-ML
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
ACS
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
XML
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
RDF
A FOAF file, a SKOS file, an OWL file.
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
zip
MagicDraw MDZIP archive, Java JAR file.
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
Example.tar file.
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
Compensation-ML
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
Gating-ML
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
OWL
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
obsolete_the supplier role of Affymetrix
An organization which supplies technology, tools and protocols for use in high throughput applications
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
GenePattern HeatMapViewer data visualization
The GenePattern process of generating Heat Maps from clustered data.
GenePattern HierarchicalClusteringViewer data visualization
The GenePattern process of generating hierarchical clustering visualization from clustered data.
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
obsolete_the manufacturer role of Agilent
obsolete_manufacturer role of Bruker Daltonics
obsolete_the manufacturer role of Thermo
obsolete_the manufacturer role of Li-Cor
obsolete_the manufacturer role of Ambion
obsolete_the manufacturer role of BIO-RAD
obsolete_the manufacturer role of Illumina
obsolete_the manufacturer role of Helicos
obsolete_manufacturer role of Bruker Corporation
obsolete_the manufacturer role of Waters
obsolete_manufacturer role of applied biosystems
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
Advanced Instruments Inc. (AI Companies)
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
3: symptomatic in bed more than 50% of the day but not bed ridden
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
2: symptomatic but in bed less than 50% of the day
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
A Karnofsky score vaue specification indicating that a patient is asymptomatic.
A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
60-70: symptomatic but in bed less than 50% of the day
A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
An organization that is developing and selling nanopore sequencing products and is based in the UK.
An organization that manufactures mosquito traps and other mosquito control products.
A manufacturer of rapid point-of-care assay devices.
A manufacturer of in vitro diagnostic assay kits in India.
A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases.
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)
relation has no temporal argument
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
A length unit which is equal to one millionth of a meter or 10^[-6] m.
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
A length unit which is equal to 10 [-10] m.
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
A mass unit which is equal to 10^[-12] g.
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
A time unit which is equal to 60 seconds.
A time unit which is equal to 3600 seconds or 60 minutes.
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
A substance unit equal to a millionth of a mol or 10^[-6] mol.
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
A unit of molarity which is equal to 10^[-12] M.
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
A volume unit which is equal to 10^[-12] L.
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
A concentration unit which a measure of viable bacterial numbers in a given volume.
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
A rate unit which is equal to one over one nanomolar second.
A rate unit which is equal to one over one molar second.
A rate unit which is equal to one over one nanomolar.
A rate unit which is equal to one over one molar.
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
A reference to a place on the Earth, by its name or by its geographical location.