2017-02-22 Pierre Grenon Bjoern Peters Matthew Pocock Liju Fan Christian Bolling Chris Taylor Chris Stoeckert 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. Tina Hernandez-Boussard Jessica Turner Allyson Lister Yongqun He Jie Zheng Tanya Gray 2009-07-31 Bill Bug Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Lawrence Hunter The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. Chris Mungall Daniel Schober Helen C. Causton James Malone Kevin Clancy Susanna-Assunta Sansone Norman Morrison Daniel Rubin Cristian Cocos Stefan Wiemann An ontology for the annotation of biomedical and functional genomics experiments. Melanie Courtot Helen Parkinson Luisa Montecchi Jennifer Fostel Jeffrey Grethe Eric Deutsch Ontology for Biomedical Investigation Philip Lord Gilberto Fragoso Philippe Rocca-Serra Elisabetta Manduchi OWL-DL Mervi Heiskanen Richard Bruskiewich Robert Stevens Dirk Derom Larisa Soldatova James A. Overton Dawn Field Trish Whetzel Alan Ruttenberg Frank Gibson Matthew Brush Richard Scheuermann John Westbrook Barry Smith Carlo Torniai en Jay Greenbaum Ryan R. Brinkman Monnie McGee Holger Stenzhorn Melissa Haendel Joe White OBI Release 2017-02-22 SVN Revision: Unversioned directory BFO OWL specification label BFO OWL specification label Really of interest to developers only Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. BFO CLIF specification label Person:Alan Ruttenberg BFO CLIF specification label Really of interest to developers only Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 editor preferred term editor preferred term~editor preferred label editor preferred label editor preferred label editor preferred term GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred label example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition textual definition textual definition definition definition 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note term editor 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 has obsolescence reason PERSON:Alan Ruttenberg PERSON:Melanie Courtot Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note is denotator type Alan Ruttenberg In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') is denotator type relates an class defined in an ontology, to the type of it's denotator imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from expand expression to Chris Mungall A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" expand expression to expand assertion to A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall 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)" expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property Alan Ruttenberg 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 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 . An alternative name for a class or property which is unique across the OBO Foundry. GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot has ID digit count 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) 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" Person:Alan Ruttenberg has ID digit count has ID range allocated to Person:Alan Ruttenberg 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 Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] has ID range allocated to has ID policy for has ID policy for 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" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg 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. Person:Alan Ruttenberg 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" has ID prefix elucidation Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation person:Alan Ruttenberg has associated axiom(nl) An axiom associated with a term expressed using natural language Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(nl) has associated axiom(fol) An axiom expressed in first order logic using CLIF syntax Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(fol) is allocated id range Add as annotation triples in the granting ontology PERSON:Alan Ruttenberg 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" is allocated id range retired from use as of Alan Ruttenberg In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp relates a class of CRID to the date after which further instances should not be made, according to the central authority retired from use as of has axiom label 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 Person:Alan Ruttenberg Person:Alan Ruttenberg has axiom label term replaced by Add as annotation triples in the granting ontology Person:Alan Ruttenberg Person:Alan Ruttenberg Use on obsolete terms, relating the term to another term that can be used as a substitute term replaced by ISA alternative term ISA tools project (http://isa-tools.org) Person: Philippe Rocca-Serra ISA alternative term Person: Alejandra Gonzalez-Beltran Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 An alternative term used by the ISA tools project (http://isa-tools.org). NIAID GSCID-BRC alternative term PERSON: Chris Stoeckert, Jie Zheng An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). NIAID GSCID-BRC alternative term NIAID GSCID-BRC metadata working group IEDB alternative term An alternative term used by the IEDB. IEDB IEDB alternative term PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters FGED alternative term An alternative term used by the Functional Genomics Data (FGED) Society. FGED alternative term PERSON: Chris Stoeckert, Jie Zheng Penn Group temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime temporal interpretation Contributor Contributor An entity responsible for making contributions to the content of the resource. Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. Coverage Coverage 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. Creator Creator An entity primarily responsible for making the content of the resource. Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. Date Date A date associated with an event in the life cycle of the resource. Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. Description Description An account of the content of the resource. Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. Format Format The physical or digital manifestation of the resource. Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). Resource Identifier Resource Identifier An unambiguous reference to the resource within a given context. 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). Language Language A language of the intellectual content of the resource. 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. Publisher Publisher An entity responsible for making the resource available 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. Relation Relation 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. Rights Management Rights Management 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. Source Source A reference to a resource from which the present resource is derived. The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. Subject and Keywords Subject and Keywords The topic of the content of the resource. Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. Title Title Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Resource Type Resource Type The nature or genre of the content of the resource. 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. shorthand shorthand label part of Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. http://www.obofoundry.org/ro/#OBO_REL:part_of Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. a core relation that holds between a part and its whole my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) part of part_of this day is part of this year (occurrent parthood) has part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. a core relation that holds between a whole and its part has part has_part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) realized in Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) is realized by realized in realized_in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation realizes Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) preceded by 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. http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by preceded_by precedes precedes occurs in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs in occurs_in unfolds in unfolds_in contains process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t contains process has measurement unit label has measurement unit label obsolete_specifically denotes 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 Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy 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. obsolete_specifically denotes see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote true is about 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. Smith, Ceusters, Ruttenberg, 2000 years of philosophy This document is about information artifacts and their representations is about is_about is a (currently) primitive relation that relates an information artifact to an entity. person:Alan Ruttenberg mentions 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition An information artifact IA mentions an entity E exactly when it has a component/part that denotes E PERSON: Jonathan Rees Person: Alan Ruttenberg mentions denotes 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically person:Alan Ruttenberg obsolete_materially denotes obsolete_materially denotes see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote true is quality measurement of 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later Alan Ruttenberg From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. is quality measurement of m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q obsolete_describes obsolete_describes true obsolete_represents obsolete_represents true has coordinate unit label has coordinate unit label relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point is duration of Person:Alan Ruttenberg is duration of relates a process to a time-measurement-datum that represents the duration of the process is quality measured as 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg inverse of the relation of is quality measurement of is quality measured as is quality specification of Person:Alan Ruttenberg Person:Bjoern Peters 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. is quality specification of quality is specified as 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters inverse of the relation of is quality specification of quality is specified as has time stamp Alan Ruttenberg has time stamp relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken has measurement datum Alan Ruttenberg has measurement datum relates a time stamped measurement datum to the measurement datum that was measured provides_service_consumer_with provides_service_consumer_with A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. is_supported_by_data Philly 2011 workshop The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. is_supported_by_data OBI OBI has_specified_input 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. PERSON: Alan Ruttenberg has_specified_input see is_input_of example_of_usage obsolete_is_concretization_of 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. PERSON: Alan Ruttenburg PERSON: Barry Smith replaced by: http://purl.obolibrary.org/obo/BFO_0000058 true obsolete_is_concretization_of is_specified_input_of PERSON:Bjoern Peters A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay obsolete_is_concretized_as 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. PERSON: Alan Ruttenberg PERSON: Barry Smith replaced by: http://purl.obolibrary.org/obo/BFO_0000059 true obsolete_is_concretized_as obsolete_has_quality 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] GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall replaced by: http://purl.obolibrary.org/obo/BFO_0000086 true obsolete_has_quality has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg has_specified_output obsolete_is_realized_by GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] executed_during has_realization is_realized_as replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' true obsolete_is_realized_by obsoleted_has_specified_output_information PERSON: Frank Gibson true 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. PERSON: Alan Ruttenberg obsoleted_has_specified_output_information is_manufactured_by Alan Ruttenberg Liju Fan 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 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) is_manufactured_by obsolete_has_function GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall Relation between an independent continuant and a function. heart has_function to-pump-blood replaced by: http://purl.obolibrary.org/obo/BFO_0000085 true obsolete_has_function obsoleted_is_reagent_in true Alan Ruttenberg Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole obsoleted_is_reagent_in 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 obsolete_realizes GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungal 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] 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. executes has_function_part involves_execution_of is_realization_of replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' true obsolete_realizes obsoleted_utilizes_reagent true Alan Ruttenberg Relationship between a protocol application and a substance that has role reagent that participates in the protocol application obsoleted_utilizes_reagent see example_of_usage for is_reagent_in obsoleted_is_device_for true Alan Ruttenberg Relationship between a device and a protocol application in which it participates obsoleted_is_device_for 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 is_specified_output_of PERSON:Bjoern Peters A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg is_specified_output_of obsoleted_utilizes_device true Alan Ruttenberg Relationship between protocol application and an intrument in which it participates obsoleted_utilizes_device see example_of_usage for is_device_for is_proxy_for 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) 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. Alan Ruttenberg is_proxy_for 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 obsoleted_has_specified_input_information PERSON: Frank Gibson consumes data true 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. PERSON:Alan Ruttenberg obsoleted_has_specified_input_information obsolete_has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. GROUP:OBI:<http://obi.sourceforge.net> PERSON:Chris Mungal replaced by: http://purl.obolibrary.org/obo/BFO_0000087 true obsolete_has_role obsolete_results_from 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 obsolete_results_from true achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' BP, AR, PPPB branch PPPB branch derived This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. achieves_planned_objective modified according to email thread from 1/23/09 in accordince with DT and PPPB branch obsoleted_is_specified_information_output_of A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. Editor PERSON: James Malone is replaced by has_specified_output_of obsoleted_is_specified_information_output_of true has grain PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg obsoleted_is_specified_information_intput_of Is the inverse relation of has_specfied_input_information is replaced by is_specified_intput_of obsoleted_is_specified_information_intput_of true is grain of 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. 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 JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic. PERSON: Alan Ruttenberg is grain of supplies A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. GROUP: Relations branch supplies has_supplier 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. PERSON: Alan Rutternberg PERSON: Cristian Cocos PERSON: Frank Gibson PERSON: Melanie Courtot has_supplier objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. objective_achieved_by OBI OBI is member of organization 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Alan Ruttenberg Person:Helen Parkinson Person:Helen Parkinson Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. is member of organization has category label has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. has disposition to bind A relationship between two material entitites that each have disposition to form a complex with the other. IEDB 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 disposition to bind has organization member Person: Jie Zheng Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 has organization member specifies value of specifies value of A relation between a value specification and an entity which the specification is about. has value specification PERSON: James A. Overton A relation between an information content entity and a value specification that specifies its value. OBI has value specification has performer has performer performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system) process is result of IEDB PERSON:Bjoern Peters 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 process is result of obsolete_is_described_by obsolete_is_described_by true bound_to bound_to 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. A relationship between two material entities that form a complex based on a selective, non-covalent interaction. inheres in A dependent inheres in its bearer at all times for which the dependent exists. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence inheres in inheres_in this fragility inheres in this vase this red color inheres in this apple bearer of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence bearer of bearer_of is bearer of this apple is bearer of this red color this vase is bearer of this fragility participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in participates_in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation has participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has_participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) 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 journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). is concretized as concretizes A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). concretizes function of A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence function of function_of is function of this catalysis function is a function of this enzyme quality of A quality inheres in its bearer at all times for which the quality exists. a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence is quality of quality of quality_of this red color is a quality of this apple role of A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence is role of role of role_of this investigator role is a role of this person has function A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence has function has_function this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) has quality A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has quality has_quality this apple has quality this red color has role A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has role has_role this person has role this investigator role (more colloquially: this person has this role of investigator) derives from This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity derives from derives_from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) derives into This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity derives into derives_into this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) location of Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a relation between two independent continuants, the location and the target, in which the target is entirely within the location location of location_of my head is the location of my brain this cage is the location of this rat located in http://www.obofoundry.org/ro/#OBO_REL:located_in Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in located_in my brain is located in my head this rat is located in this cage 2D boundary of 2D boundary of 2D_boundary_of A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity boundary of is 2D boundary of is boundary of the surface of my skin is a 2D boundary of my body has 2D boundary A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity has 2D boundary has boundary has_2D_boundary my body has 2D boundary the surface of my skin immediately preceded by starts_at_end_of David Osumi-Sutherland X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) ends_at_start_of meets David Osumi-Sutherland immediately precedes surrounded by 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 adjacent to adjacent to temporal relation move to BFO? Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation starts Chris Mungall inverse of starts with Allen starts member of An organism that is a member of a population of organisms is member of SIO is member of is a mereological relation between a item and a collection. member of member part of has member SIO has member is a mereological relation between a collection and an item. has member has measurement value has measurement value has x coordinate value has x coordinate value has z coordinate value has z coordinate value has y coordinate value has y coordinate value has_feature_value James Malone has_feature_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 specified value A relation between a value specification and a number that quantifies it. has specified value PERSON: James A. Overton A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. OBI entity entity Entity An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf Julius Caesar Verdi’s Requiem entity the Second World War your body mass index An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) 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 per discussion with Barry Smith continuant continuant Continuant (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (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 (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants continuant if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] 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) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] 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]) 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]) occurrent (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] An entity that has temporal parts and that happens, unfolds or develops through time. 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. (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) 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 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. b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) occurrent Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) occurrent 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]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) per discussion with Barry Smith 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. (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] independent continuant IndependentContinuant (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ic (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant the bottom right portion of a human torso the interior of your mouth (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] 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]) obsolete dependent continuant true A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. obsolete dependent continuant spatial region (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) s-region 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. SpatialRegion (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) spatial region (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] per discussion with Barry Smith 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]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) temporal region (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] TemporalRegion t-region (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] 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]) 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 temporal 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 per discussion with Barry Smith 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]) (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] (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) two-dimensional spatial region 2d-s-region TwoDimensionalSpatialRegion (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) an infinitely thin plane in space. the surface of a sphere-shaped part of space two-dimensional spatial region (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) spatiotemporal region (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) st-region (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] SpatiotemporalRegion (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] 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]) spatiotemporal 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 (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) 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]) (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process process the course of a disease the flight of a bird the life of an organism your process of aging. (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] 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]) disposition (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] Disposition (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. disposition If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) an atom of element X has the disposition to decay to an atom of element Y b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. disposition the cell wall is disposed to filter chemicals in endocytosis and exocytosis (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] b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) realizable entity (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) RealizableEntity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) realizable realizable entity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] zero-dimensional spatial region 0d-s-region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) ZeroDimensionalSpatialRegion (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] quality Quality (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril 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]) (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] 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] specifically dependent continuant (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key SpecificallyDependentContinuant 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. sdc b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. specifically dependent continuant the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) per discussion with Barry Smith 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 (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; 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]) 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. Role role (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) role the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) fiat object BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions fiat-object FiatObjectPart (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] b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) fiat object or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] one-dimensional spatial region (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] 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]) OneDimensionalSpatialRegion 1d-s-region an edge of a cube-shaped portion of space. one-dimensional spatial region (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] 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]) object aggregate ObjectAggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 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 defined by fiat: the aggregate of members of an organization defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container object-aggregate an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) defined through physical attachment: the aggregate of atoms in a lump of granite defined via attributive delimitations such as: the patients in this hospital object aggregate 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. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects (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] three-dimensional spatial region ThreeDimensionalSpatialRegion 3d-s-region (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) a cube-shaped region of space a sphere-shaped region of space, three-dimensional spatial region (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) site site Site (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) site the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) object object Object BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 atom b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) cell cells and organisms engineered artifacts grain of sand molecule object organelle organism planet solid portions of matter star b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) generically dependent continuant gdc (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] GenericallyDependentContinuant A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) generically dependent continuant the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] Function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. function function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar 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] process boundary (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] p-boundary ProcessBoundary Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) process boundary the boundary between the 2nd and 3rd year of your life. 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] p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) one-dimensional temporal region (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] OneDimensionalTemporalRegion 1d-t-region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). one-dimensional temporal region the temporal region during which a process occurs. A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material entity material (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (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] (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] 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]) 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. MaterialEntity 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 Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) material entity the undetached arm of a human being Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) (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 y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) (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] every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) continuant fiat boundary 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. ContinuantFiatBoundary (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO 2 Reference: 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 cf-boundary Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. immaterial entity immaterial BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 ImmaterialEntity immaterial entity one-dimensional continuant fiat boundary OneDimensionalContinuantFiatBoundary (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] 1d-cf-boundary The Equator a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) all geopolitical boundaries all lines of latitude and longitude one-dimensional continuant fiat boundary 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] process profile process-profile (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. ProcessProfile 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]) process profile (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) 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]) relational quality 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. r-quality (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] RelationalQuality a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) relational quality (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 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]) two-dimensional continuant fiat boundary (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] TwoDimensionalContinuantFiatBoundary 2d-cf-boundary 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]) two-dimensional continuant fiat boundary 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] zero-dimensional continuant fiat boundary (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. zero-dimensional continuant fiat boundary (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] requested by Melanie Courtot zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. 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]) zero-dimensional temporal region (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] ZeroDimensionalTemporalRegion 0d-t-region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) a temporal region that is occupied by a process boundary right now temporal instant. the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. zero-dimensional temporal region (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) history history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) History history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. water biotin 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. biotin peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid hydrogensulfite A sulfur oxoanion that has formula HO3S. hydrogensulfite glucose An aldohexose used as a source of energy and metabolic intermediate. glucose 5'-adenylyl sulfate 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well cytochalasin cytochalasin N-ethyl-N-nitrosourea A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. proton luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. luciferin sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. sodium chloride lead(0) An elemental lead that has formula Pb. lead(0) acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. acrylamide hydroxyl An oxygen radical that has formula HO. hydroxyl deuterium atom The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). deuterium atom ruthenium atom An iron group element atom that has formula Ru. ruthenium atom fluorescein 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. fluorescein gadodiamide hydrate The hydrate of gadodiamide. gadodiamide hydrate gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). gadoteridol phenol red 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. phenol red sodium citrate dihydrate The dihydrate of trisodium citrate. sodium citrate dihydrate atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom rare earth metal atom rare earth metal atom rhodium atom A cobalt group element atom that has formula Rh. rhodium atom gadolinium atom A lanthanoid atom that has formula Gd. gadolinium atom terbium atom A lanthanoid atom that has formula Tb. terbium atom nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid ribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid amino acid A carboxylic acid containing one or more amino groups. amino acid macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. macromolecule polymer gadolinium molecular entity gadolinium molecular entity gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). gadodiamide sodium phosphate sodium phosphate phosphorus-32 atom The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. phosphorus-32 atom phosphorus-33 atom The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. phosphorus-33 atom Cy3 dye Cy3 dye Cy5 dye Cy5 dye digoxigenin 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. digoxigenin ethylenediaminetetraacetic acid A polyamino carboxylic acid that has formula C10H16N2O8. ethylenediaminetetraacetic acid double-stranded DNA double-stranded DNA 5-bromo-2'-deoxyuridine 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. chromium-51 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. chromium-51 Alexa Fluor 532 Alexa Fluor 532 An organosulfonic acid that has formula C34H33N3O11S2. Alexa Fluor 546 Alexa Fluor 546 An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3. Alexa Fluor 555 A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. Alexa Fluor 555 tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. tritiated thymidine dimethyl sulfate The dimethyl ester of sulfuric acid. dimethyl sulfate diethyl pyrocarbonate The diethyl ester of dicarbonic acid. diethyl pyrocarbonate 1,1-dihydroxy-3-ethoxy-2-butanone 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide N-methylisatoic anhydride A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. N-methylisatoic anhydride (S)-1-(4-bromoacetamidobenzyl)EDTA (S)-1-(4-bromoacetamidobenzyl)EDTA A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. EDTA methidiumpropylamide 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. EDTA methidiumpropylamide bromophenol blue 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. bromophenol blue tris 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. tris fluorescence microscopy Any type of microscopy 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. FM fluorescence imaging fluorescence microscopic imaging fluorescence microscopy CHMO confocal fluorescence microscopy CLSM LSCM 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 fluorescence imaging confocal fluorescence microscopy confocal fluorescence microscopy confocal laser scanning fluorescence microscopy confocal laser scanning microscopy confocal-laser scanning microscopy fluorescence confocal microscopy fluorescence confocal scanning laser microscopy scanning confocal fluorescence microscopy CHMO light microscopy Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. OM light microscopy light microscopy optical microscopy CHMO liquid chromatography-tandem mass spectrometry 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. LC-MS-MS LC-MS/MS LC-MS2 LC-MSMS LC/MS/MS LCMSMS liquid chromatography tandem mass spectrometry liquid chromatography tandem mass spectroscopy liquid chromatography-tandem mass spectrometry liquid chromatography-tandem mass spectroscopy CHMO cell line cell cell line cell 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 '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 mortal cell line cell A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. immortal cell line cell immortal cell line cell 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. cell line 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). cell line immortal cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. immortal cell line mortal cell line 0 A cell line is able to support only a limited number of passages in vitro. mortal cell line cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." primary cultured cell 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. primary cultured cell native cell 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). native cell cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell fibroblast 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. fibroblast epithelial cell 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. epithelial cell T cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. T cell mast cell 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. mast cell hepatocyte 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. hepatocyte erythrocyte A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte macrophage 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. macrophage B cell A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. B cell dendritic cell 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). dendritic cell lymphocyte 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. lymphocyte experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. experimentally modified cell in vitro CD4-positive, alpha-beta T cell A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. CD4-positive, alpha-beta T cell CD8-positive, alpha-beta T cell A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. CD8-positive, alpha-beta T cell basophil 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. basophil plasma cell 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. plasma cell alpha-beta T cell A T cell that expresses an alpha-beta T cell receptor complex. alpha-beta T cell 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. CD8-positive, alpha-beta cytotoxic T cell mature NK T cell 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. mature NK T cell mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form. mononuclear cell soil 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. soil podzol 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. podzol environmental material A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. environmental material geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location core promoter binding Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. core promoter binding 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. antibody-dependent cellular cytotoxicity type IV hypersensitivity An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation. type IV hypersensitivity cytokine production The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. cytokine production cell killing 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. cell killing T cell mediated cytotoxicity T cell mediated cytotoxicity 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. adaptive immune response An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). adaptive immune response 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. cytokine production involved in immune response platelet activating factor production The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels. platelet activating factor production tolerance induction 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. tolerance induction B cell tolerance induction A process involving any mechanism for tolerance induction in B cells. B cell tolerance induction T cell tolerance induction A process involving any mechanism for tolerance induction in T cells. T cell tolerance induction hypersensitivity An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. hypersensitivity 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. cytokine production involved in inflammatory response molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. molecular_function antigen binding Interacting selectively and non-covalently with 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. antigen binding catalytic activity 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. catalytic activity RNA-directed DNA polymerase activity 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. RNA-directed DNA polymerase activity ion channel activity Catalysis of 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. ion channel activity cellular_component The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cellular_component chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. chromosome mitochondrion 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. mitochondrion glucose metabolic process 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. glucose metabolic process DNA replication DNA replication 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. DNA methylation DNA methylation The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. chromatin remodeling Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. chromatin remodeling phagocytosis An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. phagocytosis immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response 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. cellular response to DNA damage stimulus cell cycle 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. cell cycle blood coagulation 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. blood coagulation biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. biological_process opsonization 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. opsonization cell proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. cell proliferation fertilization 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). fertilization cellular process 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. cellular process gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. gene expression 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. vascular endothelial growth factor production immunoglobulin mediated immune response An immune response mediated by immunoglobulins, whether cell-bound or in solution. immunoglobulin mediated immune response histone modification The covalent alteration of one or more amino acid residues within a histone protein. histone modification immunoglobulin complex 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. immunoglobulin complex B cell receptor complex 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. B cell receptor complex antigen processing and presentation The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. antigen processing and presentation protein domain specific binding Interacting selectively and non-covalently with a specific domain of a protein. protein domain specific binding actin filament polymerization Assembly of actin filaments by the addition of actin monomers to a filament. actin filament polymerization hemopoiesis 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. hemopoiesis 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. connective tissue growth factor production chemokine production The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. chemokine production 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. granulocyte macrophage colony-stimulating factor production hepatocyte growth factor production 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. hepatocyte growth factor production type I interferon production 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. type I interferon production interferon-beta production The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interferon-beta production interferon-gamma production 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. interferon-gamma production interleukin-1 alpha production 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. interleukin-1 alpha production interleukin-1 beta production 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. interleukin-1 beta production interleukin-1 production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-1 production interleukin-10 production The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-10 production interleukin-11 production The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-11 production interleukin-12 production The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-12 production interleukin-13 production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-13 production interleukin-14 production The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-14 production interleukin-15 production The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-15 production interleukin-16 production The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-16 production interleukin-17 production 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. interleukin-17 production interleukin-18 production The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-18 production interleukin-19 production The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-19 production interleukin-2 production The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-2 production interleukin-20 production The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-20 production interleukin-21 production The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-21 production interleukin-22 production The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-22 production interleukin-23 production The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-23 production interleukin-24 production The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-24 production interleukin-25 production The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-25 production interleukin-26 production The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-26 production interleukin-27 production The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-27 production interleukin-3 production The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-3 production interleukin-4 production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-4 production interleukin-5 production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-5 production interleukin-6 production The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-6 production interleukin-7 production The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-7 production interleukin-8 production The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-8 production interleukin-9 production The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-9 production TRAIL production TRAIL production The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. tumor necrosis factor production TNF alpha production 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 production lymphotoxin A production TNF beta production The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. lymphotoxin A production 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 beta1 production 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 beta2 production 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. transforming growth factor beta3 production macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localization DNA polymerase activity 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. DNA polymerase activity type III interferon production 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. type III interferon production 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. chemokine (C-X-C motif) ligand 9 production 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 adaptive immune response 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 T cell mediated immune response 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. helper T cell enhancement of B cell mediated immune response granzyme A production The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granzyme A production perforin production 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. perforin production granulysin production The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granulysin production regulation of gene expression, epigenetic Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. regulation of gene expression, epigenetic regulation of molecular function, epigenetic Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. regulation of molecular function, epigenetic T cell proliferation T cell proliferation The expansion of a T cell population by cell division. Follows T cell activation. T cell receptor complex 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. T cell receptor complex T cell activation T cell activation 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. immunoglobulin complex, circulating 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. antibody antibody immunoglobulin complex, circulating DNA polymerase complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. DNA polymerase complex peptide antigen binding Interacting selectively and non-covalently with an antigen peptide. peptide antigen binding MHC protein complex 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. MHC protein complex membrane-bounded organelle 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. membrane-bounded organelle protein complex A ribosome is a protein complex Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. protein complex cytotoxic T cell degranulation The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. cytotoxic T cell degranulation sequence-specific DNA binding Interacting selectively and non-covalently with 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. sequence-specific DNA binding regulation of DNA methylation 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. regulation of DNA methylation 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. macrophage migration inhibitory factor production Oncostatin M production Oncostatin M production 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. chemokine (C-C motif) ligand 17 production cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. cellular developmental process response to stimulus 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. response to stimulus chromosome organization 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. chromosome organization 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. actin polymerization-dependent cell motility 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. transforming growth factor beta production 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. monocyte chemotactic protein-1 production 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. chemokine (C-C motif) ligand 4 production 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 gamma production 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. macrophage inflammatory protein-1 alpha production 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 5 production 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. chemokine (C-C motif) ligand 1 production 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. granulocyte colony-stimulating factor production IP-10 production IP-10 production The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granzyme B production The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. granzyme B production 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. tumor necrosis factor superfamily cytokine production 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. chemokine (C-C motif) ligand 22 production 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. tumor necrosis factor (ligand) superfamily member 11 production interleukin-17A production The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-17A production interleukin-17F production The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-17F production complement-dependent cytotoxicity Lysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody. complement-dependent cytotoxicity histamine secretion mediated by immunoglobulin Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface. histamine secretion mediated by immunoglobulin immune complex formation 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. immune complex formation immunoglobulin-mediated neutralization 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. immunoglobulin-mediated neutralization 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 19 production 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-C motif) ligand 21 production 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 12 production 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 13 production 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. chemokine (C-X-C motif) ligand 16 production Insulin resistance Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. Insulin resistance conditional specification OBI branch derived OBI_0000349 PlanAndPlannedProcess Branch a directive information entity that specifies what should happen if the trigger condition is fulfilled conditional specification measurement unit label 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. Examples of measurement unit labels are liters, inches, weight per volume. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. OBI Plan and Planned Process/Roles Branch OBI_0000217 PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. goal specification objective specification narrative object 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 A narrative object is an information content entity that is a set of propositions. Examples of narrative objects are reports, journal articles, and patents submission. OBI_0000013 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 group:OBI narrative object person:Chris Stoeckert action specification Alan Ruttenberg OBI Plan and Planned Process branch Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take action specification obsolete_artifact obsolete_artifact true datum label 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label GROUP: IAO datum label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n software GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot 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 software obsolete2_digital entity OBI_0000261 true 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality' 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. group:OBI obsolete2_digital entity person:Chris Stoeckert 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. OBI_0000159 a report that is published in a journal group:OBI journal article person:Alan Ruttenberg person:Chris Stoeckert information carrier 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. 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'. A quality of an information bearer that imparts the information content 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. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier 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. Person: Alan Ruttenberg manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers model number obsolete_material_entity obsolete_material_entity true obsolete2_binary digital entity OBI_0000244 true 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity' 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. MS Word document, ZIP file, DICOM file, JPEG file digital_entity group:OBI obsolete2_binary digital entity person:Chris Stoeckert obsolete_unit of measure Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy The length of a ruler. a unit of measure is the quality of some material entity compared to which another quality is some multiple of. obsolete_unit of measure true programming language 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. OBI_0000058 R, Perl, Java group:OBI person:Alan Ruttenberg person:Chris Stoeckert programming language data item 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/ 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. Data items include counts of things, analyte concentrations, and statistical summaries. JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. data data item symbol 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154). An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. PERSON: James A. Overton PERSON: Jonathan Rees a serial number such as "12324X" a stop sign a written proper name such as "OBI" based on Oxford English Dictionary symbol numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral information content entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). A generically dependent continuant that is about some thing. Examples of information content entites include journal articles, data, graphical layouts, and graphs. OBI_0000142 PERSON: Chris Stoeckert information content entity information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. integer numeral PERSON: Jonathan Rees a numeral that denotes an integer integer numeral scalar measurement datum 1 1 10 feet. 3 ml. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form PERSON: Alan Ruttenberg PERSON: Melanie Courtot Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. scalar measurement datum directive information entity 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO An information content entity whose concretizations indicate to their bearer how to realize them in a process. PERSON: Alan Ruttenberg PERSON: Bjoern Peters Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan directive information entity time trigger OBI branch derived OBI_0000331 PlanAndPlannedProcess Branch revisit? time trigger obsolete_study interpretation 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. OBI_0000005 PERSON: Alan Ruttenberg PERSON: Melanie Courtot conclusion true 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 Lawrence Hunter PERSON: Jennifer Fostel 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. obsolete_study interpretation dot plot 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. Dot plot of SSC-H and FSC-H. OBI_0000123 dot plot group:OBI person:Allyson Lister person:Chris Stoeckert 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. OBI_0000240 PERSON: Lawrence Hunter graph group:OBI person:Alan Ruttenberg person:Allyson Lister obsolete2_text based digital entity OBI_0000132 group:OBI true 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document' A text based digital entity is a digital entity that is encoded so that it only contains text characters. XML file, C++ source code file digital_entity obsolete2_text based digital entity person:Chris Stoeckert rule MSI OBI_0500021 PRS PRS a rule is an executable which guides, defines, restricts actions example to be added rule contour plot Contour plot of SSC-H, FSC-H, and FL1-H. OBI_0000246 contour plot generically_dependent_continuants group:Flow Cytometry community person:Allyson Lister person:Chris Stoeckert obsolete2_report figure OBI_0000027 true 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 group:OBI obsolete2_report figure person:Alan Ruttenberg person:Allyson Lister algorithm A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. OBI_0000270 PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. Philippe Rocca-Serra PlanAndPlannedProcess Branch adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm software interpreter 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 OBI_0000199 R program, Perl interpreter, Java virtual machine group:OBI person:Alan Ruttenberg person:Chris Stoeckert software interpreter curation status specification Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 PERSON:Bill Bug The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. curation status specification density plot 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. Density plot of SSC-H and FSC-H. OBI_0000179 density plot group:Flow Cytometry community person:Allyson Lister person:Chris Stoeckert report 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. GROUP: OBI OBI_0000099 PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert 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) disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification report obsolete_report element 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. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion OBI_0000001 PERSON: Melanie Courtot Replaced by textual entity and figure true 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). GROUP:OBI PERSON: Alan Ruttenberg PERSON: Allyson Lister 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 obsolete_report element obsolete2_binary executable OBI_0000222 true 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' 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) group:OBI obsolete2_binary executable person:Jennifer Fostel source code module A source code module is a directive information entity that specifies, using a programming language, some algorithm. OBI_0000039 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. group:OBI person:Alan Ruttenberg person:Chris Stoeckert source code module obsolete_report table 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 OBI_0000265 true 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 group:OBI obsolete_report table person:Alan Ruttenberg person:Allyson Lister data format specification 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" 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 OBI branch derived OBI_0000187 PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch data format specification data set 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). OBI_0000042 data set group:OBI person:Allyson Lister person:Chris Stoeckert 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. OBI_0000030 group:OBI image person:Alan Ruttenberg person:Allyson person:Chris Stoeckert data about an ontology part Person:Alan Ruttenberg data about an ontology part data about an ontology part is a data item about a part of an ontology, for example a term plan specification 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. Alan Ruttenberg Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI Plan and Planned Process branch OBI_0000344 PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. plan specification obsolete2_digital document OBI_0000195 true 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' 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. group:OBI obsolete2_digital document person:Jennifer Fostel measurement datum 2/2/2009 is_specified_output of some assay? A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. OBI_0000305 group:OBI measurement datum person:Chris Stoeckert obsolete_identifier _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. obsolete_identifier true version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. GROUP: IAO Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version version number 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. GROUP: IAO 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 :-) serial number lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number setting datum 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. A settings datum is a datum that denotes some configuration of an instrument. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum obsolete_digital quality Need to rework digital entity. Digital quality was suggested by Barry. obsolete_digital quality true 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 conclusion textual entity 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. Person:Alan Ruttenberg 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 material information bearer A material entity in which a concretization of an information content entity inheres. A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. GROUP: IAO a brain a hard drive material information bearer histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. GROUP:OBI PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot histogram 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. GROUP:OBI PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot heatmap Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot Venn diagram WEB: http://en.wikipedia.org/wiki/Venn_diagram obsolete_survival curve true 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm obsolete_survival curve dendrogram 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. Dendrograms are often used in computational biology to illustrate the clustering of genes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram 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. Comparison of gene expression values in two samples can be displayed in a scatter plot PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot scattergraph photograph A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph photographic print A photographic print is a material entity upon which a photograph generically depends. PERSON:Alan Ruttenberg PERSON:Melanie Courtot photographic print obsolescence reason specification PERSON: Alan Ruttenberg PERSON: Melanie Courtot The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. obsolescence reason specification textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities text textual entity citation PERSON: Lawrence Hunter 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 citation author identification A textual entity intended to identify a particular author L. Hunter PERSON: Lawrence Hunter author identification institutional identification A textual entity intended to identify a particular institution PERSON: Lawrence Hunter University of Colorado Denver School of Medicine institutional identification caption A textual entity that describes a figure 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. PERSON: Lawrence Hunter caption document title A textual entity that names a document PERSON: Lawrence Hunter Textual characteristics of traditional and Open Access scientific journals are similar document title table 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 PERSON: Lawrence Hunter table | T F --+----- T | T F F | F F table of abbreviations A table where the constituent texts are abbreviations and their expansions IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology PERSON: Lawrence Hunter table of abbreviations figure An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. Any picture, diagram or table PERSON: Lawrence Hunter figure diagram A figure that expresses one or more propositions A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. PERSON: Lawrence Hunter diagram document A collection of information content entities intended to be understood together as a whole A journal article, patent application, laboratory notebook, or a book PERSON: Lawrence Hunter document publication A document that has been accepted by a publisher A journal article or book PERSON: Lawrence Hunter publication publication about an investigation A publication that is about an investigation Most scientific journal articles PERSON: Lawrence Hunter publication about an investigation scientific publication patent A document that has been accepted by a patent authority PERSON: Lawrence Hunter US Patent 6,449,603 patent document part An abstract, introduction, method or results section. PERSON: Lawrence Hunter an information content entity that is part of a document document part abstract A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. PERSON: Lawrence Hunter 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. abstract introduction to a publication about an investigation A part of a publication about an investigation that is about the objective specification (why the investigation is being done) PERSON: Lawrence Hunter Section labelled 'introduction' of a typical scientific journal article introduction introduction to a publication about an investigation methods section A part of a publication about an investigation that is about the study design of the investigation PERSON: Lawrence Hunter The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. methods section results section A part of a publication about an investigation that is about a study design execution PERSON: Lawrence Hunter The section labelled 'results' in a typical scientific journal article results section 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 PERSON: Lawrence Hunter discussion section discussion section of a publication about an investigation references section A part of a document that has citations as parts PERSON: Lawrence Hunter The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" references section author list Lawrence Hunter and Kevin Brettonel Cohen PERSON: Lawrence Hunter author list part of a document that enumerates the authors of the document institution list PERSON: Lawrence Hunter The University of Colorado Denver School of Medicine and the University of Colorado Boulder. institution list part of a document that has parts that are institution identifications associated with the authors of the document author contributions section A part of a publication that is about the specific contributions of each author 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. PERSON: Lawrence Hunter author contributions section acknowledgements section PERSON: Lawrence Hunter Part of a publication that is about the contributions of people or institutions other than the authors. The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript acknowledgements section footnote 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. PERSON: Lawrence Hunter 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. endnote footnote supplementary material to a document PERSON: Lawrence Hunter appendix part of a document that is segregated from the rest of the document due to its size supplementary material supplementary material to a document 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). PERSON: Lawrence Hunter table of contents 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). PERSON: Lawrence Hunter table of figures running title A shorter version of a document title PERSON: Lawrence Hunter running title copyright section A document part that describes legal restrictions on making or distributing copies of the document PERSON: Lawrence Hunter This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. copyright section cartesian spatial coordinate datum 1 AR notes: We need to discuss whether it should include site. 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 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 Alan Ruttenberg cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 one dimensional cartesian spatial coordinate datum 1 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum two dimensional cartesian spatial coordinate datum 1 1 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum three dimensional cartesian spatial coordinate datum 1 1 1 A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum length measurement datum A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum denotator type A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. denotator type mass measurement datum 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A scalar measurement datum that is the result of measurement of mass quality Person:Alan Ruttenberg mass measurement datum hypothesis textual entity 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A textual entity that expresses an assertion that is intended to be tested. Person:Alan Ruttenberg hypothesis 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 time measurement datum 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A scalar measurement datum that is the result of measuring a temporal interval Person:Alan Ruttenberg time measurement datum postal address A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59 postal address email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role data item extraction from journal article a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing Person:Alan Ruttenberg data item extraction from journal article documenting 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. documenting wikipedia http://en.wikipedia.org/wiki/Documenting line graph A line graph is a type of graph created by connecting a series of data points together with a line. GROUP:OBI PERSON:Chris Stoeckert PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Line_chart line chart line graph assigning a centrally registered identifier 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity assigning a centrally registered identifier associating information with a centrally registered identifier in its registry A planned process in which a CRID registry associates an information content entity with a CRID symbol 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. associating information with a CRID in the CRID registry PERSON:Alan Ruttenberg associating information with a centrally registered identifier in its registry obsolete_establishing a CRID 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. obsolete_establishing a CRID registry true MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. centrally registered identifier symbol CRID symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. Original proposal from Bjoern, discussions at IAO calls PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. centrally registered identifier symbol centrally registered identifier CRID 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. Original proposal from Bjoern, discussions at IAO calls PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. centrally registered identifier centrally registered identifier registry CRID registry A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. Original proposal from Bjoern, discussions at IAO calls PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. centrally registered identifier registry looking up a centrally registered identifier A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot looking up a CRID looking up a centrally registered identifier time stamped measurement datum time stamped measurement datum time sampled measurement data set 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. Alan Ruttenberg experimental time series pmid:20604925 - time-lapse live cell microscopy 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. PERSON: Bill Hogan 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. http://code.google.com/p/information-artifact-ontology/issues/detail?id=114 written name software method A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software method software module A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software module software library 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. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software library software application A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software application software script A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software script 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. infection human pathogenicity disposition A disposition to initiate processes that result in a disorder in a human organism. human pathogenicity disposition Mus musculus Mus musculus house mouse mouse Rattus norvegicus Norway rat Rattus norvegicus Rattus sp. strain Wistar brown rat rat rats Viruses Viruses Euteleostomi Euteleostomi bony vertebrates Ecdysozoa Ecdysozoa Pancrustacea Pancrustacea Bacteria Bacteria eubacteria Archaea Archaea Eukaryota Eukaryota eucaryotes eukaryotes Euarchontoglires Euarchontoglires Tetrapoda Tetrapoda tetrapods Amniota Amniota amniotes Opisthokonta Opisthokonta Bilateria Bilateria Arabidopsis thaliana Arabidopsis thaliana mouse-ear cress thale cress thale-cress Murinae Murinae Mammalia Mammalia mammals Dictyostelium discoideum Dictyostelium discoideum Ascomycota Ascomycota ascomycetes sac fungi Schizosaccharomyces pombe Schizosaccharomyces pombe fission yeast Saccharomyces cerevisiae Saccharomyces cerevisiae baker's yeast brewer's yeast lager beer yeast yeast Neurospora Neurospora Caenorhabditis elegans Caenorhabditis elegans nematode Daphnia Daphnia common water fleas saccharomyceta saccharomyceta Drosophila melanogaster Drosophila melanogaster fruit fly Vertebrata <Metazoa> Vertebrata Vertebrata <Metazoa> vertebrates Danio rerio Danio rerio leopard danio zebra danio zebra fish zebrafish Xenopus <genus> Xenopus Xenopus <genus> Gallus gallus Gallus gallus bantam chicken chickens Homo sapiens Homo sapiens human human being man Rodentia Rodentia rodents role of being consumer safety officer Person:Helen Parkinson the role of a human being that is realized by enforcing regulations to ensure consumer safety Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm Jennifer Fostel OBI, CDISC Person charged with serving as CSO, FDA official who coordinates the review role of being consumer safety officer fluorescent reporter intensity group:OBI 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. fluorescent reporter intensity person:Chris Stoeckert planned process 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) 6/11/9: Edited at workshop. Used to include: is initiated by an agent Bjoern Peters Injecting mice with a vaccine in order to test its efficacy We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. branch derived A processual entity that realizes a plan which is the concretization of a plan specification. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process regulator role regulator 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 OBI Person:Jennifer Fostel a regulatory role involved with making and/or enforcing relevant legislation and governmental orders 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. Jennifer Fostel biological feature identification objective regulation-assigned role Approval letter Person: Jennifer Fostel Regulation-assigned role is a regulatory role defined by legislation or governmental orders regulation-assigned role regulatory role GROUP: Role branch OBI, CDISC 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. 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 regulatory role material supplier role Jackson Labs is an organization which provide mice as experimental material Supplier role is a special kind of service, e.g. biobank material provider role supplier PERSON:Jennifer Fostel a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. material supplier role contract research organization role contract research organization Person: Jennifer Fostel 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 group:Flow Cytometry community A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. 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. 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. list-mode data file person:Chris Stoeckert classified data set PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels 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 reference substance role reference substance 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 OBI Person:Jennifer Fostel 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 cytological stain role A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization Person:Helen Parkinson cytological stain haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin Person:Jennifer Fostel cytological stain role centrifuge pellet role 9Mar09 after discussion with process branch changed definition to include use of centrifuge; Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet GROUP: Role branch OBI centrifuge pellet role 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.. clinical research coordinator role clinical research coordinator Person:Jennifer Fostel a worker role comprised of handling the administrative duties of a trial or study. clinical research coordinator role supernatant role GROUP: Role branch OBI 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 open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. Frank Gibson chromatography column http://en.wikipedia.org/wiki/Column_chromatography drug role drug 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. OBI, CDISC Role Branch 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 drug role pump valve switch 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 OBI OBI Instrument branch pump valve switch xenotransplantation OBI branch derived PlanAndPlannedProcess Branch is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans xenotransplantation physical document GROUP: OBI PERSON: Bjoern Peters A physical document is an object serving as a record of information by means of symbolic marks. a book is a physical document physical document waiting BP: I have doubts about the utility of this. OBI branch derived PERSON:Alan Ruttenberg We need a better handling/modeling of time (January 2008) not actively doing anything to a material for a duration of time. waiting processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material chromatography device open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 Frank Gibson 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. chromatography device chromatography instrument http://en.wikipedia.org/wiki/Chromatography mass spectrometer 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 Frank Gibson LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer obsolete_platform OBI Instrument branch OBI Instrument branch suggested for deprecation https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 true A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. obsolete_platform rem1: We decided at the Philly workshop that consumables do not include reagents. FG: we could actully add a relation to platform which would be "has_part some instrument" DS: Sounds fine to me, with the restriction that I would assume a min. cardinality of 2 to be applicable for this crossproduct, so at least 2 instruments make it a platform... at least one is not enough AR:has_part is transitive, and transitive properties can't have cardinality constraints in OWL-DL. We can always put this particular constraint in the owl-full file. We need to make this a defined class when the class software is in the ontology liquid chromatography mass spectrometry platform OBI Instrument branch OBI instrument branch 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. liquid chromatography mass spectrometry platform microarray platform OBI Instrument branch OBI Instrument branch A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. microarray platform ratio of collected to emitted light Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt 10% 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:Chris Stoeckert person:Kevin Clancy ratio of collected to emitted light software optimization objective Jennifer Fostel Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. software optimization objective notified body role notified body 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 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 OBI, CDISC Person: Jennifer Fostel The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf notified body role allotransplantation OBI branch derived PlanAndPlannedProcess Branch allotransplantation is the transplantation of organs between members of the same species. gamma counter A Geiger counter A processed material which measures gamma radiation Frank Gibson gamma counter http://en.wikipedia.org/wiki/Gamma_counter trial monitor role trial monitor 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. Person:Jennifer Fostel a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study trial monitor role positive reference substance role 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 MMS mutagen Person: Jennifer Fostel 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. Philippe Rocca-Serra adapted from Wikipedia before possible import from CHEBI polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether 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 investigation Could add specific objective specification Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation study Bjoern Peters Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS OBI branch derived a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation evaluant role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. GROUP: Role Branch OBI Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role evaluant role examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") reporting party role MO:submitter mapped to this term. So, alternative term 'submitter' was added. Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. reporting party submitter Jennifer Fostel OBI The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm a study personnel role played by a party who reports the outcome of a study component reporting party role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. any method study assay 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. OBI branch derived PlanAndPlannedProcess Branch assay measuring scientific observation quantitative confidence value group:OBI A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert quantitative confidence value sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. OBI branch derived PlanAndPlannedProcess Branch sample preparation for assay study diagnosis textual entity Jennifer Fostel diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. diagnosis textual entity unplanned occurrence effecting an investigation OBI PERSON: Bjoern Peters 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. unplanned occurrence effecting an investigation eMedical record article-without-pmid-or-doi:CDISCglossary 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. eMedical record person:Jennifer Fostel culture medium a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 OBI Person: Jennifer Fostel, Jie Zheng culture medium electronic case report tabulation CDISC glossary 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. electronic case report tabulation person:Jennifer Fostel polystyrene tube PERSON: Chris Stoeckert PERSON: Chris Stoeckert Polystyrene tubes can be used to contain tissue culture cells during centrifgation a polystyrene tube is a test tube made of polystyrene polystyrene tube reagent role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. PERSON:Matthew Brush reagent (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. Buffer, dye, a catalyst, a solvating agent. PERSON:Matthew Brush reagent role role of regulator of chemical manufacturer regulator of chemical manufacture 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 OBI Person: Jennifer Fostel a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture role of regulator of chemical manufacturer detector reagent role 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 a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. detector reagent role role of certified IRB professional Person:Helen Parkinson WEB: http://en.wikipedia.org/wiki/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 certified IRB professional CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional Person:Jennifer Fostel role of certified IRB professional patient role patient CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably GROUP:Role Branch OBI, CDISC a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider patient role material processing A cell lysis, production of a cloning vector, creating a buffer. PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra A planned process which results in physical changes in a specified input material OBI branch derived PERSON: Bjoern Peters material processing material transformation protocol testing objective Jennifer Fostel Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. protocol testing objective participant under investigation role A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. OBI A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS GROUP: Role Branch participant under investigation role obsolete_role of being first subject treated OBI true 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 Rat 1A; first enrolled patient to receive treatment Role Branch first subject treated. First subject who receives the test article or placebo in a clinical trial. obsolete_role of being first subject treated measured expression level OBI Data Transformation branch 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. Examples are quantified data from an expression microarray experiment, PCR measurements, etc. measured expression level person:Chris Stoeckert responsible party role responsible party OBI Person: Jennifer Fostel a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm responsible party role principal investigator role principal investigator CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) Person: Jennifer Fostel a responsible party role played by a person responsible for the overall conduct of a study principal investigator role transplantation OBI branch derived PlanAndPlannedProcess Branch a protocol application to replace an organ or tissue of an organism transplantation biological vector role 6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector) GROUP: Role Branch OBI and Wikipedia 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. false true 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 biological vector role pH indicator dye role Person:Helen Parkinson bromophenol blue has a pH indicator dye role pH indicator dye the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity Person: Jennifer Fostel pH indicator dye role phenol red in RPMI; pH=4 indicator dye (also carries reference role) specimen role 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. GROUP: Role Branch Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. OBI liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. specimen role sequence feature identification objective Jennifer Fostel 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. sequence feature identification objective intervention design 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. OBI branch derived 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. Philppe Rocca-Serra intervention design worker role "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study worker OBI Person:Jennifer Fostel Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline worker role Bernoulli trial Bernoulli trial OBI branch derived PlanAndPlannedProcess Branch is an assay where the output data is a datum with one of two values denoted success and failure. gene list group:OBI 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. 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. gene list 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. person:Chris Stoeckert number of particles in subset Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt 500, 200, 0 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 particles in subset person:Kevin Clancy number of lost events electronic Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt 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. number of lost events electronic person:Kevin Clancy 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 Jennifer Fostel calibration substance role pH buffer used to calibrate a pH meter bears a calibration substance role molecular feature identification objective Jennifer Fostel 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. molecular feature identification objective 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. Jennifer Fostel hardware testing objective incubator Frank Gibson 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 http://www.medterms.com/script/main/art.asp?articlekey=18426 incubator obsolete_label role OBI label true http://purl.obolibrary.org/obo/REO_0000171 MHB (9-26-12): consider deprecation of this class and replacement with REO:'molecular label role' Label role is a role which inheres in a material entity and which is realized in a detection of label assay Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion Role Branch need to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entity obsolete_label role we need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1866458&amp;group_id=177891&amp;atid=886178 baseline participant role a reference participant role which is realized by making the reference to qualities at the start of the study or intervention baseline participant Person: Jennifer Fostel Subject at time = 0; subject before a stress test. baseline participant role role of independent data monitoring committee independent data monitoring committee Person: Jennifer Fostel a trial monitor role charged recommending whether to continue, modify, or end the trial role of independent data monitoring committee pathologist role Pathologist Person:Jennifer Fostel 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 Daniel Schober 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. google supernatant collection system harvesting frame filter paper Frank Gibson a device manufacture with the intent to provide a porous unsized paper used for filtering. filter paper sep:00107 cell co-culturing 2 A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay OBI branch derived PlanAndPlannedProcess Branch cell co-culturing role of Institutional Review Board Animal protocol review board Internal Review Board Person:Helen Parkinson the role of a organization that is realized by members reviewing study designs for their agreement with regulations 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 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. OBI, CDISC Person:Jennifer Fostel role of Institutional Review Board eSource document article-without-pmid-or-doi:CDISCglossary 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 eSource document person:Jennifer Fostel crossover population role a role realized when a participant serves as reference to itself crossover population Person: Jennifer Fostel crossover population role complete nutrient role 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 Person: Jennifer Fostel 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 complete nutrient role radiolabel role Jennifer Fostel a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection radiolabel radiolabel role cDNA library GROUP: PSI 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 PMID:6110205. collection of cDNA derived from mouse splenocytes. PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction cDNA library electronic case report form CDISC glossary 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. electronic case report form person:Jennifer Fostel placebo role 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 placebo 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. Person:Jennifer Fostel Pill consisting of inert materials placebo role autotransplantation OBI branch derived PlanAndPlannedProcess Branch autotransplantation is the transplantation of tissue from one part of \nthe body to another in the same individual. ) parameter threshold Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt 0.01, 0.03 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 parameter threshold person:Kevin Clancy study group role The group of randomized participants that are assigned to a treatment arm of the trial study group population Jennifer Fostel 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 May be outside the scope of OBI long term, is needed so is retained 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). WEB: http://en.wikipedia.org/wiki/P-value 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. PERSON:Chris Stoeckert p-value population 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area adapted from Oxford English Dictionnary population rem1: collection somehow always involve a selection process nuclear magnetic resonance 3D structure determination assay A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. 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). IEDB PlanAndPlannedProcess Branch, IEDB nuclear magnetic resonance 3D structure determination assay imaging assay An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. OBI branch derived PlanAndPlannedProcess Branch imaging assay protocol optimization objective Jennifer Fostel 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. protocol optimization objective role of pathology review board pathology review board Person: Jennifer Fostel a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation role of pathology review board microtiter plate A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) A microtiter_plate is a flat plate with multiple wells used as small test tubes. Melanie Courtot http://en.wikipedia.org/wiki/Microtiter_plate microplate microtiter plate role of impartial witness Person: Helen Parkinson 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 According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html Person: Jennifer Fostel 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 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 OBI 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. chromatin immunoprecipitation biological replicate role a reference participant role realized by equivalent treatment of participants biological replicate A member of a dose-time group; a patient in a given arm of a trial OBI Person:Jennifer Fostel biological replicate role radioactivity detection An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. IEDB 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. PlanAndPlannedProcess Branch, IEDB radioactivity detection investigation agent role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. investigation agent role investigator study person role GROUP: Role Branch OBI 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) 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. The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. nutrient role 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 GROUP: Role branch Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. Wikipedia, feb 29, 2008 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. nutrient role obsolete_dropout role OBI Will be modelled as defined material, ouput of some 'dropout or withdrawal process' instead of role true 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. 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) Role Branch obsolete_dropout role health care provider role health care provider Person:Jennifer Fostel a worker role of providing medical care either within or outside the study timeline health care provider role methodology testing objective Jennifer Fostel 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. methodology testing objective analytical cytology data file group:Flow Cytometry community A digital entity intended to capture data in analytical cytology domain. FCS file, ACS file, foo.fcs, foo.asc analytical cytology data file person:Chris Stoeckert proxy respondent role proxy respondent Jennifer Fostel Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel proxy respondent role fluorescence compensation matrix group:Flow Cytometry community ((1.053096, -0.22476), (-0.24877, 1.053096)) 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. fluorescence compensation matrix person:Chris Stoeckert negative reference substance role 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 Person: Jennifer Fostel Saline solution negative reference substance role role of legally acceptable representative Person:Helen Parkinson 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 OBI, CDISC 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 Person: Jennifer Fostel 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] role of legally acceptable representative investigation results report group:OBI An investigation report is a report on the results of an investigation. investigation results report person:Chris Stoeckert 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. Jennifer Fostel cellular feature identification objective reference subject role reference participant Jennifer Fostel OBI 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 vital dye role 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178 A dye role that is realized when used to detect live cells in an experiment Person: Helen Parkinson typtan blue has a vital dye vital dye Person: Jennifer Fostel vital dye role obsolete_blinded medication 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 Person:Helen Parkinson Will be modelled using a blinding process and specified output blinded medication instead true Inert pill shaped like aspirin tablet Jennifer Fostel obsolete_blinded medication role sub-investigator role sub-investigator 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 Person: Jennifer Fostel a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline sub-investigator role data encoding OBI branch derived PlanAndPlannedProcess Branch We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE a documenting process to encode an information entity into a digital document data encoding storage of measurement results from an assay into a text file, such as enzymatic cleavage OBI branch derived PlanAndPlannedProcess Branch 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 enzymatic cleavage enzymatic cleavage is a protocol application to digest 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. Jennifer Fostel hardware optimization objective obsolete_defined_material OBI Biomaterial derived Susanna Sansone false true Place holder class, Utility class to gather the defined classes obsolete_defined_material trial statistician role trial statistician 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] Person:Jennifer Fostel a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. trial statistician role standard error group:OBI 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. person:Chris Stoeckert see P-Value standard error antigen role 9Mar09 waiting for discussion with immunology terms 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 OBI Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response Role Branch antigen role software testing objective Jennifer Fostel 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. software testing objective sponsor role sponsor 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 Person: Jennifer Fostel a responsible party role involved with any of the following activities: initiating, managing and funding a study sponsor role organization GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. organization feed role 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 OBI Person: Jennifer Fostel 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 feed role technical replicate role technical replicate technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay Aliquots of a tissue subjected to parallel assays Person: Jennifer Fostel 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 dye Jennifer Fostel dye role cluster group:OBI A data set which is a subset of data that are a similar to each other in some way. Cluster of the lymphocytes population. cluster person:Allyson person:Chris Stoeckert cohort role 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. 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 Jennifer Fostel 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. cohort role artificially induced nucleic acid hybridization 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. OBI branch derived PlanAndPlannedProcess Branch 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 DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. DNA extraction OBI branch derived PlanAndPlannedProcess Branch plan The plan of researcher X to perform an experiment according to a protocol. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. AR, BP, JM, MC, PRS branch derived plan obsolete_sample population 03/21/2010: BP, obsoleting this term, as it is duplicated by 'material sample'. Use that instead term instead, which now also has 'sample population' as an alternative label. GROUP: OBI Biomaterial Branch PERSON: Jennifer Fostel PERSON: Philippe Rocca-Serra true 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. 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 obsolete_sample population recruited population organism feature identification objective Jennifer Fostel 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. organism feature identification objective number of lost events computer Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt 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 number of lost events computer person:Kevin Clancy protocol study protocol A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. PlanAndPlannedProcess Branch protocol role of regulator of consumables and medical devices drug regulatoy authority 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 OBI, CDISC Person: Jennifer Fostel 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 role of regulator of consumables and medical devices adding a material entity into a target BP Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. branch derived adding a material entity into a target is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. analyte role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. GROUP: Role Branch Glucose in blood (measured in an assay to determine the concentration of glucose). OBI 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. A 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 analyte role disease stage PERSON: Bjoern peters 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 intraperitoneal injection BP 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 GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra 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 precipitate precipited material protein-protein interaction detection 20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays. An assay with the objective to determine interactions between proteins, such as protein-protein binding. protein-protein interaction detection transcription factor binding site assay OBI Philippe Rocca-Serra JZ: fixed inconsistency issue and relabel the term see tracker: https://sourceforge.net/p/obi/obi-terms/767/ An assay with objective to find DNA region specifically recognized by proteins that function as transcription factors JZ: add equivalent axiom for classification add alternative term 'TF binding' which was used in BCBC database TF binding Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031 transcription factor binding site assay obsolete_enrollment merged with 'enrollment of human subjects true Bjoern Peters 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 IEDB enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules obsolete_enrollment adverse event trigger OBI branch derived PERSON:Alan Ruttenberg adverse event trigger revisit? eluate OBI Bionaterial PERSON: Philippe Rocca-Serra 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 eluate eluted material need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role material to be added role 9 March 09 from discussion with PA branch OBI Role Branch drug added to a buffer contained in a tube; substance injected into an animal; material to be added role material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process obsolete_peritoneum true BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection is the serous membrane that forms the lining of the abdominal cavity obsolete_peritoneum drawing a conclusion based on data Bjoern Peters Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. PERSON: Bjoern Peters PERSON: Jennifer Fostel A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion drawing a conclusion based on data planning 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification planning obsolete_documenting 6/11/9: Edited at workshop. Should go into IAO. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters IAO_0000572 Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. true wikipedia http://en.wikipedia.org/wiki/Documenting obsolete_documenting histological sample preparation OBI branch derived PERSON:Bjoern Peters 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 inductive reasoning Bjoern Peters wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning 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. 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. inductive reasoning mass analyzer Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer 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. The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation mass analyzer hypothesis driven investigation OBI branch derived PlanAndPlannedProcess Branch hypothesis driven investigation is an investigation with the goal to test one or more hypothesis hypothesis generating investigation OBI branch derived PlanAndPlannedProcess Branch hypothesis generating investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis ion source Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source 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 source of a Voyager-DE??? STR Biospectrometry Workstation ion source ion detector Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector 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. The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation ion detector metabolite profiling OBI Philippe Rocca-Serra metabolite assay Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 metabolite profiling metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism light emission function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. light emission function record function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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 record function magnify function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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. magnify function contain function A syringe, a beaker Bill Bug Daniel Schober Frank Gibson Melanie Courtot A contain function is a function to constrain a material entities location in space contain function heat function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A heat function is a function that increases the internal kinetic energy of a material heat function material separation function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. material separation function ionize process 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize Electrospray ionization in mass spectrometry Person:Bjoern Peters 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. ionize process excitation function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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. excitation function freeze function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. freeze function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function perturb function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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. http://en.wikipedia.org/wiki/Perturbation_biology perturb function filter function Frank Gibson A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through filter function mechanical function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). http://en.wikipedia.org/wiki/Mechanical_work mechanical function gas filter function Frank Gibson A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture gas filter function liquid filter function Frank Gibson A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture liquid filter function transfer function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A transfer function is a function to displace a material from one location to another. transfer function electricity supply function Daniel Schober Frank Gibson Melanie Courtot 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. electricity supply function power supply ionization function Bill Bug Daniel Schober Frank Gibson Melanie Courtot The ion source in amass spectrometer 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. http://en.wikipedia.org/wiki/Ionization ionization function cool function Daniel Schober Frank Gibson Melanie Courtot A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. cool function connection function An electricity cable Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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. connection function isoelectric focusing device Frank Gibson sep:00097 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. isoelectric focusing device isoelectric focusing unit thermostatic circulator Frank Gibson sep:00098 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 thermostatic circulator energy supply function Frank Gibson An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy energy supply function information processor function Frank Gibson 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 information processor function signal conversion function Bill Bug Daniel Schober Frank Gibson Melanie Courtot transduction 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. signal conversion function blot module Frank Gibson sep:00092 A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised blot module signal amplification function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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. signal amplification function image acquisition function Frank Gibson An image acquisition function is a function to acquire an image of a material image acquisition function image creation device Frank Gibson sep:00096 An image creation device is a device which captures a digitized image of an object image acquisition device image creation device solid support function Daniel Schober Frank Gibson Melanie Courtot Taped, glued, pinned, dried or molecularly bonded to a solid support A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement solid support function display function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A display function is a function to present information by translating that information through some lookup process into visual form. display function environment control function Bill Bug Daniel Schober Frank Gibson Melanie Courtot An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. environment control function sort function Daniel Schober Frank Gibson Melanie Courtot 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. sort function gel dryer Frank Gibson sep:00094 A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels gel dryer primer role (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 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. primer role PCR product GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. PCR product We are using PCR and not the written out words, as this is the most common used. is double stranded DNA that is the specified output of a polymerase chain reaction viral RNA extraction Person:Bjoern Peters 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 nucleic acid template role 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 GROUP: OBI Biomaterial Branch PERSON: Bjoern Peters PERSON: Kevin Clancy PERSON: Melanie Courtot a plasmid in which extraneous DNA has been inserted. recombinant plasmid cloning vector role PERSON: Helen Parkinson 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 cell cycle synchronization Bjoern Peters and Nicole Washington OBI PA 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 polymerase chain reaction OBI Plan adapted from wikipedai Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 PCR 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. polymerase chain reaction cloning insert role 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" GROUP: Role branch OBII and Wikipedia cloning insert role 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. measuring glucose concentration in blood serum An assay that determines the concentration of glucose molecules in a blood serum sample Person:Bjoern Peters measuring glucose concentration in blood serum reverse transcriptase group:OBI person:Melanie Courtot enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) reverse transcriptase obsolete_trypsinized material A material entity that has undergone a process of digestion with trypsin A trypsinized suspension of cells Person:Bjoern Peters decided to be deprecated on Aug 2, 2010 dev call true Test Class: to evaluate OBI design pattern obsolete_trypsinized material syringe OBI Instrument adapted from Wikipedia Philippe Rocca-Serra 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 syringe extract GROUP: OBI Biomatrial Branch PERSON: Philippe Rocca-Serra Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process extract extracted material transcription profiling assay OBI Philippe Rocca-Serra transcription profiling An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot 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 gene expression profiling transcription profiling assay averaging objective Elisabetta Manduchi PERSON: Elisabetta Manduchi A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. James Malone averaging objective injection OBI Biomaterial Philippe Rocca-Serra 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 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. enzyme GROUP:OBI 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. person: Melanie Courtot (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) enzyme intraperitoneal administration Person:Bjoern Peters 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 group:OBI person:Melanie Courtot plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 injection into organ section A process in which an input substance is injected into a organ section. Person:Bjoern Peters Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology injection into organ section polyacrylamide gel GROUP: OBI Biomaterial Branch PERSON: Jie Zheng PERSON: Philippe Rocca-Serra 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 polyacrylamide gel DNA sequence feature detection An assay with the objective to determine a sequence feature of DNA OBI Person:Bjoern Peters Philippe Rocca-Serra genotyping using an Affymetrix chip DNA sequence feature detection should be a defined class where interpretation of data generated by assay qualifies a DNA sequence adding material objective BP creating a mouse infected with LCM virus adding material objective is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity genotyping assay OBI Biomaterial Philippe Rocca-Serra SNP analysis 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. genotype profiling, SNP genotyping genotyping assay needle OBI Instrument Philippe Rocca-Serra 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. needle analyte measurement objective PERSON: Bjoern Peters PPPB branch 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 DNA sequence variation detection OBI Biomaterial Philippe Rocca-Serra Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 DNA sequence variation detection DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule. agarose gel GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra 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 agarose gel assay objective PPPB branch PPPB branch the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) assay objective obsolete_heart Alan Ruttenberg's heart Person:Bjoern Peters The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions http://en.wikipedia.org/wiki/Heart true unused class. decided to be deprecated on Aug 2, 2010 dev call. Will be imported when need. MC: should be imported obsolete_heart analyte assay PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration')) 2013-09-23: simplify equivalent axiom An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. analyte assay 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 target of material addition role From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. GROUP: Role Branch OBI peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. target of material addition role is a role realized by an entity into which a material is added in a material addition process target of material addition role mass measurement assay Helen Parkinson OBI Philippe Rocca-Serra The patients was weighed and mass was determined to be 47 kilograms a process to determine the mass of an evaluant mass measurement assay obsolete_identification Alan Ruttenberg 2010/11/22: After OBI call. A specific identification objective should be used instead, as necessary Philippe Rocca-Serra See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178 true 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 obsolete_identification intra cellular electrophysiology recording An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular PERSON: Frank Gibson PERSON: Frank Gibson intra cellular electrophysiology recording packed column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 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. PERSON:Daniel Schober WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> packed column obsolete_defined_output PERSON: Alan Ruttenberg PERSON: James Malone PERSON: Melanie Courtot true 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. 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. obsolete_defined_output regulatory agency GROUP: OBI Biomaterial Branch The US Environmental Protection Agency WEB: en.wikipedia.org/wiki/Regulator A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. regulatory agency normalized data set PERSON: James Malone PERSON: Melanie Courtot 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. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. measure function extracellular electrophysiology recording An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data PERSON: Frank Gibson PERSON: Frank Gibson, Helen Parkinson 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 extracellular electrophysiology recording consume data function PERSON: Daniel Schober PERSON: Frank Gibson PERSON: Melanie Courtot 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. consume data function material transformation objective GROUP: OBI PlanAndPlannedProcess Branch PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. artifact creation objective material transformation objective manufacturing GROUP: OBI PlanAndPlannedProcess Branch Manufacturing implies reproducibility and responsibility AR PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process This includes a single scientist making a processed material for personal use. manufacturing manufacturing objective GROUP: OBI PlanAndPlannedProcess Branch PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra is the objective to manufacture a material of a certain function (device) manufacturing objective column chromatography detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077 PERSON:Daniel Schober 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. WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html> chromatography detector, defined class/xps column chromatography detector Bruker autosampler http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 A Bruker autosampler is an autosampler made by Bruker. Bruker autosampler GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober organic acid column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober organic acid column thermal conductivity detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 PERSON:Daniel Schober TCD, hot wire detector 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). WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html> thermal conductivity detector Bruker US 2 NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189 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. Bruker US 2 NMR magnet NMR instrument PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html> protein column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober protein column refactor as defined class solvent mixer http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober check on definition ! solvent mixer mass spectrometry assay An assay that identifies the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles. 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. Philippe Rocca-Serra Philippe Rocca-Serra mass spectrometry assay study design execution 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. a planned process that carries out a study design a planned process that realizes the concretization of a study design branch derived injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. study design execution Bruker NMR Case sample changer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 Bruker NMR Case sample changer NMR instrument PERSON:Daniel Schober 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. WEB:<http://www.bruker-biospin.com/automation.html> nano pump system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052 A pump system optimized for nano flow chromatography. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober nano pump system Bruker AutoClean system http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 Bruker AutoClean system 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. PERSON:Daniel Schober WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> washing system/NMR tube washing system, XPS: device has function washing manual injection system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. manual injection system Varian GEMINI spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239 An older Varian Broadband NMR spectrometer. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober Varian GEMINI spectrometer column connector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography device column connector solid NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243 An NMR probe that is designed to hold a solid sample. GROUP:<http://msi-ontology.sourceforge.net> NMR device PERSON:Daniel Schober solid NMR probe Bruker high resolution probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 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. Bruker high resolution probe GROUP:<http://msi-ontology.sourceforge.net> HR Probe NMR probe PERSON:Daniel Schober chromatography detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> chromatography detector normal phase column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober normal phase column APOLLO console http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249 APOLLO console NMR instrument/NMR console PERSON:Daniel Schober 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. WEB:<http://www.tecmag.com/apollo.htm> NMR sample holder http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212 An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. GROUP:<http://msi-ontology.sourceforge.net> NMR device NMR sample holder PERSON:Daniel Schober chromatography instrument http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 Any instrument that is used to carry out a chromatography experiment. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography device, defined class? chromatography instrument continuous wave NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283 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). NMR instrument PERSON:Daniel Schober WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> continuous wave NMR instrument fourier transformation NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284 GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> 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. NMR instrument PERSON:Daniel Schober fourier transformation NMR instrument nitrogen phosphorous detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 PERSON:Daniel Schober 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. WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> nitrogen phosphorous detector cation exchange column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 A cation exchange column is a chromatography column that is used in cation exchange chromatography. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober cation exchange column direct detection NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 An NMR probe designed to allow the direct detection of acquisition nuclei. GROUP:<http://msi-ontology.sourceforge.net> NMR device PERSON:Daniel Schober direct detection NMR probe Bruker B-ACS system http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 Bruker B-ACS system NMR instrument PERSON:Daniel Schober 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. WEB:<http://www.bruker-biospin.com/automation.html> rapid resolution column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober rapid resolution column liquid chromatography autosampler http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061 Designed to perform capillary LC with injection of sample volumes ranging from nL to L. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober liquid chromatography autosampler vacuum degasser http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/vacuum.html> vacuum degasser capillary column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober capillary column sample inlet http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 PERSON:Daniel Schober 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. WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> chromatography device sample inlet NMR tube washing system http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204 An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument NMR tube washing system PERSON:Daniel Schober NMR console http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015 A component of an NMR instrument that controls the activities of the other components. GROUP:<http://msi-ontology.sourceforge.net> NMR console NMR instrument, TODO: same as or part of acquisition computer? PERSON:Daniel Schober dual loop autosampler http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063 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). PERSON:Daniel Schober WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149> dual loop autosampler variable wavelength detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober variable wavelength detector Bruker LC-NMR platform http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276 hyphenated NMR instrument platform Bruker LC-NMR platform NMR instrument PERSON:Daniel Schober 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. WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html> sample injection system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography device sample injection system multiple wavelength detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078 A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober multiple wavelength detector photoionization detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 PERSON:Daniel Schober PID 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. WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> photoionization detector gas generator http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html> gas chromatography equipment gas generator column jacket http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography device column jacket electron capture detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085 ECD PERSON:Daniel Schober 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. WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> electron capture detector reversed phase column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober reversed phase column injector lubricant http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118 A lubricant used in liquid chromatography that eases sample injector penetration. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober injector lubricant isolation of cell population Person: Bjoern Peters a process in which a population of cells with certain characteristics is isolated from a larger population isolation of cell population removing CD4+ cells from PBMCs using magnetic beads. DISCOVERY console http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247 DISCOVERY console GROUP:<http://msi-ontology.sourceforge.net> NMR instrument/NMR console PERSON:Daniel Schober 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. Bruker AMX series NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 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. Bruker AMX series NMR instrument NMR instrument PERSON:Daniel Schober WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> chromatofocusing column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 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. PERSON:Daniel Schober WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> chromatofocusing column NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014 GROUP:<http://msi-ontology.sourceforge.net> NMR instrument NMR probe PERSON:Daniel Schober 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. NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 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. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument NMR magnet PERSON:Daniel Schober trap column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober trap column flow probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131 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. NMR device PERSON:Daniel Schober WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH> flow probe clinical chemistry assay 3/26/09: There needs to be a restriction set that specifies which type of evaluants are used in the assay, somewhere along the lines of 'sample derived of bodily fluid' Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Mueller T, Schimetta W, Dieplinger B, Loeffler P, Rehm M, Kreimeier U, Poelz W, Haltmayer M. Clin Chem Lab Med. 2008;46(4):558-62. PMID: 18605936 Person: Philippe Rocca-Serra a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism. adapted from Wikipedia chemical pathology clinical chemistry clinical chemistry assay detection of analyte in blood sample flame ionization detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 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. FID PERSON:Daniel Schober WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> flame ionization detector vial http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 A vial is a cylindrical container often made from glass tubing. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober vial magic angle spinning rotor http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 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. MAS rotor NMR instrument PERSON:Daniel Schober WEB:<http://www.freepatentsonline.com/4352066.html> magic angle spinning rotor Varian VXR spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 A Varian NMR spectrometer. NMR instrument PERSON:Daniel Schober Varian VXR spectrometer WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> splitless GC injector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 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. PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> splitless GC injector preparative autosampler http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 For preparative LC with injection of sample volumes ranging from L to mL ranges. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober preparative autosampler flow high resolution probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 GROUP:<http://msi-ontology.sourceforge.net> 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. NMR probe PERSON:Daniel Schober flow HR-probe flow high resolution probe liquid chromatography valve http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> chromatography device liquid chromatography valve JEOL NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 An NMR probe that is manufactured by JEOL. GROUP:<http://msi-ontology.sourceforge.net> JEOL NMR probe NMR device PERSON:Daniel Schober Bruker UltraShield Plus NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 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. Bruker UltraShield Plus NMR magnet NMR instrument PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> Bruker CryoProbe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 Bruker CryoProbe GROUP:<http://msi-ontology.sourceforge.net> NMR probe PERSON:Daniel Schober 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 widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient. column cartridge http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography device, check on definition ! column cartridge affinity column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober affinity column tecmag NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 An NMR instrument that is manufactured by tecmag. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober tecmag NMR instrument gel filtration column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober gel filtration column fraction collector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> fraction collector copy number variation profiling CNV analysis Philippe Rocca-Serra Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796 copy number variation profiling copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping. in-line filter http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 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. PERSON:Daniel Schober WEB:<http://www.appliedporous.com/frits-chromatography.htm> in-line filter imaging NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 An NMR probe that is designed for generating pictures from sample states via NMR imaging. GROUP:<http://msi-ontology.sourceforge.net> NMR device PERSON:Daniel Schober imaging NMR probe isolation of adherent cells 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. isolation of adherent cells Bruker AC series NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 A series of older Bruker NMR magnets, now out of production. Bruker AC series NMR instrument GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober gas chromatography equipment http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 Any device used in a gas chromatography experiment. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober gas chromatography equipment will become defined class/xps syringe filter http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122 A small membrane filter of defined pore size, that filters samples from a syringe. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober syringe filter Bruker SampleRail system http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207 Bruker SampleRail system NMR instrument PERSON:Daniel Schober 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. WEB:<http://www.bruker-biospin.com/automation.html> column compartment http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober column compartment capillary pump system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051 A pump system optimized for capillary chromatography. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober capillary pump system evaporative light scattering detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 PERSON:Daniel Schober 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. WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html> evaporative light scattering detector isolation of PBMCs PERSON: bjoern peters a process in which cells with a single nucleus are isolated from a blood sample 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. isolation of PBMCs wiki http://en.wikipedia.org/wiki/PBMC column cartridger http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 A chromatography device where the column cartridge is inserted into and stabilised. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober check on definition ! column cartridger nitrogen generator http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034 A gas generator that generates nitrogen gas. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober nitrogen generator needle assembly http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet chromatography device, check on definition ! needle assembly reverse transcribed polymerase chain reaction 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation 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 Philippe Rocca-Serra RT-PCR 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. reverse transcribed polymerase chain reaction reverse transcription polymerase chain reaction Bruker Capillary LC-NMR platform http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279 hyphenated NMR instrument platform Bruker Capillary LC-NMR platform 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. NMR instrument PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html> gas chromatography oven http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober gas chromatography equipment gas chromatography oven autosampler http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002 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. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober autosampler isocratic pump system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 A pump system optimized for isocratic chromatography. PERSON:Daniel Schober WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> isocratic pump system flash pump system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048 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). GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober flash pump system Varian UNITY INOVA spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236 NMR instrument PERSON:Daniel Schober 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. Varian UNITY INOVA spectrometer WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH> liquid NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242 An NMR probe that is designed to hold a liquid sample. GROUP:<http://msi-ontology.sourceforge.net> NMR device PERSON:Daniel Schober liquid NMR probe ion exchange column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober ion exchange column Bruker NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 An NMR probe that is manufactured by Bruker. Bruker NMR probe GROUP:<http://msi-ontology.sourceforge.net> NMR device, TODO: May need no definition. PERSON:Daniel Schober anion trap column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober anion trap column fluorescene detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> fluorescene detector tecmag EAGLE probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 GROUP:<http://msi-ontology.sourceforge.net> NMR probe PERSON:Daniel Schober 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. tecmag EAGLE probe electrical conductivity detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 PERSON:Daniel Schober 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. WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> electrical conductivity detector NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 An Instrument which is used to carry out a NMR analysis of some sample. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument NMR instrument NMR instrument PERSON:Daniel Schober Bruker UltraShield NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187 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. Bruker UltraShield NMR magnet NMR instrument PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> piston-seal http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116 PERSON:Daniel Schober 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. WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html> piston-seal mass selective detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198 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. PERSON:Daniel Schober WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> mass selective detector mass spectrometry detector spin column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober spin column manufacturer role GROUP: Role Branch Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. OBI With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. manufacturer role transfer line http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235 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. PERSON:Daniel Schober WEB:<http://www.freepatentsonline.com/5702671.html> chromatography device transfer line gradient pump system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050 A pump system optimized for gradient chromatography. PERSON:Daniel Schober WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html> gradient pump system high temperature column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober high temperature column Bruker Ultrastabilized NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 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. Bruker Ultrastabilized NMR magnet NMR instrument PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> scattered molecular aggregate the sodium and chloride ions in a glass of salt water Collective 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 PERSON: Alan Ruttenberg 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 scattered molecular aggregate obsolete_molecular concentration 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. JZ: Can we replace the term by PATO: http://purl.obolibrary.org/obo/PATO_0000033 If not, we will wait the term available in PATO. Although specified that obsolete reason is 'term imported', the term has not imported yet. Will keep tracking this term until import the replaced term. Term depracted since the object property 'towards' used in the axioms is not avaliable in BFO2. PERSON: Alan Ruttenberg This term represent a quality of molecular concentration. If there is need for some other sort of concentration - e.g. ratio of counts of cells, another term is needed. OBI uses a standard unit for representing concentration qualities but this still needs to be decided on. A relation needs to be defined that relates the quality instance to the representation of its quantitative value in the chosen units. See http://en.wikipedia.org/wiki/Concentration Measurements of concentration may be in any appropriate unit. Note that precise concentrations are virtually never known. Finally, note that there is no such thing as a concentration of 0. A concentration is a *relational* quality and so can't exist unless both entities it inheres in exist. However one map make concentration measurements that turn out not to be about concentrations qualities, if it happens that the scattered molecular aggregate doesn't actually exist. logical definition in OBI: 'quality of related physical entities' ('inheres in' some material_entity) and (towards some 'scattered molecular aggregate') the phosphate concentration should be 0.1M true obsolete_molecular concentration NMR sample tube http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 GROUP:<http://msi-ontology.sourceforge.net> NMR device NMR sample tube PERSON:Daniel Schober The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. Varian UNITY spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237 NMR instrument PERSON:Daniel Schober The predecessor series of the Varian UNITY INOVA spectrometer. Varian UNITY spectrometer WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php> AVANCE II spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197 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. AVANCE II spectrometer NMR instrument PERSON:Daniel Schober WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93> y-column connector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober y-column connector Bruker LC-NMR/MS platform http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 hyphenated NMR instrument platform Bruker LC-NMR/MS platform GROUP:<http://msi-ontology.sourceforge.net> Includes the connection to a high-resolution TOF-LC-MS system. NMR instrument PERSON:Daniel Schober refractive index detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html> refractive index detector anion exchange column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober anion exchange column plunger column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober plunger column flame photometric detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 FPD PERSON:Daniel Schober 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. WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> flame photometric detector chromatography pump system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046 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). PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Column_chromatography> chromatography pump system Bruker 1mm MicroProbe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194 Bruker 1mm MicroProbe GROUP:<http://msi-ontology.sourceforge.net> NMR probe 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 properties\n virtually no salt effect\n discrete samples in tubes that can be sealed and stored\n automation accessory for sample preparation and handling available. PERSON:Daniel Schober Bruker BEST NMR system http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 Bruker BEST NMR system Bruker Efficient Sample Transfer NMR NMR instrument PERSON:Daniel Schober 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. WEB:<http://www.bruker-biospin.com/automation.html> chromatography detector filter http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121 An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography detector filter cation trap column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278 A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober cation trap column column adapter http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 An Adapter that enabled the connection of a column to additional devices. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography device column adapter pulsed amperometric detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240 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). PAD PERSON:Daniel Schober WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L> pulsed amperometric detector Bruker NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 An NMR instrument that is manufactured by Bruker. Bruker NMR instrument GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober Bruker NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186 An NMR magnet that is manufactured by Bruker. Bruker NMR magnet GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober ozone-induced chemiluminescence detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 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. PERSON:Daniel Schober WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> ozone-induced chemiluminescence detector tecmag NMR console http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 An NMR console manufactured by tecmac. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober tecmag NMR console JEOL NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 An NMR instrument that is manufactured by JEOL. GROUP:<http://msi-ontology.sourceforge.net> JEOL NMR instrument NMR instrument PERSON:Daniel Schober chromatography consumable http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 A chromatography consumable is a consumable that is used in a chromatography experiment. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober chromatography consumable chromatography device column frit http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070 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). PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/radial/columns.html> chromatography device column frit liquid chromatography column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober liquid chromatography column detector lamp http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html> detector lamp chart recorder http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober 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. chart recorder chromatography device open tubular column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 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. PERSON:Daniel Schober WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> open tubular column high resolution magic angle spin probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 GROUP:<http://msi-ontology.sourceforge.net> NMR probe PERSON:Daniel Schober 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. high resolution MAS, hr-MAS high resolution magic angle spin probe hydrogen generator http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035 A gas generator that generates hydrogen gas. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober hydrogen generator glass column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober glass column auto injector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 A gas chromatography device that can auto-inject a small number of samples an inlet. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober auto injector Varian NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234 An NMR instrument that is manufactured by Varian. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober Varian NMR instrument Bruker MATCH tube holder system http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 Bruker MATCH tube holder system Bruker Multiple Adjustable Tube Clamp Holder GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober 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 SPE-NMR platform http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278 hyphenated NMR instrument platform 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. Bruker SPE-NMR platform GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober guard column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111 GROUP:<http://msi-ontology.sourceforge.net> 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. PERSON:Daniel Schober chromatography device guard column protein expression profiling OBI branch derived Phlippe Rocca-Serra Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ. Proteome Sci. 2008 Dec 10;6(1):34.PMID: 19077203 a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays protein expression profiling proteomic analysis high resolution probe with automatic tuning and matching http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 GROUP:<http://msi-ontology.sourceforge.net> High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM NMR probe PERSON:Daniel Schober 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 probe with automatic tuning and matching fluorine-induced chemiluminescence detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087 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. PERSON:Daniel Schober WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm> fluorine-induced chemiluminescence detector size exclusion column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober size exclusion column chromatography splitter http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html> chromatography device chromatography splitter Bruker micro imaging probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 Bruker micro imaging probe 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. NMR probe PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/probes_microimaging.html> custom made column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 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. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober custom made column gel permeation column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 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. PERSON:Daniel Schober WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> gel permeation column NMR spectroscopy 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 NMR spectroscopy NMR spectroscopy is a process which 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. Nuclear magnetic resonance spectroscopy Philippe Rocca-Serra adapted from Wikipedia Bruker SampleJet system http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208 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. Bruker SampleJet system NMR instrument PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> JEOL ECX NMR spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227 JEOL ECX NMR spectrometer NMR instrument PERSON:Daniel Schober 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. WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx> DNA sequencing DNA sequencing DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858 OBI Branch derived Philippe Rocca-Serra nucleotide sequencing quaternary pump system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047 A pump system that pump and mix up to four different solvents in parallel. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober quaternary pump system carbon nanotube column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 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. PERSON:Daniel Schober WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> carbon nanotube column Bruker solid magic angle spinning probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193 Bruker solid magic angle spinning probe GROUP:<http://msi-ontology.sourceforge.net> 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. NMR probe PERSON:Daniel Schober solid MAS probe hematology Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943 OBI branch derived Philippe Rocca-Serra blood analysis, haematology hematology hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments Varian MERCURY spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 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. NMR instrument PERSON:Daniel Schober Varian MERCURY spectrometer WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> Bruker Metabolic Profiler http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 hyphenated NMR instrument platform 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. Bruker Metabolic Profiler NMR instrument PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> column heater http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 PERSON:Daniel Schober 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. WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> column heater DNA methylation profiling assay DNA methylation profiling DNA methylation profiling assay 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. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979 OBI branch derived Philippe Rocca-Serra an assay which aims to provide information about 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. JEOL CapNMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 JEOL CapNMR probe NMR probe PERSON:Daniel Schober 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. WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> acquisition computer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 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. GROUP:<http://msi-ontology.sourceforge.net> NMR instrument PERSON:Daniel Schober acquisition computer gas chromatography detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 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. FID PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> chromatography detector, defined class/xps gas chromatography detector gas purifier http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 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. PERSON:Daniel Schober WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> gas chromatography equipment gas purifier material separation objective PPPB branch PPPB branch The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. material separation objective indirect detection probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 An NMR probe designed to allow the indirect detection of acquisition nuclei. GROUP:<http://msi-ontology.sourceforge.net> NMR device PERSON:Daniel Schober indirect detection probe JEOL ECA NMR spectrometer http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 JEOL ECA NMR spectrometer NMR instrument PERSON:Daniel Schober 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. WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> atomic emission detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 AED 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. PERSON:Daniel Schober WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> atomic emission detector clustered data set A clustered data set is the output of a K means clustering data transformation AR thinks could be a data item instead PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels 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. clustered data set data set of features PERSON: James Malone PERSON: Monnie McGee 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 objective differential expression analysis and that consists of James Malone Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation urine specimen 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 a portion of urine collected from an organism are we happy calling collection of urine a material separation? urine specimen material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. bp bp created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. material combination fuzzy clustering objective PERSON: James Malone PERSON: Ryan Brinkman 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. James Malone fuzzy clustering objective device setting 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 PERSON: Frank Gibson a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device device setting blood specimen Bjoern Peters Bjoern Peters a material entity derived from a portion of blood collected from an organism blood drawn from a human for glucose assay blood specimen data set of predicted values according to fitted curve PERSON: James Malone PERSON: Monnie McGee 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 set of predicted values according to fitted curve data representational model 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 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. GROUP: OBI Melanie Courtot data representational model data structure data structure specification gene regulatory graph model phylogenetic tree protein interaction network specimen collection process 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop A planned process with the objective of collecting a specimen. Bjoern Peters Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. specimen collection process 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. specimen collection 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/ 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 background corrected data set PERSON: James Malone PERSON: Melanie Courtot A data set that is produced as the output of a background correction data transformation. background corrected data set enzyme-linked immunosorbent assay 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. ELISA IEDB IEDB enzyme-linked immunosorbent assay error corrected data set PERSON: James Malone PERSON: Monnie McGee 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 James Malone supervised classification data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. PERSON: James Malone class prediction data transformation BrdU incorporation assay 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. BrdU incorporation assay IEDB IEDB 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. obsolete intracellular cytokine staining assay ICS ICCS IEDB IEDB 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. intracellular cytokine staining (ICS) obsolete intracellular cytokine staining assay true background correction data transformation James Malone A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. PERSON: James Malone background correction data transformation obsolete MHC multimer staining assay 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 IEDB IEDB MHC tetramer assay MHC tetramer/multimer staining 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. obsolete MHC multimer staining assay true error correction data transformation EDITORS Monnie McGee 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. James Malone error correction data transformation tritiated thymidine incorporation assay 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. IEDB IEDB 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. tritiated thymidine incorporation assay sample from organism 5/29: This is a helper class for now a material obtained from an organism in order to be a representative of the whole sample from organism we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. statistical hypothesis test James Malone A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. PERSON: James Malone statistical hypothesis test center value PERSON: James Malone PERSON: Monnie McGee median 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 Person:Helen Parkinson WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing 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 James Malone statistical hypothesis test objective reduced dimension data set PERSON: James Malone PERSON: Monnie McGee 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 portioning objective A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. The objective to obtain multiple aliquots of an enzyme preparation. portioning objective average value PERSON: James Malone PERSON: Monnie McGee arithmetic mean A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. average value whole organism preparation 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. putting a mouse in the blender. Not: putting a mouse on a scale whole organism preparation separation into different composition objective A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). The objective to obtain cells contained in a sample of blood. We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective obsolete_study result 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 GROUP: OBI Study result is an information content entity that is a specified data output of a study. obsolete_study result true specimen collection objective A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. specimen collection objective creating a mixture of molecules in solution Bjoern Peters PERSON: Helen Parkinson The production of PBS 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. material combination objective PPPB branch bp is an objective to obtain an output material that contains several input materials. material combination objective nucleotide overhang cloning Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs Helen Parkinson Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation nucleotide overhang cloning rodent care protocol A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. Bjoern Peters Bjoern Peters Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. rodent care protocol 454 Genome Sequence 20 454 Genome Sequence 20 GS 20 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. Philippe Rocca-Serra is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. immunoprecipitation OBI plan and planned process branch PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. Philippe Rocca-Serra immunoprecipitation is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity ABI 377 automated sequencer ABI 377 automated sequencer Applied Biosystems Philippe Rocca-Serra 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. recombination enzyme based cloning 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 recombination enzyme based cloning MeDIP-seq assay MeDIP-seq assay Methylated DNA immunoprecipitation sequencing assay PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. Philippe Rocca-Serra adapted from wikipedia is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on 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. animal feeding Bjoern Peters In an investigation, this will typically be part of an animal care process animal feeding animal feeding is a process in which animals are provided with food branch derived giving crickets to a snake. chain termination sequencing PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. Philippe Rocca-Serra Sanger sequencing adapted from wikipedia chain termination sequencing dye terminator sequencing is a DNA sequencing 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 AB SOLiD System AB SOLiD System Applied Biosystems PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. Philippe Rocca-Serra is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Helicos sequencing Helicos sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9. Philippe Rocca-Serra adapted from wikipedia is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. true single molecule sequencing obsolete_DNA ligase 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule Kevin Clancy, Bjoern Peters ligase obsolete_DNA ligase replaced by imported PRO: DNA ligase true survival assessment Need to point out more specifically that survival / death is measured. Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time survival assessment support vector machine 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. James Malone PERSON: Ryan Brinkman Ryan Brinkman SVM support vector machine self-organizing map 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. James Malone PERSON: Ryan Brinkman Ryan Brinkman SOM self-organizing map 454 Genome Sequencer FLX 454 GS FLX 454 Genome Sequencer FLX GS-FLX 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. Philippe Rocca-Serra 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 is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Illumina Genome Analyzer II Illumina Corporation Illumina Genome Analyzer II PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. Philippe Rocca-Serra 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 decision tree induction objective 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. James Malone decision tree induction objective Edman degradation 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. Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. Edman degradation IEDB IEDB SOLiD sequencing 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. Philippe Rocca-Serra SOLiD sequencing adapted from Wikipedia and Applied Biosystems web site is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. 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 James Malone A decision tree building data transformation is a data transformation that has objective decision tree induction. PERSON: James Malone decision tree building data transformation laboratory animal care a process that realizes an animal care protocol that specifies how animals are kept and maintained laboratory animal care yeast artificial chromosome vector Kevin Clancy, Bjoern Peters YAC 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 yeast artificial chromosome vector Li-Cor 4300 DNA Analysis System Li-Cor 4300 DNA Analysis System OBI and Li-Cor Philippe Rocca-Serra is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing library preparation 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. Philippe Rocca-Serra 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. library construction library preparation pathogen challenge A pathogen challenge is the administration of a live pathogenic organism to a host pathogen challenge GenePattern software GenePattern software James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. graph of vertices 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. Bjoern Peters Chris Stoeckert For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. James Malone WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html graph of vertices animal care protocol An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes Bjoern Peters Bjoern Peters Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. animal care protocol ChIP-seq assay ChIP-seq assay PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9. Philippe Rocca-Serra adapted from Wikipedia an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. chromatin immunoprecipitation sequencing assay made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes HeliScope Single Molecule Sequencer HeliScope Single Molecule Sequencer Philippe Rocca-Serra is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry pathogen role 6 April 2009: from the Vaccine Community GROUP: Role Branch OBI 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 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 vaccine preparation OBI The production of B. pertussis vaccine. vaccine preparation vaccine preparation is a planned process with specified output a vaccine immunologic adjuvant role 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'. 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 GROUP: Role branch 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 The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. Vaccine Ontology, Wikipedia, OBI immunologic adjuvant role glucose tolerance test NuGO OBI plan branch PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9. Philippe Rocca-Serra glucose tolerance test is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. 30-10-2013:[author: PRS] removing "realizes some (concretizes some 'time series design')" axiom as it causes 'gtt' to be classified under study design execution instead of assay paired-end library 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. Philippe Rocca-Serra adapted from information provided by Solid web site is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs mate-paired library paired-end library paired-end tag (PET) library DNA sequencing by ligation DNA sequencing by ligation PERSON: Philippe Rocca-Serra PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22. is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step. Solexa sequencing PMID: 18987734 Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9. Philippe Rocca-Serra Solexa sequencing adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009) is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow 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. reversible terminator sequencing host role 30 Mar09 submitted by vaccine community 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 GROUP: Role Branch 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 OBI host role 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 http://en.wikipedia.org/wiki/Host_(biology) peak matching James Malone PERSON: Ryan Brinkman 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 Ryan Brinkman peak matching k-nearest neighbors k-NN 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. James Malone PERSON: James Malone k-nearest neighbors rodent care PPPB branch PPPB branch keeping animal rodent care 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. cloning plasmid 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 cloning plasmid pyrosequencing Philippe Rocca-Serra Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review. Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site is a DNA sequencing which allows sequencing of 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. pyrosequencing recombinant vector 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. recombinant vector restriction enzyme 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments Kevin Clancy, Bjoern Peters The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG an enzyme that has a specific target cleavage sites within nucleic acids restriction enzyme DNA sequencing by synthesis DNA sequencing by synthesis PERSON: Philippe Rocca-Serra PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25. is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. NTP-2000 Jennifer Fostel, Bjoern Peters NTP-2000 a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents single fragment library Philippe Rocca-Serra fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs single fragment library cloning vector 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. cloning vector restriction enzyme based cloning Kevin Clancy, Bjoern Peters restriction enzyme based cloning 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. Student's t-test James Malone 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. Student's t-test WEB: http://en.wikipedia.org/wiki/T-test material sample role 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. material sample role topologically preserved clustered data set 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. James Malone PERSON: James Malone the output data set generated from a self-organizing map. topologically preserved clustered data set nucleic acid restriction enzyme digest 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 Kevin Clancy, Bjoern Peters nucleic acid restriction enzyme digest immune response assay an assay with the objective to determine information about an immune response immune response assay material sampling process A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity material sampling process material sample A material entity that has the material sample role OBI: workshop blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. material sample sample sample population bisulfite sequencing 8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing. An assay which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. 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. Genome Res. 2009 Jul 6. Philippe Rocca-Serra adapted from Wikipedia bisulfite sequencing CART classification and regression trees 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. CART James Malone study design independent variable 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables study factor 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. 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 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 independent variable experimental factor 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. study design independent variable study design dependent variable 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 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. dependent variable 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 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. study design dependent variable anticoagulant-containing test tube 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A 'blue top' test tube that contains anticoagulant for storing blood specimens' Person:Alan Ruttenberg anticoagulant-containing test tube study design controlled variable 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Control_variable In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling 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. 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 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. controlled variable study design controlled variable human antithrombin-III (AT-III) in blood assay An assay to measure the amount of antithrombin III in blood. PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. Person:Alan Ruttenberg WEB:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 human antithrombin-III (AT-III) in blood assay fluorescently labeled MHC multimer 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 fluorescently labeled MHC multimer survival rate 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. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate recombinant BAC cloning 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 http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome recombinant BAC cloning multiple testing correction objective A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously Application of the Bonferroni correction http://en.wikipedia.org/wiki/Multiple_Testing_Correction multiple comparison correction objective multiple testing correction objective statistical model validation A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson 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 http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation double blind study execution 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 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 Person:Alan Ruttenberg double blind study execution http://clinicaltrials.gov/ct2/info/glossary#double transcription factor binding site PLace_holder for sequence ontology term SO:0000235 transcription factor binding site glucometer A measurement device with the function to measure and record the level/amount of glucose in a blood sample Diabetic patients use glucometers to determine their glucose levels PERSON:Frank Gibson PERSON:Helen Parkinson glucometer glucose meter http://en.wikipedia.org/wiki/Glucose_meter purification objective 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality BP PERSON:Bjoern Peters 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 isolation objective purification objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. obsolete_primary structure of protein Person:Bjoern Peters 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 obsolete_primary structure of protein replaced by SO_0000104 polypeptide true capsule shell 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg a small rounded gelatinous container capsule shell http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n recombinant phage cloning Helen Parkinson 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. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 recombinant phage cloning cross linking A process in which bonds are created that link one polymer to another PERSON: Chris Stoeckert cross linking cross linking can be used as a probe to link proteins together, to check protein protein interactions http://en.wikipedia.org/wiki/Cross-link spike train datum A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. Helen Parkinson, Alan Ruttenberg Jessica Turner, NIF Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog needs more work to see exactly what the data set looks like - HP spike train datum spike train measurement prothrombin time assay 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). Person:Alan Ruttenberg The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma. WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 prothrombin time assay denaturing Denaturing DNA in alcohol Is a process in which the tertiary or secondary structure of a polymer is disrupted denaturing http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 informing investigator of subject study arm 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 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 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. Person:Alan Ruttenberg informing investigator of subject study arm antithrombin-III (AT-III) berichrome assay 1 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 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 WEB:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 antithrombin-III (AT-III) berichrome assay todo Reagents from Berichrom(r) Antithrombin III (A) and standard human plasma material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters material maintenance objective PERSON: Bjoern Peters presentation of stimulus Helen Parkinson, Jessica Turner, Dirk Derom Helen Parkinson, Jessica Turner, Dirk Derom 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 presentation of stimulus stimulation of organism spectrolyse heparin antifactor-Xa assay 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma. The principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, 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. PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). Person:Alan Ruttenberg WEB:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 spectrolyse heparin antifactor-Xa assay amplified DNA Alan Ruttenberg Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg amplified DNA informed consent process 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed informed consent process primary structure of DNA macromolecule BP et al a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO primary structure of DNA macromolecule measuring neural activity in the caudate nucleus 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 Helen Parkinson Jessica Turner, NIF, Dirk Derom, OBI The process of measuring neural activity in the caudate nucleus measuring neural activity in the caudate nucleus to be treated with active ingredient role 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 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 PERSON: Helen Parkinson Person:Alan Ruttenberg Role of a patient in a group treated with an active substance in a clinical trial to be treated with active ingredient role guar gum 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. Helen Parkinson guar gum http://en.wikipedia.org/wiki/Guar_gum Berichrom(r) Antithrombin III (A) Kit 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Berichrom(r) Antithrombin III (A) Kit 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 Person:Alan Ruttenberg WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06 micro electrode 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. Helen Parkinson, Jessica Turner, Dirk Derom Jessica Turner, Dirk Derom micro electrode micro electrode measuring device fucoidan 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). Helen Parkinson fucoidan http://en.wikipedia.org/wiki/Fucoidan calibration 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. GROUP: OBI Philly workshop WEB:http://en.wikipedia.org/wiki/calibration calibration the process of using pH buffer adjust a pH meter anticoagulant tube storage of blood specimen 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg Storage of a blood specimen in a tube with anticoagulant anticoagulant tube storage of blood specimen activated partial thromboplastin time (aPTT) assay 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms. PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent. Person:Alan Ruttenberg WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06 activated partial thromboplastin time (aPTT) assay filled capsule 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A pill in the form of a small rounded gelatinous container with medicine inside. Person:Alan Ruttenberg filled capsule http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n single blind study execution 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 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 Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#single single blind study execution thrombin time assay 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time PMID:19696660#The thrombin time was determined using thromboclotin assay kit. Person:Alan Ruttenberg WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 thrombin time assay recombinant YAC cloning Helen Parkinson 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 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 recombinant YAC cloning to be treated with placebo role 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 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 Person:Alan Ruttenberg to be treated with placebo role treatment portion of study execution 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A planned process, part of a study design execution, during which the treatment of subjects is ongoing Person:Alan Ruttenberg treatment portion of study execution pill 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A dose of medicine or placebo in the form of a small pellet. Person:Alan Ruttenberg http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n pill research organization An organization formed with a goal to have its members conduct investigations Person:Bjoern Peters The SALK institute is a research organization. research organization obsolete_primary structure of sequence macromolecule 2010-06-28 Alan Ruttenberg. This term and its children to be replaced by sequence ontology terms once we figure out what the right terms are . 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 Person:Bjoern Peters These are all placeholders and should be replaced by SO terms obsolete_primary structure of sequence macromolecule replaced by SO_0000001 region these are not in great shape yet; need to clarify how what a 'sequence macromolecule is' and how it differes from molecules in general (directivity of certain bonds, linear connectivity along that type of bond etc.) true DNA residue methylation DNA residue methylation a quality of a DNA residue that has a methyl group attached to it measurement device A device in which a measure function inheres. A ruler, a microarray scanner, a Geiger counter. GROUP:OBI Philly workshop OBI measurement device high molecular weight DNA extract Extraction of chromosomal DNA from mammalian cells by first isolating nucei OBI PERSON:Chris Stoeckert The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. high molecular weight DNA extract manufacturer A person or organization that has a manufacturer role manufacturer test tube A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material Bjoern Peters collection tube http://en.wikipedia.org/wiki/Test_tube sample tube test tube oral ingestion of pill 2009/09/28 Alan Ruttenberg. Fucoidan-use-case An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg oral ingestion of pill material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance labeled oligonucleotide 2010-01-31: Philippe Rocca-Serra placeholder Person: Philippe Rocca-Serra 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 labeled oligonucleotide unblinding process 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg 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 unblinding process subject agrees they understand informed consent document 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 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A process in which a subject receives an informed consent document and agrees that they have understood it Person:Alan Ruttenberg subject agrees they understand informed consent document informing subject of study arm 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 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 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. Person:Alan Ruttenberg informing subject of study arm Sysmex CA-6000 Coagulation Analyzer 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg Sysmex CA-6000 Coagulation Analyzer The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 hospital 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A medical organization at which sick or injured people are given clinical care Person:Alan Ruttenberg Person:Helen Parkinson hospital http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n 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] modified from the wording of the wordnet definition primary structure of RNA molecule Person:Bjoern Peters 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 primary structure of RNA molecule test substance role 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 Group:OBI Person:Alan Ruttenberg fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally test substance role polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction organellar RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group organellar RNA extraction obsolete_diethyl pyrocarbonate Replaced by CHEBI_59051 Diethylpyrocarbonate obsolete_diethyl pyrocarbonate true record of missing knowledge A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. Bjoern Peters This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. a information content entity created to indicate that information about something is not available to the person recording it. record of missing knowledge western blot analysis 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. Philippe Rocca-Serra, IEDB Philippe Rocca-Serra, IEDB 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. western blot analysis total RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group total RNA extraction 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. intracellular staining obsolete intracellular material detection by flow cytometry assay true complementary nucleotide probe role 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 PERSON:Bjoern Peters complementary nucleotide probe role record of unknown sex 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. Bjoern Peters 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 record indicating that the biological sex of an organism is not known. record of unknown sex cytoplasmic RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group cytoplasmic RNA extraction northern blot analysis 2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K. Person: Philippe Rocca-Serra a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager northern blot northern blot analysis Likelihood-ratio test 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. Likelihood-ratio test Tina Boussard nuclear RNA extract 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. 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) PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group nuclear RNA extract 96-well neutralization assay 96-well neutralization assay A serum neutralization of viral infectivity assay which done in a 96-well plate. MC: 20100217: microneutralization is used by the influenza community, to refer to a nutralizationassay at a smaller scale. However smaller is difficult to define accurately, and we therefore chose a label being more specific. microneutralization assay person: Bjoern Peters person: Melanie Courtot establishing cancer cell line Establishment of HeLa immortal cell line Helen Parkinson establishing cancer 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 pattern matching objective 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. Tina Boussard http://en.wikipedia.org/wiki/Pattern_matching pattern matching objective polyA RNA extract 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. PERSON: Chris Stoeckert PERSON: Jie Zheng 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.) UPenn Group polyA RNA extract single-nucleotide-resolution nucleic acid structure mapping assay 2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy. Person: Philippe Rocca-Serra RNAO is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. single-nucleotide-resolution nucleic acid structure mapping assay viral hemagglutination assay HA HI The viral hemagglutination assay (HA) is a quantification of viruses by hemagglutination. WEB: http://en.wikipedia.org/wiki/Hemagglutination_assay person: Bjoern Peters person: Melanie Courtot viral hemagglutination assay viral hemeagglutination assay serum neutralization of viral infectivity assay A quantitative assay where 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 simple process of dilution provides a way to compare the virus- neutralizing abilities of different sera. The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. MC, 20100217: I added influenza neutralization assay as alternative term. This should be tagged with a community specific value, eg "influenza ontology" or else. WEB: http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ influenza neutralization assay person: Bjoern Peters person: Melanie Courtot serum neutralization of viral infectivity assay pre-mortem specimen Bjoern Peters a specimen that was taken from a live organism material obtained through a liver biopsy from a human patient pre-mortem specimen MO_705 premortem detection of specific nucleic acid polymers with complementary probes 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. IEDB IEDB Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. detection of specific nucleic acid polymers with complementary probes viral hemagglutination inhibition assay 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 hemagglutination inhibition by the antibody. Bjoern and Melanie Bjoern and Melanie 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. viral hemagglutination inhibition assay cytoplasmic RNA extract A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. 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.) PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group cytoplasmic RNA extract cell line immortalization 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. Bjoern Peters OBI 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 cell line immortalization 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' random primed DNA labeling 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. PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9. Person: Bjoern Peters Person: Chris Stoeckert Person: Philippe Rocca-Serra 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 random primed DNA labeling RNA extract Group: UPenn Group PERSON: Chris Stoeckert PERSON: Jie Zheng RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. cell-cell killing assay A cytometry assay that monitors a cell population to track how many are killed by other cells. 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. IEDB IEDB cell-cell killing assay in vivo cell killing assay A cell killing assay that measures if and how many target cells are killed within an organism. IEDB IEDB 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. in vivo cell killing assay secondary structure of sequence macromolecule 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 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. Person: Philippe Rocca-Serra Wikipedia secondary structure of sequence macromolecule nuclear RNA extraction A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group nuclear RNA extraction 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm survival curve cell proliferation assay A cytometry assay which measures the degreee to which input cells are replicating. IEDB IEDB Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. cell proliferation assay Southern blot analysis 2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe' 2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern. OBI & Wikipedia PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3. Person: Philippe Rocca-Serra Southern blot Southern blot analysis Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. real time polymerase chain reaction assay A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify 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. Q-PCR WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction kinetic polymerase chain reaction person: Bjoern Peters person: Melanie Courtot qPCR quantitative real time polymerase chain reaction real time PCR real time polymerase chain reaction assay protein extract OBI & wikipedia 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. Person: Philippe Rocca-Serra 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, protein extract total RNA extract A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. Extraction of total RNA from cells with Qiagen mini RNeasy kit. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group total RNA extract secondary structure of RNA molecule 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 PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. Person: Philippe Rocca-Serra secondary structure of RNA molecule DEPC structure mapping assay DEPC structure mapping assay PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. Person: Philippe Rocca-Serra RNA ontology is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure organellar RNA extract 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. Extraction of organellar RNA from plant cells using organellar RNA binding protein. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group organellar RNA extract post mortem specimen Bjoern Peters a specimen that was taken from a dead organism post mortem specimen the spleen taken from a dead mouse MO_416 postmortem in vitro cell killing assay A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. 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. IEDB IEDB in vitro cell killing assay reporter cell line analyte detection bioassay 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. 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. IEDB IEDB reporter cell line analyte detection bioassay sequence feature annotation Bjoern Peters Bjoern Peters Information about a sequence region place holder for sequence ontology term sequence feature annotation induced hemagglutination 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'. The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination hemeagglutination induced hemagglutination person: Bjoern Peters person: Melanie Courtot supplying 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. Jackson Labs supplies mouse strains. Jennifer Fostel Jennifer Fostel The planned process of providing material entities to be used in an investigation. supplying labeled DNA extract Group: OBI group Group: OBI group 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 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. labeled DNA extract cloacal specimen 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. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf cloacal specimen type of sample used in the PCIRN influenza network radio immuno 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. IEDB IEDB To evaluate the specificity of antibody binding to 35S-labeled IA-2(256‰ÛÒ760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256‰ÛÒ760) fragments were tested. Unlabeled recombinant IA-2(256‰ÛÒ760) 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 4å¡C with patient sera. The following day, after incubation with radiolabeled 35S‰ÛÒIA-2(256‰ÛÒ760) or 35S‰ÛÒIA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. radio immuno assay real time reverse-transcription polymerase chain reaction assay Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) PERSON: Bjoern Peters PERSON: Melanie Courtot RRT-PCR RT-rt PCR qRT-PCR real time reverse-transcription polymerase chain reaction assay X-ray crystallography assay A 3D 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. Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. IEDB IEDB X-ray crystallography assay 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. IEDB IEDB promoter activity detection by reporter gene assay nasopharyngeal aspirate specimen A speciemn which derives from nasopharyngeal mucosa after aspiration. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasopharyngeal aspirate specimen type of sample used in the PCIRN influenza network freezing storage 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. A storage process in temperature that maintenance the frozen status of the stored entities. OBI Person: Alan Ruttenberg, Mathias Brochhausen a fozen pellet used for later assay freezing storage MO_481 frozen_storage flow cytometry assay 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. IEDB IEDB 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. flow cytometry assay nasal swab specimen 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. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasal swab specimen type of sample used in the PCIRN influenza network Dulbecco's modified Eagle medium A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. D-MEM DMEM Dulbecco's modified Eagle medium Logical definition should contain all components listed in textual definition at some point. PERSON:Bjoern Peters animal euthanization 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 Helen Parkinson and Melissa Haendel Melissa Haendel Rats were euthanized with CO2 animal euthanization animal sacrifice may later be refined with more specific list of organisms cytometric bead array assay An analyte assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes. IEDB IEDB Luminex assay Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. cytometric bead array assay labeled RNA extract Group: OBI group Group: OBI group 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 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. labeled RNA extract frozen specimen A specimen that has been frozen in order to store it. Frozen blood plasma MO_610 frozen_sample Person:Alan Ruttenberg frozen specimen surface plasmon resonance binding assay 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. IEDB IEDB 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. surface plasmon resonance binding assay labeled specimen A specimen that has been modified in order to be able to detect it in future experiments OBI group added during call 3/1/2010 labeled specimen infectious agent IEDB IEDB infectious agent is a material entity bearing the disposition to infect an organism obsolete_ambidexterious handedness obsolete_ambidexterious handedness true lyophilization storage PERSON: Chris Stoeckert PERSON: Jie Zheng a storage process with input material entity and output freeze dried material for long time storage can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed lyophilization storage material combination function A material separation function is a function that decreases the resolution between two or more material entities. A stirrer has a material combination function Helen Parkinson OBI material combination function obsolete_training service provider role EBI provides training on databases and tools and has a training service provider role OBI PERSON:Helen Parkinson a service provider role which is realized by a servicer provider organization performing some training obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service. obsolete_training service provider role true calorimeter A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. PERSON:Bjoern Peters calorimeter calorimetry instrument? http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm study intervention GROUP: OBI PERSON: Bjoern Peters study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study material separation device A device with a separation function realized in a planed process flow cytometer material separation device positron emission tomography scanner 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. PERSON:Bjoern Peters PET scanner? http://en.wikipedia.org/wiki/Positron_emission_tomography positron emission tomography scanner intramuscular injection intramuscular injection 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 micromanipulator 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. PERSON:Bjoern Peters http://en.wikipedia.org/wiki/Micromanipulator micromanipulator obsolete_material access provider role A person or organization who provides access to a DNA sequencer. OBI PERSON:Helen Parkinson a service provider role which is realized by a servicer provider organization performing access to some material obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service. obsolete_material access provider role true obsolete_left handedness obsolete_left handedness true categorical measurement datum A measurement datum that is reported on a categorical scale Bjoern Peters Bjoern Peters categorical measurement datum nominal mesurement datum training process a process that achieves a training objective e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility training process optical microscope A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range PERSON:Bjoern Peters optical microscope service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer OBI Person:Helen Parkinson a role which inheres in a person who uses a service service consumer role intradermal injection PERSON: Melanie Courtot intradermal injection 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 chemical cleavage PERSON:Philippe Rocca-Serra 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. RNA ontology group chemical cleavage 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 handedness assay A handedness assay 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. Helen Parkinson The Edinburgh handedness assay is a specific method of determing handedness handedness assay handedness test http://en.wikipedia.org/wiki/Handedness vibration isolation table A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. PERSON:Bjoern Peters United States Patent 6877711 vibration isolation table sterilization function a function to remove viable organisms from an input material sterilization function service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. PERSON:Helen Parkinson is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person service provider role oscilloscope 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). PERSON:Bjoern Peters http://en.wikipedia.org/wiki/Oscilloscope oscilloscope accessed material role 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 accessed material role is realized in a planned process where the bearer participates the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism paraffin specimen MO_990 paraffin_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin liver tissue embedded in paraffin paraffin specimen compound treatment design MO_555 compound_treatment_design PERSON: Bjoern Peters This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. an intervention design in which the treatment is the administration of a compound compound treatment design oral administration PERSON: Melanie Courtot The administration of a substance into the mouth of an organism oral administration processed specimen A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A tissue sample that has been sliced and stained for a histology study. subcutaneous injection PERSON: Melanie Courtot 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 subcutaneous injection electrode puller 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. PERSON:Bjoern Peters electrode puller http://faculty.plattsburgh.edu/donald.slish/Puller1.html obsolete_handedness obsolete_handedness true http://purl.obolibrary.org/obo/PATO_0002201 self reported handedness assessment An assay in which a person makes a statement that indicates what handedness he has from a choice of different categories. self reported handedness assessment vibrotome A preparation device that uses a vibrating razor blade to cut through tissue. vibrotome reagent application function 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? A function that is realized when a reagent is automatically added to some research material. An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. PERSON: Nicole Vasilevsky, Matthew Brush PERSON: Nicole Vasilevsky, Matthew Brush reagent application function addition of molecular tracer function A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. Immunohistochemical labeling of tissue sections by an autostainer staining system. PERSON: Nicole Vasilevsky, Matthew Brush PERSON: Nicole Vasilevsky, Matthew Brush addition of molecular tracer function training objective A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package An training objective which is fulfilled by the provision of some training Helen Parkinson OBI training objective categorical label A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters 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. categorical label in live cell assay An assay in which a measurement is made by observing entities located in a live cell. in live cell assay lyophilized specimen MO_589 freeze_dried_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. freezing dried DNA lyophilized specimen in live organism assay An assay in which a measurement is made by observing entities located in an organism. Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. PERSON:Bjoern Peters in live organism assay in vivo assay container 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) A device that can be used to restrict the location of material entities over time PERSON: Bjoern Peters container device 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. OBI development call 2012-12-17. PERSON: Helen Parkinson device instrument dose specification a directive information entity that describes the dose that will be administered to a target a protocol specifying to administer 1 ml of vaccine to a mouse dose specification scalar score from composite inputs 1 questionaire score scalar score from composite inputs 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. JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? Person: Jessica Turner Person: Jessica Turner fresh specimen MO_730 fresh_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a liver freshly removed from a rat a specimen that is output of a specimen creation process used for an investigation without storage. fresh specimen obsolete_electrically powered device a processed material created to have a function and which requires electrical power to execute obsolete_electrically powered device true sequence data A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. GROUP: OBI Person:Chris Stoeckert example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. sequence data obsolete_right handedness obsolete_right handedness true cell-cell binding detection by flow cytometry assay 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. IEDB IEDB 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. cell-cell binding detection by flow cytometry assay 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 PERSON:Alan Ruttenberg PERSON:Jessica Turner handedness categorical measurement datum paraffin storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage need to specify paraffin or wax is one of specified input of the process paraffin storage in container assay an assay in which a measurement is made by observing entities located in a container. in container assay obsolete_protocol service provider role DNA sequencing of a sample by a core lab which returns data to the consumer PERSON:Helen Parkinson a service provider role which is realized by a servicer provider organization performing a protocol execution obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service. obsolete_protocol service provider role true agar stab specimen MO_971 agar_stab PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a process that cell culture inoculated into agar for long term storage. agar stab specimen computed tomography scanner 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. CT scanner PERSON:Bjoern Peters X-ray computed tomography scanner computed tomography scanner http://en.wikipedia.org/wiki/X-ray_computed_tomography intranasal mucosal administration PERSON: Melanie Courtot The administration of a substance into the intranasal mucosis of an organism intranasal mucosal administration dose 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. An organism has been injected 1ml of vaccine dose growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing MO_588 growth_condition_design PERSON: Bjoern Peters growth condition intervention design obsolete_DNA sequencing training service 03/22/2010:workshop: there is a user requirement that not in all cases of the training the trainee gains the skills. A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments obsolete_DNA sequencing training service true obsolete_general scalar measurement datum 4/10/2011 BP: It is unclear to me why we need this, and don't just use the scalar measurement datum. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178 obsolete_general scalar measurement datum true performing a diagnosis 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 performing a diagnosis PCR instrument 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 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. PCR instrument electron microscope A microscope that produces an image of an object by targeting it with an electron beam electron microscope Edinburgh score 1 Edinburgh score PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 Person: Alan Ruttenberg Person:Jessica Turner WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html A score that measures the dominance of a person's right or left hand in everyday activities. DNA sequencing service A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. DNA sequencing service Eagle-i will supply better English definition service provision objective A sequencing centre has a service provision objective An objective which is fulfilled by the provision of some service e.g. a training service Helen Parkinson OBI service provision objective intravenous injection PERSON: Melanie Courtot intravenous injection 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 administration of material to specimen Bjoern Peters Bjoern Peters Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. administration of material to specimen device creation objective OBI PERSON: Helen Parkinson an objective which aims to create a device with a specified function device creation objective growth environment OBI group PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters Right now this may be incomplete. Should also cover e.g. sound, light as well. The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. growth environment questionnaire Need to clarify if this is a document or a directive information entity (or what their connection is)) questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Merriam-Webster PERSON: Jessica Turner Edinburgh handedness assay Edinburgh handedness assay PERSON:Jessica Turner Person:Alan Ruttenberg The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, 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. WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory Faraday cage A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. Faraday cage Faraday shield PERSON:Bjoern Peters Wikipedia http://en.wikipedia.org/wiki/Faraday_cage isolation function? HP agar stab storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group a storage process with input cell culture and agar and output agar stab for long time storage agar stab storage need to specify that agar is one of input for this process RNASE CL3 structure mapping assay PMID:16453415 Person:Philippe Rocca-Serra RNA ontology RNASE CL3 structure mapping assay a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse CL3 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 RNAse CL3 CMCT structure mapping assay CMCT structure mapping assay PMID:2422386 and PMID:2446263 Person: Philippe Rocca-Serra RNA ontology 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 image creation A planned process that captures an image of an object. PERSON: Jie Zheng Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel image acquisition image creation MPE-Fe(II) structure mapping assay MPE-Fe(II) structure mapping assay PMID:6209709 Person: Philippe Rocca-Serra RNA ontology a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-MP 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 Fe-MP probe obsolete_qualitative binding detection assay true 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 obsolete_qualitative binding detection assay nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract ENU structure mapping assay ENU structure mapping assay PMID:7002606 and PMID:2446263 Person: Philippe Rocca-Serra RNA ontology a single-nucleotide-resolution nucleic acid structure mapping assay which uses ENU 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 ENU probe RNASE V1 structure mapping assay PMID:7031604 Person:Philippe Rocca-Serra RNA ontology RNASE V1 structure mapping assay a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse V1 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 RNAse V1 kethoxal structure mapping assay Person: Philippe Rocca-Serra RNA ontology is a single-nucleotide-resolution nucleic acid structure mapping assay which uses kethoxal as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure kethoxal structure mapping assay single nucleotide resolution mapping assay using Kethoxal probe single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing Person: Philippe Rocca-Serra RNAO and OBI a single-nucleotide-resolution nucleic acid structure mapping assay which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study. single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing DMS structure mapping assay DMS structure mapping assay PMID:6159633 and PMID:2446263 Person: Philippe Rocca-Serra RNA Ontology a single-nucleotide-resolution nucleic acid structure mapping assay which uses DMS 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 DMS probe DNASE 1 structure mapping assay DNASE 1 structure mapping assay DNAse footprinting assay PMID:3773731 Person:Philippe Rocca-Serra RNA ontology 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 Person: Philippe Rocca-Serra RNAO and OBI a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study. single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing Rhodium DNA structure mapping assay PMID:2843807 Person:Philippe Rocca-Serra RNA ontology Rhodium DNA structure mapping assay a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhodium 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 Rhodium probe RNA ADA I RNA structure mapping assay PMID:7527340 Person: Philippe Rocca-Serra RNA ADA I RNA structure mapping assay RNA ontology a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNA adenosine deaminase I 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 RNA adenosine deaminase I Lead structure mapping assay Lead structure mapping assay PMID:2686708 Person:Philippe Rocca-Serra RNA ontology a single-nucleotide-resolution nucleic acid structure mapping assay which uses lead 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 Lead probe RNASE T2 structure mapping assay PMID:6207483 Person:Philippe Rocca-Serra RNA ontology RNASE T2 structure mapping assay a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T2 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 RNAse T2 gene dosage assay David Osumi Sutherland PERSON: Bjoern Peters an assay of changes in phenotype due to increased or decreased dosage of a single allele of a gene. gene dosage assay Fe-BABE RNA structure mapping assay Fe-BABE RNA structure mapping assay PMID: 7862644 Person:Philippe Rocca-Serra RNA ontology a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-BABE 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 Fe-BABE probe RNASE U2 structure mapping assay PMID:409999 Person:Philippe Rocca-Serra RNA ontology RNASE U2 structure mapping assay a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAase U2 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 RNAse U2 binding constant determination assay 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 PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant determination assay NMIA RNA structure mapping assay NMIA RNA structure mapping assay PMID: 15796531 Person:Philippe Rocca-Serra RNA ontology SHAPE mapping assay a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses NMIA 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 NMIA probe Terbium RNA structure mapping assay PMID:10772868 Person:Philippe Rocca-Serra RNA ontology Terbium RNA structure mapping assay a single-nucleotide-resolution nucleic acid structure mapping assay which uses Terbium 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 Terbium probe feature extraction A planed process with objective of obtaining quantified values from an image. MO_928: feature_extraction PERSON: Jie Zheng feature extraction OH-radical structure mapping assay MOHCA assay OH footprinting assay OH-radical structure mapping assay PMID:2501870 Person:Philippe Rocca-Serra RNA ontology a single-nucleotide-resolution nucleic acid structure mapping assay which uses hydroxyl radical 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 OH-radical probe RNASE T1 structure mapping assay PMID:114514 Person:Philippe Rocca-Serra RNA ontology RNASE T1 structure mapping assay a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T1 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 RNAse T1 array image creation An image creation process that generate an image from the array. MO_929: image_acquisition PERSON: Jie Zheng array image acquisition array image creation light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) OBI Person:Helen Parkinson a device which has a function to emit light. light emission device perturbation device A homogenizer is a perturbation device. A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson perturbation device environmental control device A growth chamber is an environmental control device. An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. Helen Parkinson OBI environmental control device Nuclease S1 structure mapping assay Nuclease S1 structure mapping assay PMID:363143 Person: Philippe Rocca-Serra RNA ontology 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 Nuclease S1 specimen fixation function EAGLE-I a function that allows specific identification of individual speciment from one another. e.g the function of a bar code reader used to read slide bar codes specimen fixation function obsolete_specimen fixation function A specimen fixation function is a function that holds or fastens an entity in a fixed position. EAGLE-I duplicate term obsolete_specimen fixation function true Ruthenium structure mapping assay PMID:3016894 Person:Philippe Rocca-Serra RNAOntology Ruthenium structure mapping assay is a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhutenium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure inline probing RNA structure mapping PMID:10573122 and PMID: 18369975 Person: Philippe Rocca-Serra RNA ontology inline probing RNA structure mapping is a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses intromolecular reactivity to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure current amplification function A current amplification function is an amplification function that increases the amplitude of a current. EAGLE-I current amplification function stabilization function 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. EAGLE-I isolation function stabilization function pump function EAGLE-I a transfer unction where the transfer requires work to move the entity, often against a gradient. pump function cell transfer function A cell harvester has a cell transfer function. EAGLE-I cell transfer function is a transfer function that displaces cells from one place to another angiograph A device that records the patterns of pulse waves inside blood vessels. PERSON: Erik Segerdell angiograph http://medical-dictionary.thefreedictionary.com/angiograph capillary blotter 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. PERSON: Erik Segerdell capillary blotter http://www.biometra.de/ bioreactor A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT PERSON: Erik Segerdell bioreactor http://en.wikipedia.org/wiki/Bioreactor pH meter A device that is used to measure the pH (acidity or alkalinity) of a liquid. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/PH_meter pH meter digital camera An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. PERSON: Erik Segerdell digital camera http://en.wikipedia.org/wiki/Digital_camera chip spotting device 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. PERSON: Erik Segerdell United States Patent 7416705 chip spotting device RNA extraction/purification instrument A device that is used to isolate and collect RNA for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell RNA extraction/purification instrument DNA extract DNA extract Group: UPenn group Person: Jie Zheng The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. two-photon laser/detector 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy two-photon laser/detector electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell electrophoresis system http://en.wikipedia.org/wiki/Category:Electrophoresis PET synthesizer A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. PERSON: Erik Segerdell PERSON: Erik Segerdell PET synthesizer spinning-disk confocal microscope A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Nipkow_disk spinning-disk confocal microscope DNA synthesizer An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. DNA synthesizer PERSON: Erik Segerdell http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers 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. PERSON: Erik Segerdell high performance liquid chromatography instrument http://en.wikipedia.org/wiki/High_performance_liquid_chromatography microplate reader A measurement device that detects biological, chemical or physical events of samples in microtiter plates. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Plate_reader microplate reader ELISA microplate reader A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). ELISA microplate reader PERSON: Erik Segerdell PERSON: Erik Segerdell spot cutter A robotic device that is used to excise spots from gels. PERSON: Erik Segerdell PERSON: Erik Segerdell spot cutter microwave synthesis system A device that is used to apply microwave irradiation to chemical reactions. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Microwave_chemistry microwave synthesis system densitometer A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. PERSON: Erik Segerdell densitometer http://en.wikipedia.org/wiki/Densitometer automatic staining machine A device that is used to automatically stain tissue sections on slides or tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell automatic staining machine automatic tissue processor A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. PERSON: Erik Segerdell United States Patent 3762362 automatic tissue processor stereo microscope 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope stereo microscope top loading balance A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. PERSON: Erik Segerdell PERSON: Erik Segerdell top loading balance perfusion station A device or system in which perfusion units are integrated. PERSON: Erik Segerdell PERSON: Erik Segerdell perfusion station SPECT scanner 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. PERSON: Erik Segerdell SPECT scanner http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography array manufacturer role a manufacturer role which is played by the person or organization that manufactured the array MO_695 array_manufacturer PERSON: Chris Stoeckert, Jie Zheng array manufacturer role scintillation counter A device that is used to measure ionizing radiation. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Scintillation_counter scintillation counter programmable array microscope A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. PERSON: Erik Segerdell Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8 programmable array microscope cryostat A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION PERSON: Erik Segerdell cryostat http://en.wikipedia.org/wiki/Cryostat microtome knife maker A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. PERSON: Erik Segerdell PERSON: Erik Segerdell microtome knife maker cryofixation device A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. PERSON: Erik Segerdell cryofixation device http://en.wikipedia.org/wiki/Cryofixation hybridization oven A device that creates an appropriate environment for nucleic acid hybridization. PERSON: Erik Segerdell PERSON: Erik Segerdell hybridization oven incubator shaker An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). PERSON: Erik Segerdell PERSON: Erik Segerdell incubator shaker small-animal image acquisition device A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. PERSON: Erik Segerdell PERSON: Erik Segerdell small-animal image acquisition device infrared image acquisition device An image acquisition device that is responsive to an infrared emissive target within a given field of view. PERSON: Erik Segerdell United States Patent 4107530 infrared image acquisition device confocal microscope 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. PERSON: Erik Segerdell confocal microscope http://en.wikipedia.org/wiki/Confocal_microscopy patch clamp device A device used in electrophysiology that allows the study of single or multiple ion channels in cells. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Patch_clamp patch clamp device gel imaging system A device that is used to acquire images of laboratory gels. PERSON: Erik Segerdell PERSON: Erik Segerdell gel imaging system protein separation apparatus A device that is used for the separation of proteins. PERSON: Erik Segerdell PERSON: Erik Segerdell protein separation apparatus multichannel electronic pipette 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. PERSON: Erik Segerdell http://www.faqs.org/patents/app/20090196797 multichannel electronic pipette vitrification apparatus A device that is used to effect the transition of a substance into a glass. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Glass_transition vitrification apparatus radiography instrument An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Medical_radiography radiography instrument radiation measurement device A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. PERSON: Erik Segerdell PERSON: Erik Segerdell radiation measurement device lyophilizer A device that is used to freeze dry material. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Freeze_drying lyophilizer tandem mass spectrometer 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. PERSON: Erik Segerdell http://goldbook.iupac.org/T06250.html tandem mass spectrometer microhardness tester A hardness testing device that is used in light-optical microscopes. PERSON: Erik Segerdell United States Patent 4611487 microhardness tester multimode microplate reader A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. PERSON: Erik Segerdell PERSON: Erik Segerdell multimode microplate reader mechanical balance A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). PERSON: Erik Segerdell http://www.britannica.com/EBchecked/topic/49765/balance mechanical balance computer cluster A group of linked computers, working together closely so that in many respects they form a single computer. PERSON: Erik Segerdell computer cluster http://en.wikipedia.org/wiki/Cluster_(computing) microtome knife sharpener A device that is used to sharpen knives used in microtomy. PERSON: Erik Segerdell PERSON: Erik Segerdell microtome knife sharpener plate shaker A device that provides shaking motion for microplates. PERSON: Erik Segerdell PERSON: Erik Segerdell plate shaker coagulation analyzer A device for automatically analyzing blood coagulation in a clinical laboratory. PERSON: Erik Segerdell United States Patent 5439646 coagulation analyzer laser capture microdissection microscope A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. PERSON: Erik Segerdell http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine laser capture microdissection microscope liquid extraction robot A liquid handling device that provides automatic liquid extraction. PERSON: Erik Segerdell PERSON: Erik Segerdell liquid extraction robot ultrasound machine A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Sonography ultrasound machine immunoblot scanner A device that is used for the imaging of immunoblots. PERSON: Erik Segerdell PERSON: Erik Segerdell immunoblot scanner microcentrifuge 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Laboratory_centrifuge microcentrifuge electronic repeater pipette 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. PERSON: Erik Segerdell electronic repeater pipette http://www.faqs.org/patents/app/20090196797 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. PERSON: Erik Segerdell electron paramagnetic resonance spectrometer http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance rocker A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). PERSON: Erik Segerdell PERSON: Erik Segerdell rocker analytical balance 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. PERSON: Erik Segerdell analytical balance http://en.wikipedia.org/wiki/Weighing_scale scanning force microscope A microscope that forms images of surfaces using a physical probe that scans the specimen. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Scanning_probe_microscopy scanning force microscope pulsed-field gel electrophoresis system A gel electrophoresis system that is used to separate very large molecules of DNA. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis pulsed-field gel electrophoresis system tissue embedding station A device that is used to perform paraffin embedding of tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell tissue embedding station nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer bead array reader A device that is used to acquire and image bead array data. PERSON: Erik Segerdell PERSON: Erik Segerdell bead array reader real-time PCR machine An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real-time PCR machine paraffin oven A device that is used for the warming of paraffin embedding medium. PERSON: Erik Segerdell PERSON: Erik Segerdell paraffin oven autoclave 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 PERSON: Erik Segerdell autoclave microplate washer A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? PERSON: Erik Segerdell http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 microplate washer nucleic acid extraction/purification instrument A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid extraction/purification instrument ELISA microplate washer A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). ELISA microplate washer PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum manifold 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. PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum manifold DNA extraction/purification instrument A device that is used to isolate and collect DNA for subsequent molecular analysis. DNA extraction/purification instrument PERSON: Erik Segerdell http://en.wikipedia.org/wiki/DNA_extraction multichannel pipette A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. PERSON: Erik Segerdell PERSON: Erik Segerdell multichannel pipette cell harvester A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? PERSON: Erik Segerdell PERSON: Erik Segerdell cell harvester portable fluorometer A compact fluorometer that can be carried or moved with ease. PERSON: Erik Segerdell PERSON: Erik Segerdell portable fluorometer gel electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell electrophoresis system gel electrophoresis system http://en.wikipedia.org/wiki/Category:Electrophoresis diffractometer 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. PERSON: Erik Segerdell diffractometer http://en.wikipedia.org/wiki/Diffractometer microdissection instrument A device that is used for the dissection of tissues under magnification. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/microdissection microdissection instrument micropipette puller A device that is used to fabricate glass micropipettes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Micropipette micropipette puller laser scanning confocal microscope 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy laser scanning confocal microscope digital microscope A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. PERSON: Erik Segerdell digital microscope http://en.wikipedia.org/wiki/Digital_microscope freeze substitution system 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. PERSON: Erik Segerdell doi:10.1017/S143192760707866X freeze substitution system micropipette A microinjection device that is used to measure very small volumes of liquids. PERSON: Erik Segerdell http://www.answers.com/topic/micropipette micropipette voltage clamp device 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Voltage_clamp voltage clamp device vacuum oven A device that heats materials in a vacuum. PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum oven slide warmer A device that is used to heat microscope slides. PERSON: Erik Segerdell PERSON: Erik Segerdell slide warmer capillary electrophoresis instrument An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. PERSON: Erik Segerdell capillary electrophoresis instrument http://en.wikipedia.org/wiki/Capillary_electrophoresis 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. PERSON: Erik Segerdell denaturing high-performance liquid chromatography instrument doi:10.1385/1-59259-850-1:173 agarose gel electrophoresis system 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. PERSON: Erik Segerdell agarose gel electrophoresis system http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis balance A measuring instrument that is used to determine the weight or mass of an object. PERSON: Erik Segerdell balance http://en.wikipedia.org/wiki/Weighing_scale surface plasmon resonance instrument A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Surface_plasmon_resonance surface plasmon resonance instrument protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer X-ray source A device that is used to generate X-rays. PERSON: Erik Segerdell X-ray source http://en.wikipedia.org/wiki/X-ray_generator x-ray generator liquid chromatography instrument 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 PERSON: Matthew Brush PERSON: Matthew Brush liquid chromatography instrument spike-in quality control role MO_937 spike_quality_control PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter 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 spike-in quality control role individual organism identifier PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual a CRID symbol used to distinguish one individual organism from another. individual organism identifier dye swap quality control role MO_524 dye_swap_quality_control PERSON: Chris Stoeckert, Jie Zheng 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 dye swap quality control role labeled nucleic acid extract MO_221 labeledExtract Person: Jie Zheng 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. labeled extract labeled extract labeled nucleic acid extract binding constant 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. A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum 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". binding constant 3D structure determination of bound complex assay 3D structure determination of bound complex assay A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration. Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. IEDB IEDB binding assay An assay with the objective to characterize the disposition of two or more material entities to form a complex. 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.nnThe 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. PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum binding assay cell culture expansion 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. MO_758 grow PERSON: Chris Stoeckert, Jie Zheng a processual entity that results in the increase of cell numbers cell culture expansion including grow of yeast and bacteria gene knock out MO_771 gene_knock_out PERSON: Chris Stoeckert, Jie Zheng 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. gene knock out gene knock in PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/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. 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 PERSON: Chris Stoeckert, Jie Zheng chromosomal substitution genetically modified material GROUP: OBI PERSON: Jie Zheng a material entity, organism or cell, that is the output of a genetic transformation process. genetically modified material term is proposed by BP on Oct 25, 2010 dev call transfection MO_366 transfection PERSON: Chris Stoeckert, Jie Zheng 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 suggested to be added by BP and AR during Oct 25, 2010 dev call Person: Jie Zheng Person: Jie Zheng a material transformation objective aims to create genetically modified organism or cell genetic transformation objective induced mutation MO_564 induced_mutation PERSON: Chris Stoeckert, Jie Zheng a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. induced mutation 3D structural organization datum 3D structural organization datum A measurement datum that describes the structural orientation of a material entity in 3D space. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. age since planting measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call MO_495 planting PERSON:Chris Stoeckert, Jie Zheng age since planting measurement datum age since hatching measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. MO_745 hatching PERSON:Chris Stoeckert, Jie Zheng age since hatching measurement datum age measurement assay An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted. OBI group PERSON: Alan Ruttenberg This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. age measurement assay age since egg laying measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. MO_767 egg laying PERSON:Chris Stoeckert, Jie Zheng age since egg laying measurement datum assay validation objective GROUP: Penn Group PERSON: Chris Stoeckert, Jie Zheng an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results assay validation objective age since germination measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. MO_590 germination PERSON:Chris Stoeckert, Jie Zheng age since germination measurement datum validation by reverse transcription PCR design MO_986 reverse_transcription_PCR_quality_control PERSON: Chris Stoeckert, Jie Zheng a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results validation by reverse transcription PCR design age since eclosion measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. MO_876 eclosion PERSON:Chris Stoeckert, Jie Zheng age since eclosion measurement datum age since sowing measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. MO_748 sowing PERSON:Chris Stoeckert, Jie Zheng age since sowing measurement datum age since coitus measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. MO_783 coitus PERSON:Chris Stoeckert, Jie Zheng age since coitus measurement datum validation by real time PCR design MO_434 real_time_PCR_quality_control PERSON: Chris Stoeckert, Jie Zheng 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 validation by real time PCR design age measurement datum A time measurement datum that is the result of measurement of age of an organism In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class MO_178 Age PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng discussed on Nov 15, dev call All subtype will be defined by textual definition now. note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage age measurement datum age since fertilization measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. Definition of fertilization comes from GO. MO_701 fertilization PERSON:Chris Stoeckert, Jie Zheng age since fertilization measurement datum age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. MO_710 birth PERSON:Chris Stoeckert, Jie Zheng age since birth measurement datum reverse transcription polymerase chain reaction assay GROUP: Penn Group PERSON: Chris Stoeckert, Jie Zheng an assay that evaluates 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. reverse transcription polymerase chain reaction assay half life datum (t 1/2) Bjoern Peters Bjoern Peters The time it takes for 50% of a class of stochastic processes to occur. half life datum (t 1/2) t 1/2 dose response curve 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. Bjoern Peters; Randi Vita dose response curve service A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony service passive immunization 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. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum 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. adoptive transfer passive immunization selective organism creation objective PERSON: Chris Stoeckert, Jie Zheng WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 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. selective organism creation objective Individual epitope immunization in vivo 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. An immunization in which an individual epitope is administered into a host organism. Individual epitope immunization in vivo Injection of a peptide T cell epitope into a mouse PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita RNA sequencing BP 12/21:Created based on a request from Melanie Bjoern Peters Bjoern Peters RNA sequencing RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact efficacy of epitope intervention experiment An experiment that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. Bjoern Peters efficacy of epitope intervention experiment efficacy of in vivo intervention 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. Bjoern Peters epitope protection from infectious challenge experiment protection from infectious challenge half maximal effective concentration (EC50) Bjoern Peters; Randi Vita 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) 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. wikipedia binding datum 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. Bjoern Peters; Randi Vita binding datum negative binding datum A binding datum that states that there is no significant disposition of two or more entities to form a complex negative binding datum 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. Bjoern Peters epitope protection from tumor challenge experiment tumor burden after challenge epitope protection experiment Bjoern Peters an epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. epitope protection experiment protection from challenge 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 cultivar ecotype strain selectively maintained organism 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. Bjoern Peters epitope protection from infectious challenge experiment based on pathogen burden pathogen burden after infectious challenge infectious agent detection assay 2/22/2011, BP: This should probably be an analyte assay, but the logical definition of those is currently restricted to 'scattered molecular aggregates', which excludes using infectious agents as analytes. See below (realizes some ('evaluant role' and (role_of some material_entity))) and (realizes some ('analyte role' and (role_of some 'infectious agent'))) and (achieves_planned_objective some 'analyte measurement objective') An assay in which the presence or amount of an infectious agent in an input material is detected in an evaluant Bjoern Peters, Randi Vita, Jason Greenbaum Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers. infectious agent detection assay epitope disease exacerbation experiment Bjoern Peters an 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 disease exacerbation experiment exacerbation assay epitope protection experiment based on survival Bjoern Peters an epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. epitope protection experiment based on survival host survival after challenge epitope treatment experiment Bjoern Peters 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 epitope treatment experiment half maximal inhibitory concentration (IC50) Bjoern Peters; Randi Vita 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. Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. half maximal inhibitory concentration (IC50) wikipedia epitope specific immune intervention An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope Person: Bjoern Peters, Randi Vita, Jason Greenbaum epitope specific immune intervention 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific cytokine production by T cells ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TGFb release|ELISPOT operator variation design Person: Chris Stoeckert, Jie Zheng A study design that assesses the operator performance and relation to data consistency and quality. MO_519 operator_variation_design operator variation design cytometric bead array assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses a cytometric bead array assay. CXCL10/IP-10 release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific IP-10 production by T cells comparative genome hybridization by array design Person: Chris Stoeckert, Jie Zheng A study design that detects genomic copy number variations using microarray technology. MO_856 comparative_genome_hybridization_design comparative genome hybridization by array design biological activity 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. IEDB IL-27 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-27 production by T cells in vivo design Person: Chris Stoeckert, Jie Zheng A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. MO_454 in_vivo_design in vivo design genotyping by high throughput sequencing design MO_560 genotyping_design Person: Chris Stoeckert, Jie Zheng A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. genotyping by high throughput sequencing design epitope specific tolerance induction by T cells A process of tolerance induction 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific tolerance induction by T cells innate behavior design Person: Chris Stoeckert, Jie Zheng A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. MO_355 innate_behavior_design innate behavior design detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TGFb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells SNP microarray EFO_0002703 SNP array Person: Helen Parkinson a DNA microarray used to detect polymorphisms in DNA samples SNP microarray cell component comparison design A study design that compares samples from different cell components. Person: Chris Stoeckert, Jie Zheng MO_1019 cell_component_comparison_design cell component comparison design ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells GM-CSF release|ELISPOT IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific macrophage inflammatory protein-1 alpha production by T cells epitope specific T cell activation A process of T cell activation 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific T cell activation biological activity 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. IEDB IL-10 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-10 production by T cells cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a cytometric bead array assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TGFb release|cytometric bead array cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells ex vivo design Person: Chris Stoeckert, Jie Zheng 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. MO_808 ex_vivo_design ex vivo design 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific type IV hypersensitivity by T cells normalization testing design Person: Chris Stoeckert, Jie Zheng A study design that tests different normalization procedures. MO_729 normalization_testing_design normalization testing design intracellular material detection assay measuring epitope specific perforin release A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular material detection assay measuring epitope specific perforin release perforin release|intracellular staining cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a cell culture analyte detection bioassay. IEDB IL-2 release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells biological activity 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. IEDB IL-22 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-22 production by T cells biological activity 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. IEDB IL-8 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-C motif) ligand 1 production by T cells cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a cell culture analyte detection bioassay. IEDB IL-10 release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells ChIP-chip by SNP array assay Group: ArrayExpress production team An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology ChIP-chip by SNP array assay EFO_0002764 ChIP-chip by SNP array ELISA measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an ELISA. CCL5/RANTES release|ELISA ELISA measuring epitope specific RANTES production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses a cytometric bead array assay. IEDB IL-1b release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells genetic population background information Group: OBI group Group: OBI group a genetic characteristics information which is a part of genotype information that identifies the population of organisms genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information proposed and discussed on San Diego OBI workshop, March 2011 environmental history design MO_698 environmental_history_design Person: Chris Stoeckert, Jie Zheng A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. environmental history design ELISPOT assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-6 production by T cells IEDB IL-6 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity 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. IEDB IEDB antibody help|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex A T cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters dissociation constant KD|surface plasmon resonance (SPR)|nM plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex biological activity 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. IEDB IL-5 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-5 production by T cells ELISA measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISA. ELISA measuring epitope specific transforming growth factor-beta production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TGFb release|ELISA biological activity assay measuring epitope specific RANTES production by T cells A T cell epitope specific cytokine production assay that detects RANTES production by T cells. CCL5/RANTES release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific RANTES production by T cells biological activity 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. GM-CSF release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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 epigenetic modification identification objective transcription profiling by tiling array assay Person: James Malone An assay in which the transcriptome of a biological sample is analysed using a tiling path array. EFO_0002769 transcription profiling by tiling array transcription profiling by tiling array assay ELISA measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-22 production by T cells IEDB IL-22 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity 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. IEDB IL-21 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-21 production by T cells ELISA measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-9 production by T cells IEDB IL-9 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters transcription profiling by high throughput sequencing design Person: Chris Stoeckert, Jie Zheng 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 Group: ArrayExpress production team transcription profiling by high throughput sequencing design intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-6 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a cell culture analyte detection bioassay. IEDB IL-4 release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNFa release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a cytometric bead array assay. CCL2/MCP-1 release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells ELISA measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-23 production by T cells IEDB IL-23 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release perforin release|RNA/DNA detection ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISA. ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNF release|ELISA genotyping by high throughput sequencing assay Person: James Malone An assay in which high througput sequencer is used to detect polymorphisms in DNA samples EFO_0002771: genotyping by high throughput sequencing genotyping by high throughput sequencing assay ChIP-chip assay ChIP-on-chip assay Person: James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/ChIP-on-chip an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis. ChIP-chip assay epitope specific T cell tolerance induction A process of T cell tolerance induction 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific T cell tolerance induction 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters T cell degranulation by intracellular staining obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation true biological activity 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. IEDB IL-13 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-13 production by T cells array platform variation design Person: Chris Stoeckert, Jie Zheng A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. MO_899 array_platform_variation_design array platform variation design biological activity assay measuring interleukin-9 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. IEDB IL-9 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-3 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-5 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific lymphotoxin A production by T cells 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-1 alpha production by T cells ChIP-seq design http://en.wikipedia.org/wiki/Chip-Sequencing 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. ChIP-seq design Person: Chris Stoeckert, Jie Zheng translational bias design Person: Chris Stoeckert, Jie Zheng A study design that characterizes the association of transcripts and translation machinery. MO_939 translational_bias_design translational bias design ELISA measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-3 production by T cells IEDB IL-3 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-1 alpha production by T cells IEDB IL-1a release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-27 production by T cells biological activity 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters T cell help|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response biological activity 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TGFb release|biological activity biological activity assay measuring epitope specific transforming growth factor-beta production by T cells FWER adjusted p-value FWER adjusted p-value 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) http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html DNA methylation profiling by high throughput sequencing assay EFO_0002761 methylation profiling by high throughput sequencing Group: ArrayExpress production team, James Malone, Helen Parkinson Philippe Rocca-Serra An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology DNA methylation profiling by high throughput sequencing assay 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific transforming growth factor-beta production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-12 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells biological activity assay measuring epitope specific cytotoxic T cell degranulation A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific cytotoxic T cell degranulation degranulation|biological activity cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a cell culture analyte detection bioassay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TGFb release|bioassay cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells RNA-seq assay JZ: should be inferred as 'DNA sequencing'. Will check in the future. An assay 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 EFO_0002770 transcription profiling by high throughput sequencing PERSON: James Malone RNA-seq assay an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq transcription profiling by high throughput sequencing ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNF release|ELISPOT cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a cell culture analyte detection bioassay. IEDB IL-5 release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells genotyping by array assay Group: ArrayExpress production team An assay in which an array is used to detect polymorphisms in DNA samples EFO_0002767: genotyping by array genotyping by array assay 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-16 production by T cells biological activity 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. CCL1/TCA-3 release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-2 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells DNA methylation profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which the methylation state of DNA is determined and is compared between samples using array technology. DNA methylation profiling by array design GROUP: ArrayExpress production team detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-22 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells biological activity 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. IEDB IL-16 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-16 production by T cells ELISA measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an ELISA. CXCL10/IP-10 release|ELISA ELISA measuring epitope specific IP-10 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters translation profiling assay 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. EFO_0001033 translation profiling PERSON: James Malone translation profiling assay ELISA measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-15 production by T cells IEDB IL-15 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses a cytometric bead array assay. IEDB IL-12 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-12 production by T cells in vitro design Person: Chris Stoeckert, Jie Zheng 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. MO_347 in_vitro_design in vitro design RNAi profiling by array design Person: Chris Stoeckert, Jie Zheng 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. Group: ArrayExpress production team RNAi profiling by array design ELISA measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an ELISA. ELISA measuring epitope specific lymphotoxin A production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters lymphotoxin A/TNFb release|ELISA cytometric bead array assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a cytometric bead array assay. IEDB IL-5 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-5 production by T cells transcription profiling by array design MO_533 transcript_identification_design Person: Chris Stoeckert, Jie Zheng A study design that identifies forms and abundance of transcripts in the genome using microarray technology. transcription profiling by array design detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-17 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells biological activity 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. IEDB IL-15 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-15 production by T cells disease state design Person: Chris Stoeckert, Jie Zheng 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. MO_902 disease_state_design disease state design wild type organism genotype information C57BL/6J wild type Group: OBI group Group: OBI group 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. proposed and discussed on San Diego OBI workshop, March 2011 wild type organism genotype information biological activity 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. IEDB IL-17 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-17 production by T cells cytometric bead array assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses a cytometric bead array assay. IEDB IL-17 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-17 production by T cells cytometric bead array assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-10 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-10 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-21 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-5 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells cytometric bead array assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a cytometric bead array assay. IEDB IL-2 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-2 production by T cells cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses a cell culture analyte detection bioassay. IEDB IL-16 release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISA. CCL3/MIP-1a release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. GM-CSF release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells RNAi profiling by array assay 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. EFO_0001030 RNAi profiling by array PERSON: James Malone RNAi profiling by array assay 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 Group: OBI group Group: OBI group 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 genotype information RNA stability design Person: Chris Stoeckert, Jie Zheng A study design that examines the stability and/or decay of RNA transcripts. MO_553 RNA_stability_design RNA stability design tiling microarray EFO_0002704: tiling array Person: Helen Parkinson 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. genome tiling array tiling microarray biological activity 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 IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific IP-10 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-13 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells species comparison design A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex 3D structure|x-ray crystallography|angstroms A T cell epitope 3D structure determination assay that uses an X-ray crystallography assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex transcription profiling by RT-PCR design Person: Chris Stoeckert, Jie Zheng A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Group: ArrayExpress production team transcription profiling by RT-PCR design 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific T cell enhancement of B cell mediated immune response ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISA. CCL1/TCA-3 release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-21 production by T cells flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex A T cell epitope qualitative binding assay that uses a cell-cell binding detection by flow cytometry assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters T cell- APC binding|binding assay flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex proteomic profiling by array assay Person: James Malone An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology EFO_0002765 proteomic profiling by array proteomic profiling by array assay cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a cell culture analyte detection bioassay. IEDB IFNg release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells ELISPOT assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an ELISPOT assay. ELISPOT assay measuring epitope specific granzyme B release by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters granzyme B release|ELISPOT microRNA profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. Group: ArrayExpress production team microRNA profiling by array design 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters in vivo assay measuring T cell epitope specific tolerance induction tolerance|in vivo assay detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL5/RANTES release|RNA/DNA detection IEDB IEDB detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells cytometric bead array assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a cytometric bead array assay. IEDB IL-4 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-4 production by T cells biological activity 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific lymphotoxin A production by T cells lymphotoxin A/TNFb release|biological activity organism development design Person: Chris Stoeckert, Jie Zheng A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. MO_892 development_or_differentiation_design organism development design family history design Person: Chris Stoeckert, Jie Zheng A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. MO_544 family_history_design family history design ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISA. CXCL9/MIG release|ELISA ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells IEDB IEDB transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Group: Penn Group Person: Chris Stoeckert, Jie Zheng transcription profiling identification objective DNA methylation profiling by array assay Person: James Malone Philippe Rocca-Serra An assay in which the methylation state of DNA is determined and is compared between samples using array technology DNA methylation profiling by array assay EFO_0002759 methylation profiling by array biological activity 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. CCL3/MIP-1a release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific granulocyte colony stimulating factor production by T cells microRNA profiling by array assay An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome. EFO_0000753 microRNA profiling by array PERSON: James Malone microRNA profiling by array assay quality control testing design Person: Chris Stoeckert, Jie Zheng A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. MO_981 quality_control_testing_design quality control testing design clinical history design Person: Chris Stoeckert, Jie Zheng A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. MO_832 clinical_history_design clinical history design detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-4 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cell culture analyte detection bioassay. GM-CSF release|bioassay IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-21 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific 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 An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL2/MCP-1 release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISA. CCL2/MCP-1 release|ELISA ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity 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. CCL4/MIP-1b release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells ELISA measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-21 production by T cells IEDB IL-21 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters in vivo skin test assay measuring T cell 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 An assay of epitope specific interleukin-13 production by T cells that uses a cytometric bead array assay. IEDB IL-13 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-13 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IFNg release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific tumor necrosis factor superfamily cytokine production by T cells allele information MO_58 Allele Person: Chris Stoeckert, Jie Zheng 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. allele information discussed on San Diego OBI workshop, March 2011 genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a cytometric bead array assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNFa release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells ELISPOT assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-17 production by T cells IEDB IL-17 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IFNb release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. GM-CSF release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells post-transcriptional modification design Person: Chris Stoeckert, Jie Zheng A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. MO_392 cellular_modification_design post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases post-transcriptional modification design ELISA measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-8 production by T cells IEDB IL-8 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a cytometric bead array assay. IEDB IL-6 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-6 production by T cells transcription profiling by RT-PCR assay An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR) EFO_0002943: transcription profiling by RT-PCR Person: Anna Farne transcription profiling by RT-PCR assay 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-C motif) ligand 4 production by T cells biological activity 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. IEDB IL-23 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-23 production by T cells genetic alteration information Group: OBI group Group: OBI group a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. genetic alteration information proposed and discussed on San Diego OBI workshop, March 2011 cellular process design Person: Chris Stoeckert, Jie Zheng 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. MO_810 cellular_process_design cellular process design epitope specific RANTES production by T cells A process of RANTES 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific RANTES production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-10 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a cytometric bead array assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNF release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells wild type allele information MO_605 genotype Person: Chris Stoeckert, Jie Zheng an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. discussed on San Diego OBI workshop, March 2011 wild type allele information intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an intracellular cytokine staining assay. CCL4/MIP-1b release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific granzyme B production by T cells 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-8 production by T cells injury design Person: Chris Stoeckert, Jie Zheng A study design in which the response of an organism(s) to injury or damage is studied. MO_726 injury_design injury design intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-3 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells organism status comparison design Person: Chris Stoeckert, Jie Zheng A study design that compares samples from live and dead organisms. MO_841 organism_status_design organism status comparison design ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISA. CCL4/MIP-1b release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a cytometric bead array assay. IEDB IFNg release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interferon-gamma production by T cells biological activity 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. IEDB IL-18 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-23 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-27 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CXCL10/IP-10 release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a cell culture analyte detection bioassay. IEDB IL-3 release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an intracellular cytokine staining assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNF release|ICS intracellular cytokine staining assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific monocyte chemotactic protein-1 production by T cells genotyping by array design MO_560 genotyping_design Person: Chris Stoeckert, Jie Zheng A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. genotyping by array design biological activity 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. IEDB IL-1a release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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 An assay of epitope specific interleukin-6 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-6 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells biological activity 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. IEDB IFNb release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interferon-beta production by T cells biological activity 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. IEDB IL-12 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-12 production by T cells in vivo assay measuring epitope specific T cell killing A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytotoxicity|in vivo assay in vivo assay measuring epitope specific T cell killing comparative genomic hybridization by array assay Philippe Rocca-Serra An assay in which changes in DNA sequence copy number are analysed 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. EFO_0000749: comparative genomic hybridization by array Person: James Malone array CGH comparative genomic hybridization by array assay epitope specific cytotoxic T cell degranulation A process of cytotoxic T cell degranulation 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific cytotoxic T cell degranulation detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-23 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells stimulus or stress design Person: Chris Stoeckert, Jie Zheng 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. MO_568 stimulus_or_stress_design stimulus or stress design cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a cytometric bead array assay. G-CSF release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific 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 Person: Chris Stoeckert, Jie Zheng protein and DNA interaction identification objective 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-22 production by T cells biological activity 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNF release|biological activity biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells protocol optimization design Person: Chris Stoeckert, Jie Zheng A study design where different protocols or protocol parameters are compared aims to find an optimized protocol MO_934 optimization_design protocol optimization design promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a promoter activity detection by reporter gene assay. IEDB IEDB IL-2 release|reporter gene assay promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells ChIP-chip design ChIP-on-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. ChIP-chip design MO_933 binding_site_identification_design Person: Chris Stoeckert, Jie Zheng genetic characteristics information MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) MO_66 IndividualGeneticCharacteristics Person: Chris Stoeckert, Jie Zheng a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. genetic characteristics information cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a cytometric bead array assay. CCL3/MIP-1a release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells biological activity 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. IEDB IL-3 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-3 production by T cells biological activity assay measuring epitope specific T cell activation A T cell epitope dependent biological activity assay that detects T cell activation. IEDB IEDB activation|biological activity biological activity assay measuring epitope specific T cell activation imprinting design Person: Chris Stoeckert, Jie Zheng 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. MO_914 imprinting_design imprinting design cell cycle design Person: Chris Stoeckert, Jie Zheng 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. MO_822 cell_cycle_design cell cycle design translation profiling design Person: Chris Stoeckert, Jie Zheng 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. Group: ArrayExpress production team translation profiling design cell type comparison design Person: Chris Stoeckert, Jie Zheng A study design that compares cells of different type, for example different cell lines. MO_764 cell_type_comparison_design cell type comparison design cytometric bead array assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses a cytometric bead array assay. CCL5/RANTES release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific RANTES production by T cells cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a cell culture analyte detection bioassay. IEDB IL-6 release|bioassay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells biological activity 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. IEDB IFNg release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-9 production by T cells biological activity assay measuring epitope specific tumor necrosis factor production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNFa release|biological activity biological activity assay measuring epitope specific tumor necrosis factor production by T cells ChIP-chip by tiling array design Group: ArrayExpress production team Person: Chris Stoeckert, Jie Zheng A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. ChIP-chip by tiling array design dose response design Person: Chris Stoeckert, Jie Zheng A study design that examines the relationship between the size of the administered dose and the extent of the response. MO_485 dose_response_design dose response design ChIP-chip by tiling array assay Group: ArrayExpress production team An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology ChIP-chip by tiling array assay EFO_0002762 ChIP-chip by tiling array 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific helper T cell enhancement of T cell mediated immune response 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interferon-beta production by T cells organism part comparison design A study design that compares tissues, regions, organs within or between organisms Person: Chris Stoeckert, Jie Zheng MO_953 organism_part_comparison_design organism part comparison design intracellular material detection measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters granzyme B release|intracellular staining intracellular material detection measuring epitope specific granzyme B release by T cells protein binding site identification design A study design that investigates protein binding sites on nucleic acids. MO_933 binding_site_identification_design Person: Chris Stoeckert, Jie Zheng protein binding site identification design sex comparison design A study design that assays differences associated with an organism's sex, gender or mating type. Person: Chris Stoeckert, Jie Zheng MO_575 sex_design sex comparison design transcription profiling by tiling array design MO_507 tiling_path_design Person: Chris Stoeckert, Jie Zheng 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. transcription profiling by tiling array design cell differentiation design Person: Chris Stoeckert, Jie Zheng A study design that assays events associated with cell development or differentiation. MO_892 development_or_differentiation_design cell differentiation design transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. MO_533 transcript_identification_design Person: Chris Stoeckert, Jie Zheng transcription profiling design operon identification design Person: Chris Stoeckert, Jie Zheng A study design that identifies locations and members of operons in a genome. MO_772 operon_identification_design operon identification design radio immuno assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a radio immuno assay. IEDB IFNg release|radio immuno assay (RIA) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters radio immuno assay measuring epitope specific interferon-gamma production by T cells DNA methylation profiling by high throughput sequencing design Person: Chris Stoeckert, Jie Zheng A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. DNA methylation profiling by high throughput sequencing design GROUP: ArrayExpress production team biological activity 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific granzyme B release by T cells granzyme B release|biological activity intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an intracellular cytokine staining assay. CXCL9/MIG release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific 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 assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISA. CCL9/MIP-1g release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-X-C motif) ligand 9 production by T cells all pairs design Person: Chris Stoeckert, Jie Zheng A study design in which all specimens are compared to every other specimen. MO_565 all_pairs all pairs design proteomic profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology Group: ArrayExpress production team proteomic profiling by array design q-value 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)" q-value 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. Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html FDR adjusted p-value PERS:Philippe Rocca-Serra genotyping design Person: Chris Stoeckert, Jie Zheng A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. MO_560 genotyping_design genotyping design biological activity 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. IEDB IL-2 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-15 production by T cells 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific macrophage inflammatory protein-1 gamma production by T cells individual genetic characteristics comparison design Person: Chris Stoeckert, Jie Zheng A study design where genotype, haplotype, or other individual genetic characteristics are compared. MO_527 individual_genetic_characteristics_design individual genetic characteristics comparison design biological activity 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. IEDB IL-1b release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-1 beta production by T cells biological activity 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. IEDB IL-4 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-4 production by T cells biological activity 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. IEDB IL-6 release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-6 production by T cells cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a cell culture analyte detection bioassay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNFa release|bioassay cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an intracellular cytokine staining assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells lymphotoxin A/TNFb release|ICS pathogenicity design Person: Chris Stoeckert, Jie Zheng 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. MO_807 pathogenicity_design pathogenicity design ELISPOT assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-5 production by T cells IEDB IL-5 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity 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. CCL9/MIP-1g release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells cytometric bead array assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses a cytometric bead array assay. IEDB IL-8 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-8 production by T cells biological activity 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. CXCL9/MIG release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells genetic modification design Person: Chris Stoeckert, Jie Zheng 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. MO_447 genetic_modification_design genetic modification design ELISA measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an ELISA. ELISA measuring epitope specific granzyme B release by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters granzyme B release|ELISA 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. Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific IP-10 production by T cells transcription profiling by array assay An assay in which the transcriptome of a biological sample is analysed using array technology. Person: James Malone EFO_0002768: transcription profiling by array RNA profiling by array assay JZ: add alternative term: 'RNA profiling by array assay' requested by ENCODE developer. See tracker: https://sourceforge.net/p/obi/obi-terms/757/ transcription profiling by array assay strain comparison design Person: Chris Stoeckert, Jie Zheng A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. MO_462 strain_or_line_design strain comparison design biological activity 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. CCL2/MCP-1 release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-12 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific 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. IEDB IEDB disease exacerbation|in vivo assay in vivo assay measuring T cell epitope specific disease exacerbation cell specimen A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. MO_612 cell PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl 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/ cell specimen 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ligand presentation|T cell recognition monospecific T cell recognition assay measuring MHC ligand processing and presentation 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-17F production by T cells T cell epitope specific immune intervention An epitope specific immune intervention in which the induced response targets a T cell epitope IEDB Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters T cell epitope specific immune intervention specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. MO_95 BiosourceType PERSON: Chris Stoeckert, Jie Zheng specimen with known storage state in vivo assay measuring T cell epitope specific protection from tumor challenge A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on tumor burden. IEDB IEDB in vivo assay measuring T cell epitope specific protection from tumor challenge 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. MO_861 lowess_group_normalization Person: Elisabetta Manduchi lowess group transformation in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on pathogen burden. IEDB IEDB in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden pathogen burden after challenge|in vivo assay phage display binding assay 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. IEDB IEDB 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. phage display binding assay 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. MO_720 lowess_normalization Person: Elisabetta Manduchi lowess transformation 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 IEDB IEDB ligand presentation|mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). MO_954 organism_part PERSON: Chris Stoeckert, Jie Zheng specimen from organism tissue specimen phage display library panning IEDB, http://en.wikipedia.org/wiki/Phage_display Jason Greenbaum, Randi Vita, Bjoern Peters 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. 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 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. MO_692 lowess_global_normalization Person: Elisabetta Manduchi lowess global transformation intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specifictransforming growth factor-beta production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB TGFb release|ICS intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells cell collecting A planned process that collects cells from culture. MO_982 harvest PERSON: Chris Stoeckert, Jie Zheng cell collecting biological activity 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. IEDB IEDB biological activity assay measuring T cell epitope specific in vivo activity in vivo activity|biological activity purified MHC molecule preparation 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. Bjoern Peters HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody purified MHC molecule preparation disposition to be bound by an MHC protein complex IEDB 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. MHC ligand disposition PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters disposition to be bound by an MHC protein complex B cell epitope specific immune intervention An epitope specific immune intervention in which the induced response targets a B cell epitope B cell epitope specific immune intervention IEDB Injecting a mouse with recombinant antibody targeting an anthrax epitope PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters epitope tolerance induction experiment An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response IEDB IEDB epitope tolerance induction experiment tolerance induction 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. IEDB IEDB ligand presentation|cellular MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cytometric bead array assay. GM-CSF release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells radioactivity detection binding assay IEDB PERSON:Bjoern Peters, Randi Vita binding assay that uses radioactivity detection as an indicator of binding radioactivity detection binding assay in vivo assay measuring T cell epitope specific protection based on survival A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on survival. IEDB IEDB in vivo assay measuring T cell epitope specific protection based on survival survival from challenge|in vivo assay 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. IEDB IEDB cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition qualitative binding|cellular MHC/T cell inhibition linear amplification An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies. MO_997 linear_amplification PERSON: Chris Stoeckert, Jie Zheng linear amplification biological activity 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. IEDB IEDB biological activity assay measuring epitope specific T cell helper activity helper response|biological activity intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-22 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells biological activity 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. IEDB IEDB biological activity assay measuring epitope specific perforin release by T cells perforin release|biological activity atmosphere A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. MO_219 atmosphere PERSON: Chris Stoeckert, Jie Zheng atmosphere fluorescence detection binding assay IEDB PERSON:Bjoern Peters, Randi Vita binding assay that uses fluorescence detection as an indicator of binding fluorescence detection binding assay 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand ligand presentation|coelution fluorescence detection assay An assay in which a material's fluorescence is determined. IEDB IEDB 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. fluorescence detection assay epitope specific perforin production by T cells PERSON: Bjoern Peters, Randi Vita 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 production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. epitope specific perforin production by T cells MHC protein complex binding to ligand 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. IEDB MHC protein complex binding to ligand PERSON: Bjoern Peters; Randi Vita 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 dissection A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. EFO_0003856 dissection MO_374 dissect PERSON: Chris Stoeckert, Jie Zheng dissection 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 MO_406 purify PERSON: Chris Stoeckert, Jie Zheng purification 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. MO_84 OrganismStatus PERSON: Chris Stoeckert, Jie Zheng organizational term, used in description of specimen that is created from known pre- or post-mortem status specimen with 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. IEDB IEDB decreased disease|in vivo assay in vivo assay measuring T cell epitope specific treatment of 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. MO_738 timepoint Person: Chris Stoeckert sampling time measurement datum time point 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 Edman degradation assay measuring MHC ligand processing and presentation IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ligand presentation|Edman degradation 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. IEDB IEDB ligand presentation|secreted MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC disposition to be a product of antigen processing and presentation 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. IEDB IEDB 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. disposition to be a product of antigen processing and presentation cytometric bead array assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses a cytometric bead array assay. IEDB IEDB IL-17A release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17A production by T cells purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection A purified MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection qualitative binding|purified MHC/competitive/radioactivity minimal inhibitory concentration 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. Bjoern Peters, coordinated with Albert Goldfain Created following request by Albert Goldfain PERSON:Bjoern Peters minimal inhibitory concentration material maintenance service A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material maintenance service model organism colony maintanance cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand binding half maximal effective concentration (EC50) determination assay that uses radioactivity detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection A cell lysate MHC binding assay that uses fluorescence detection to detect direct binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection qualitative binding|lysate MHC/direct/fluorescence cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISA. ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells G-CSF release|ELISA IEDB IEDB 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 Assembly Algorithm NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng sequence assembly algorithm cytometric bead array assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses a cytometric bead array assay. IEDB IEDB IL-17F release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17F production by T cells cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding equilibrium association constant (KA) determination assay that uses fluorescence detection to detect direct binding. IEDB IEDB association constant KA|cellular MHC/direct/fluorescence|1/M cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection PDB file 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. PDB file PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 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. Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-17A production by T cells support service 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. An help desk for an instrument or a software. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON; Carlo Torniai support service material service A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Carlo Torniai PERSON: Matthew Brush material service data analysis 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. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush Statistaical analysis service, data visualization service data analysis service data service A service that has some information content entity as input and output. Data analysis service such statistical abalysis or storage service such data backup. Information content entity was used as specified input and output since it was more appropriate then data item or dataset. PERSON: Carlo Torniai PERSON: Carlo Torniai PERSON: Matthew Brush data service purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection A purified MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB half life|purified MHC/direct/fluorescence|min purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection cytometric bead array assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-9 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-9 production by T cells data storage service A service offering data backup 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. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data storage service purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection A purified MHC binding assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection 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. Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific interleukin-7 production by T cells equilibrium dissociation constant (KD) A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) IEDB KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb PERSON: Bjoern Peters, Randi Vita equilibrium dissociation constant (KD) purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters dissociation constant KD|purified MHC/competitive/fluorescence|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection training service A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. A service that offers training for a specific instrument or technique. A course to learn how to use a microscope PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush training service cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection dissociation constant KD|cellular MHC/competitive/fluorescence|nM obsolete T cell recognition of eluted MHC ligand assay An assay that identifies an MHC ligand using a T cell response assay as a readout IEDB PERSON: Randi Vita, Bjoern Peters T cell recognition 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. obsolete T cell recognition of eluted MHC ligand assay true purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB on rate|purified MHC/direct/fluorescence|nM^-1s^-1 purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-13 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to measure direct ligand binding and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. IEDB IEDB dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection dissociation constant KD|lysate MHC/competitive/radioactivity|nM intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an intracellular cytokine staining assay. CCL3/MIP-1a release|ICS IEDB IEDB intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells comparative phenotypic assessment 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 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 Philly workshop 2011 Philly workshop 2011 comparative phenotypic assessment material analysis service A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush Services performing DNA sequencing or Cell Analysis material analysis service equilibrium association constant (KA) A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) IEDB KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. PERSON: Bjoern Peters, Randi Vita equilibrium association constant (KA) cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection dissociation constant KD|cellular MHC/competitive/radioactivity|nM cell bound MHC binding assay measuring binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay measuring MHC ligand binding using MHC present on cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC binding assay measuring binding of a MHC:ligand complex qualitative binding|cellular MHC access service 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. A service that provides acess to a mass spectrometer. 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. PERSON: Matthew Brush PERSON: Carlo Torniai PERSON: Matthew Brush access service intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A T cell epitope specific tumor necrosis factor (ligand) superfamily member 11 production assay that uses an intracellular cytokine staining assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNFSF11/RANKL release|ICS intracellular cytokine staining assay measuring epitope specific 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. IEDB IEDB assay measuring a binding constant of a MHC:ligand complex binding constant|binding assay rate measurement datum A scalar measurement datum that represents the number of events occuring over a time interval IEDB PERSON: Bjoern Peters, Randi Vita 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. rate measurement datum purified MHC binding assay measuring binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay using MHC in a purified MHC molecule preparation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters purified MHC binding assay measuring binding of a MHC:ligand complex qualitative binding|purified MHC cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection A cell lysate MHC binding assay that uses radioactivity detection to detect direct binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection qualitative binding|lysate MHC/direct/radioactivity material storage service A service that offers liquid nitrogen stroage. A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material storage service cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection A cell bound MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. IEDB IEDB cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection half life|cellular MHC/direct/radioactivity|min cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection 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. IEDB PERSON: Bjoern Peters obsolete cell lysate MHC binding constant determination assay true cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses an intracellular cytokine staining assay. IEDB IEDB IL-17F release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells material processing service 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. PERSON: Carlo Torniai PERSON: Carlo Torniai PERSON: Matthew Brush material processing service purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. IEDB IEDB dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection half life|lysate MHC/direct/radioactivity|min 50% dissociation of binding temperature (Tm) 50% dissociation of binding temperature (Tm) A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. IEDB PERSON: Bjoern Peters, Randi Vita 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. melting temperature (Tm) cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection A cell lysate MHC ligand binding off rate measurement (koff) determination assay that uses radioactivity detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection off rate|lysate MHC/direct/radioactivity|1/s purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB off rate|purified MHC/direct/fluorescence|1/s purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection biological activity 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. IEDB IEDB VEGF release|biological activity biological activity assay measuring epitope specific 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. PERSON: Bjoern Peters, Randi Vita equilibrium dissociation constant (KD) approximated by IC50 http://dx.doi.org/10.1016/0006-2952(73)90196-2 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. IEDB PERSON: Bjoern Peters obsolete cell bound MHC binding constant determination assay true DNA sequence data 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. A sequence data item that is about the primary structure of DNA DNA sequence data OBI call; Bjoern Peters OBI call; Melanie Courtout The part of a FASTA file that contains the letters ACTGGGAA obsolete cell lysate MHC competitive binding assay using radioactivity detection IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC competitive binding using radioactivity competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate obsolete cell lysate MHC competitive binding assay using radioactivity detection true 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. Philly workshop 2011 Philly workshop 2011 assigning gene property based on phenotypic assessment 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. IEDB PERSON: Bjoern Peters obsolete purified MHC binding constant determination assay true cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-22 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells ELISA measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISA. ELISA measuring epitope specific vascular endothelial growth factor production by T cells IEDB IEDB VEGF release|ELISA cell lysate MHC binding assay measuring binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay using MHC in a cell lysate. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell lysate MHC binding assay measuring binding of a MHC:ligand complex qualitative binding|lysate MHC material transport service A service for chemical disposal A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. PERSON: Carlo Torniai PERSON: Carlo Torniai PERSON: Matthew Brush material transport service 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 PERSON: Bjoern Peters, Randi Vita equilibrium dissociation constant (KD) approximated by EC50 obsolete cell bound MHC direct binding assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC direct binding direct binding assay measuring MHC ligand binding using MHC derived from a cell obsolete cell bound MHC direct binding assay true half life of binding datum A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. IEDB PERSON: Bjoern Peters, Randi Vita The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. half life of binding datum purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display A purified MHC binding assay that uses a phage display binding assay to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display qualitative binding|purified MHC/direct/phage display cytometric bead array assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-7 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-7 production by T cells purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection A purified MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters half life|purified MHC/direct/radioactivity|min purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection biological activity 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. IEDB IEDB IL-7 release|biological activity biological activity assay measuring epitope specific interleukin-7 production by T cells binding 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. A peptide binding to an MHC molecule to form a complex. IEDB PERSON: Bjoern Peters, Randi Vita The process of material entities forming complexes. binding intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses an intracellular cytokine staining assay. IEDB IEDB IL-17A release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection A purified MHC binding assay that uses fluorescence detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection qualitative binding|purified MHC/direct/fluorescence direct binding assay 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. IEDB PERSON:Bjoern Peters, Randi Vita a binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. direct binding assay purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB IEDB half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection competitive inhibition of binding assay 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. 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. IEDB IEDB competitive inhibition of binding assay cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection A cell bound MHC binding assay that uses fluorescence to detect loss of binding of a known reference ligand due to competition by the ligand under investigation IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection qualitative binding|cellular MHC/competitive/fluorescence X-ray crystallography assay determining the 3D structure of a MHC:ligand complex 3D structure|x-ray crystallography|angstroms A MHC binding 3D structure determination of MHC molecule:epitope complex assay that uses an X-ray crystallography assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters X-ray crystallography assay determining the 3D structure of a MHC:ligand complex PDB file chain 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 IEDB PDB file chain PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex 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. IEDB IEDB cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM data maintenance service 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. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data maintenance service cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection A cell bound MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection qualitative binding|cellular MHC/competitive/radioactivity biological activity 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. G-CSF release|biological activity IEDB IEDB biological activity assay measuring epitope specific 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 An assay of epitope specific interleukin-21 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-21 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection A cell bound MHC binding assay that uses radioactivity detection to detect direct binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection qualitative binding|cellular MHC/direct/radioactivity binding off rate measurement datum (koff) A rate measurement datum of how quickly bound complexes disassociate IEDB PERSON: Bjoern Peters, Randi Vita binding off rate measurement datum (koff) purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection 50% dissociation temperature|purified MHC/direct/fluorescence|�C A purified MHC binding assay that uses fluorescence detection to measure the 50% dissociation of binding temperature of direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection binding on rate measurement datum (kon) A rate measurement datum of how quickly bound complexes form IEDB PERSON: Bjoern Peters, Randi Vita binding on rate measurement datum (kon) cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection A cell bound MHC binding assay that uses fluorescence detection to detect direct binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection qualitative binding|cellular MHC/direct/fluorescence biological activity 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. IEDB IEDB TNFSF11/RANKL release|biological activity biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection A purified MHC binding assay that uses radioactivity detection to measure direct ligand binding. IEDB IEDB purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection qualitative binding|purified MHC/direct/radioactivity intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-8 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses a cytometric bead array assay. IEDB IEDB IL-23 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells obsolete purified MHC direct binding assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation obsolete purified MHC direct binding assay purified MHC direct binding true 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. Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific vascular endothelial growth factor production by T cells purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection GenBank ID GenBank ID GenBank Record ID NIAID GSCID-BRC A CRID symbol uniquely indentifies the submitted GeneBank sequence record. NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng investigation description study description A textual entity that describes an investigation. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng investigation description project description specimen identifier NIAID GSCID-BRC A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Specimen ID NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng specimen ID specimen identifier PubMed ID 1 Publication Citation 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/ NIAID GSCID-BRC PMID Person: Chris Stoeckert, Jie Zheng PubMed ID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID average depth of sequence coverage NIAID GSCID-BRC An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. Depth of Coverage - Average NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng average depth of sequence coverage specimen collection time measurement datum Specimen Collection Date A time measurement datum that is the measure of the time when the specimens are collected. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng collection date specimen collection time measurement datum latitude coordinate measurement datum NIAID GSCID-BRC Specimen Collection Location - Latitude A measurement datum that is the measure of the latitude coordinate of a site. NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng latitude latitude coordinate measurement datum longitude coordinate measurement datum Specimen Collection Location - Longitude A measurement datum that is the measure of the longitude coordinate of a site. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng longitude longitude coordinate measurement datum investigation title study title A textual entity that denotes an investigation. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person:Chris Stoeckert, Jie Zheng investigation title project title organism identification objective A biological feature identification objective to identify the organism species in a specimen. Penn Group Person: Chris Stoeckert, Jie Zheng organism identification objective organism identification assay An assay that identifies the organism species in a specimen. Organism Detection Method NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng organism identification assay sequence annotation algorithm NIAID GSCID-BRC Annotation Algorithm An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng sequence annotation algorithm 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 Bioinformatics Resource Center NIAID GSCID-BRC Person: Chris Stoeckert, Jie Zheng Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers country name NIAID GSCID-BRC Specimen Collection Location - Country 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. NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng Website: http://en.wikipedia.org/wiki/Country country name investigation identifier A CRID symbol used to identify an investigation. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zhneg investigation identifier project ID grant identifier NIAID GSCID-BRC A CRID symbol used to identify a grant. NIAID GSCID-BRC metadata working group Person: Chris Stoeckert, Jie Zheng grant ID grant identifier analytical chromatography 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. 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. IEDB IEDB analytical chromatography electron microscopy imaging assay 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. IEDB IEDB 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. electron microscopy imaging assay immuno staining assay A detection of molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. 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. IEDB IEDB immuno staining assay purified material 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 mixture of peptide molecules that has been run through an HPLC column to remove 65 GROUP: OBI call OBI conference call purified material calorimetric binding assay 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. A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (ΔH) 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 . IEDB IEDB calorimetric binding assay antibody binding detection by fluorescence quenching 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). IEDB IEDB 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). antibody binding detection by fluorescence quenching grant AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 Group: OBI OBI grant 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 dissociation constant KD|antigen inhibition (~ IC50)|nM biological activity assay measuring epitope specific Ig-mediated histamine release A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific Ig-mediated histamine release histamine release|biological activity biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation A B cell epitope dependent biological activity determination assay that detects antigen activation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters antigen activation|biological activity biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation biological activity assay measuring epitope specific complement-dependent cytotoxicity A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific complement-dependent cytotoxicity complement-dependent cytotoxicity|biological activity biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters antibody-dependent cellular cytotoxicity|biological activity biological activity assay measuring epitope specific 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific immunoglobulin-mediated neutralization neutralization |biological activity biological activity assay measuring epitope specific opsonization A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific opsonization opsonization|biological activity calorimetry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a calorimetric binding assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters calorimetry assay measuring binding of a B cell epitope:antibody complex qualitative binding|calorimetry electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex 3D structure|electron microscopy A B cell epitope 3D structure determination assay that uses an electron microscopy imaging assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex NMR assay determining the 3D structure of a B cell epitope:antibody complex 3D structure|nuclear magnetic resonance (NMR) A B cell epitope 3D structure determination assay that uses a nuclear magnetic resonance assay. IEDB NMR assay determining the 3D structure of a B cell epitope:antibody complex PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cross blocking assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an antibody cross-blocking assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cross blocking assay measuring binding of a B cell epitope:antibody complex qualitative binding|cross blocking RIA measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a radio immuno assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters RIA measuring binding of a B cell epitope:antibody complex qualitative binding|radio immuno assay (RIA) immunoblot assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunoblot assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters immunoblot assay measuring binding of a B cell epitope:antibody complex qualitative binding|western blot plasmon resonance assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a surface plasmon resonance assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters plasmon resonance assay measuring binding of a B cell epitope:antibody complex qualitative binding|surface plasmon resonance (SPR) immuno staining assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immuno staining assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters immuno staining assay measuring binding of a B cell epitope:antibody complex qualitative binding|immuno staining immunoprecipitation assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunoprecipitation assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters immunoprecipitation assay measuring binding of a B cell epitope:antibody complex qualitative binding|immunoprecipitation mass spectrometry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a mass spectrometry assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters mass spectrometry assay measuring binding of a B cell epitope:antibody complex qualitative binding|mass spectrometry phage display assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a phage display binding assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters phage display assay measuring binding of a B cell epitope:antibody complex qualitative binding|phage display electron microscopy assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an electron microscopy imaging assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters electron microscopy assay measuring binding of a B cell epitope:antibody complex qualitative binding|electron microscopy ELISA measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunosorbent assay. ELISA measuring binding of a B cell epitope:antibody complex IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters qualitative binding|ELISA ELISPOT assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunospot assay. ELISPOT assay measuring binding of a B cell epitope:antibody complex IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters qualitative binding|ELISPOT flow cytometry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a flow cytometry assay. IEDB IEDB flow cytometry assay measuring binding of a B cell epitope:antibody complex qualitative binding|flow cytometry intracellular material detection assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay. IEDB IEDB granzyme A release|intracellular staining intracellular material detection assay measuring epitope specific granzyme A release by T cells chromatography assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an analytical chromatography assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters chromatography assay measuring binding of a B cell epitope:antibody complex qualitative binding|chromatography 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. IEDB NMR assay measuring binding of a B cell epitope:antibody complex PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters qualitative binding|nuclear magnetic resonance (NMR) ELISA measuring epitope specific granulysin release by T cells A T cell epitope specific granulysin release assay that uses an ELISA. ELISA measuring epitope specific granulysin release by T cells IEDB IEDB granulysin release|ELISA intracellular material detection assay measuring epitope specific granulysin release by T cells A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay. IEDB IEDB granulysin release|intracellular staining intracellular material detection assay measuring epitope specific granulysin release by T cells cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection off rate|cellular MHC/direct/fluorescence|1/s cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection A cell bound MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection on rate|cellular MHC/direct/fluorescence|nM^-1s^-1 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection split-ubiquitin assay PERSON:Philippe Rocca-Serra; Marcus Chibucos 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. Nikko E, André B. Eukaryot Cell. 2007 Aug;6(8):1266-77. Epub 2007 May 18. PMID: 17513562 adapted from wikipedia add regulatory region DNA binding;sequence-specific DNA binding;obo:GO:0000975;obo:GO:0043565; is a kind of yeast 2 hybrid system which enables membrane soluble proteins to be screened. two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (\"Cub\", residues 35–76) and an N-terminal ubiquitin moiety (\"Nub\", residues 1–34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait–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. split-ubiquitin assay far-Western blot PERSON:Philippe Rocca-Serra; Marcus Chibucos Studying protein-protein interactions via blot overlay or Far Western blot. Hall RA. Methods Mol Biol. 2004;261:167-74. Review. PMID: 15064457 adapted from ECO, PMID:18079728 far-Western blot is a adaptation on the western blot assay to explore protein-protein interaction. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. RNA protection 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. Wildey GM, Billetz AC, Matyas JR, Adams ME, McDevitt CA. J Orthop Res. 2001 Jul;19(4):650-8. PMID: 11518275 PERSON:Philippe Rocca-Serra; Marcus Chibucos RNA protection assay RPA is a technique to assess the presence and estimate 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. RPA; RNAse protection assay adapted from wikipedia + PMID:16491611 electrophoretic mobility shift assay EMSA,gel shift assay, gel mobility shift assay, band shift assay, gel retardation assay Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. Puranik S, Kumar K, Srivastava PS, Prasad M. Plant Signal Behav. 2011 Oct;6(10):1588-90. Epub 2011 Oct 1. PMID: 21918373 PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:6269071 electrophoretic mobility shift assay is an assay which aims to provide information about Protein-DNA or Protein-RNA interaction and which used gel electrophoresis and relies 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. gene knock-down assay PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:17430206 gene knock-down assay is 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 Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. PMID:20543846 PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID: 20543846 nano-CAGE nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples nano-cap analysis of gene expression cap analysis of gene expression 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160 An assay which aims at monitoring 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 CAGE PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:14663149 cap analysis of gene expression ELISA measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses an ELISA. ELISA measuring epitope specific interleukin-17A production by T cells IEDB IEDB IL-17A release|ELISA detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-7 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific granulysin production by T cells 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. Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific granzyme A production by T cells yeast 2-hybrid PERSON:Philippe Rocca-Serra; Marcus Chibucos Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. Reuter T, Herterich S, Bernhard O, Hoehn H, Gross HJ. Blood. 2000 Jan 15;95(2):719-20. PMID: 10627486 Y2H adapted from wikipedia add regulatory region DNA binding;GO:0043565; yeast 2 hybrid screen is an assay meant to discover 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.[1][2] The Y2H is thus a protein-fragment complementation assay. yeast 2-hybrid Sos-recruitment assay PERSON:Philippe Rocca-Serra; Marcus Chibucos SRS Sos-recruitment assay The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. Schönhofer-Merl S, Torres-Ruiz RA. Mol Genet Genomics. 2010 May;283(5):439-49. Epub 2010 Mar 19. PMID: 20300944 adapted from the original publication by Aronheim et al, 1997. PMID: 9154808 add regulatory region DNA binding;GO:0043565; is a kind of yeast 2 hybrid system 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, interacting proteins for targeted domain can be detected. yeast one-hybrid PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID: 22218861 The one-hybrid variation of this technique is designed to investigate protein–DNA interactions and uses a single fusion protein in which the AD is linked directly to the binding domain. Y1H Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764. PMID: 22037702 add regulatory region DNA binding;obo:GO:0000975; yeast one-hybrid bacterial one-hybrid is a method for identifying 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 A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. Nucleic Acids Res. 2008 May;36(8):2547-60. Epub 2008 Mar 10. PMID: 18332042 B1H PERSON:Philippe Rocca-Serra; Marcus Chibucos add regulatory region DNA binding;obo:GO:0000975; bacterial one-hybrid http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system chromosome organization assay by fluorescence in situ hybridization Changed label from fluorescence in situ hybridization as per tracker item #788 Duplication of intrachromosomal insertion segments 4q32→q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization.PMID:22384449 FISH PERSON:Philippe Rocca-Serra; Marcus Chibucos chromosome organization assay by fluorescence in situ hybridization is an in situ hybridization assay that uses fluorescence as means of detection chromosomal integrity methylation-specific polymerase chain reaction 2015-03-30 OBI dev call: The assay was defined as equvivalent to (assay and (has_specified_input some 'binding complex 3D structure determination assay') and (has_specified_output some ('data item' and ('is about' some 'regulation of DNA methylation')))) and (achieves_planned_objective some 'epigenetic modification identification objective') 'binding complex 3D structure determination assay' is a process and cannot be the input of another process which cause inconsistent. In the call, we decided to remove axiom and will discuss it in the assay harmonization discussion. see tracker: https://sourceforge.net/p/obi/obi-terms/747/ MSP 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 PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:8790415 is an assay which 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. methylation-specific polymerase chain reaction amplification of intermethylated sites (AIMS) assay amplification of intermethylated sites (AIMS) is an assay appropriate for genome-wide estimates of DNA methylation and the discovery of specific methylated 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. AIMS assay,intermethylated site amplification Analysis of DNA methylation by amplification of intermethylated sites (AIMS).PMID:18987810 PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID: 18987810 amplification of intermethylated sites (AIMS) assay in situ hybridization ISH PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:9021518 Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 in situ hybridization is an assay using artificially induced nucleic hybridization to localize a specific DNA or RNA sequence in a portion or section of tissue contact representative role A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. Person: Chris Stoeckert Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 NIAID GSCID-BRC contact representative role cytochalasin-induced inhibition of actin polymerization assay PERSON:Philippe Rocca-Serra; Marcus Chibucos add ;actin filament polymerization obo:GO:0070358; cytochalasin-induced inhibition of actin polymerization assay is 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 OBI group PERSON:Philippe Rocca-Serra is an objective specification which aims to discover molecular function realized by a molecular entity molecular function identification objective cellular structure feature identification objective OBI group PERSON:Philippe Rocca-Serra 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 protection from challenge in vivo intervention experiment based on reduction of fertility. IEDB PERSON:Randi Vita, James Overton, Bjoern Peters in vivo assay measuring B cell epitope specific protection from fertility protection from fertility|in vivo assay 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters in vivo assay measuring B cell epitope specific tolerance induction tolerance|in vivo assay 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters hypersensitivity|in vivo assay in vivo assay measuring B cell epitope specific induction of hypersensitivity biological activity assay measuring epitope specific immune complex formation A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters agglutination|biological activity biological activity assay measuring epitope specific immune complex formation in vivo assay measuring B cell epitope specific protection based on survival A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on survival. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters in vivo assay measuring B cell epitope specific protection based on survival survival from challenge|in vivo assay 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters decreased disease|in vivo assay in vivo assay measuring B cell epitope specific treatment of disease biological activity 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring B cell epitope specific in vivo activity in vivo activity|biological activity antibody cross-blocking assay 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. IEDB IEDB 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. antibody cross-blocking assay antibody inhibition of antibody binding immunoprecipitation assay 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. 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. IEDB IEDB immunoprecipitation assay 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters antigen inhibition assay measuring binding of a B cell epitope:antibody complex qualitative binding|antigen inhibition immunoglobulin binding to epitope Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus IEDB PERSON: Bjoern Peters, Randi Vita a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). immunoglobulin binding to epitope assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope recognition assay that detects qualitative binding. IEDB IEDB assay measuring qualitiative binding of a B cell epitope:antibody complex qualitative binding|binding assay biological activity 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. IEDB IEDB biological activity assay measuring epitope specific activation of additional immune response in vitro secondary in vitro activity|biological 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. IEDB IEDB antibody activity inhibition|biological activity biological activity assay measuring epitope specific antigen inhibition of antibody activity assay measuring B cell epitope specific biological activity A B cell epitope recognition assay that detects biological activity. IEDB IEDB assay measuring B cell epitope specific biological activity biological activity|any method immunoglobulin mediated histamine release 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. IEDB PERSON: Bjoern Peters, Randi Vita The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. immunoglobulin mediated histamine release 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring a binding constant of a B cell epitope:antibody complex binding constant|binding assay in vivo assay measuring B cell epitope specific protection from challenge An efficacy of B cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters in vivo assay measuring B cell epitope specific protection from challenge protection from challenge|in vivo assay 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters disease exacerbation|in vivo assay in vivo assay measuring B cell epitope specific disease exacerbation obsolete B cell epitope direct binding assay A direct binding assay using a assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters direct binding assay obsolete B cell epitope direct binding assay true B cell epitope specific opsonization B cell epitope specific opsonization Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters opsonization resulting from antibody binding to epitope B cell epitope specific immunoglobulin-mediated neutralization B cell epitope specific immunoglobulin-mediated neutralization Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters competitive binding assay obsolete B cell epitope competitive binding assay true B cell epitope specific complement-dependent cytotoxicity B cell epitope specific complement-dependent cytotoxicity Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters complement-dependent cytotoxicity resulting from antibody binding to epitope B cell epitope specific antibody-dependent cellular cytotoxicity B cell epitope specific antibody-dependent cellular cytotoxicity Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the on rate [kon] of a B cell epitope:antibody complex on rate|binding assay|M^-1s^-1 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the association constant [KA] of a B cell epitope:antibody complex association constant KA|binding assay|1/nM B cell epitope specific immune complex formation B cell epitope specific immune complex formation Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters immune complex formation resulting from antibody binding to epitope 3D structure determining assay of a 3D B cell epitope:antibody complex 3D structure determining assay of a 3D B cell epitope:antibody complex 3D structure|any method A B cell epitope recognition assay that characterizes the 3D structure of an antibody / BCR with a ligand. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters B cell epitope specific hypersensitivity B cell epitope specific hypersensitivity Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the off rate [koff] of a B cell epitope:antibody complex off rate|binding assay|1/s biological activity assay measuring epitope specific hemagglutination inhibition A B cell epitope qualitative binding to antibody assay that uses a viral hemagglutination inhibition assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific hemagglutination inhibition hemagglutination inhibition|biological activity B cell epitope specific histamine secretion mediated by immunoglobulin B cell epitope specific histamine secretion mediated by immunoglobulin Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope quenching assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an antibody binding detection by fluorescence quenching. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters qualitative binding|quenching quenching assay measuring binding of a B cell epitope:antibody complex RIA 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 radio immuno assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex dissociation constant KD|radio immuno assay (RIA)|nM ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an enzyme-linked immunosorbent assay. ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters dissociation constant KD|ELISA|nM quenching 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 an antibody binding detection by fluorescence quenching assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters dissociation constant KD|quenching|nM quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a surface plasmon resonance assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters association constant KA|surface plasmon resonance (SPR)|1/nM surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex surface plasmon resonance 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 surface plasmon resonance assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters dissociation constant KD|surface plasmon resonance (SPR)|nM surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an antibody binding detection by fluorescence quenching assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters association constant KA|quenching|1/nM quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a calorimetric binding assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters association constant KA|calorimetry|1/nM calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex calorimetry 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 calorimetric binding assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex dissociation constant KD|calorimetry|nM ELISA measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an enzyme-linked immunosorbent assay. ELISA measuring the association constant [KA] of a B cell epitope:antibody complex IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters association constant KA|ELISA|1/nM RIA measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a radio immuno assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters RIA measuring the association constant [KA] of a B cell epitope:antibody complex 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters X-ray crystallography [Ã…] obsolete B cell epitope specific X-ray crystallography assay true X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex 3D structure|x-ray crystallography|angstroms A B cell epitope 3D structure determination assay that uses an X-ray crystallography assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope binding off rate measurement (koff) determination assay that uses a surface plasmon resonance assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters off rate|surface plasmon resonance (SPR)|1/s surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope binding off rate measurement (koff) determination assay that uses an antibody binding detection by fluorescence quenching assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters off rate|quenching|1/s quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope on rate measurement (kon) determination assay that uses a surface plasmon resonance assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters on rate|surface plasmon resonance (SPR)|M^-1s^-1 surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope on rate measurement (kon) determination assay that uses an antibody binding detection by fluorescence quenching assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters on rate|quenching|M^-1s^-1 quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-1b release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an intracellular cytokine staining assay. IEDB IL-1a release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells IEDB IL-1a release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-1a release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses a cytometric bead array assay. IEDB IL-1a release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells ELISPOT assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interferon-beta production by T cells IEDB IFNb release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an intracellular cytokine staining assay. IEDB IFNb release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. G-CSF release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells ELISA measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an ELISA. ELISA measuring epitope specific interferon-beta production by T cells IEDB IFNb release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. G-CSF release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells G-CSF release|ELISPOT IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a cytometric bead array assay. CXCL9/MIG release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells selection criterion A directive information entity which defines and states a principle of standard by which selection process may take place. OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ Person: Philippe Rocca-Serra rats should be aged between 6 and 8 weeks and weight between 180-250grams selection criterion selection rule ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISPOT assay. CXCL9/MIG release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CXCL9/MIG release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISPOT assay. CCL4/MIP-1b release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells IEDB IEDB detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CXCL12/SDF-1 release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-X-C motif) ligand 13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CXCL13/BLC release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-X-C motif) ligand 16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CXCL16 release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-C motif) ligand 21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL21/SLC release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL22/MDC release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a cytometric bead array assay. CCL4/MIP-1b release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL4/MIP-1b release|RNA/DNA detection IEDB IEDB detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific vascular endothelial growth factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB VEGF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-C motif) ligand 19 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL19/MIP-3b release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an intracellular cytokine staining assay. CCL1/TCA-3 release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells specimen collector role NIAID GSCID-BRC Person: Jie Zheng, Chris Stoeckert Penn Group An Investigation agent role borne by a person or organization which is realized in a specimen collection process. specimen collector role intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB VEGF release|ICS intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells IEDB IEDB VEGF release|ELISPOT biological activity 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. IEDB IL-17F release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-17F production by T cells biological activity 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. IEDB IL-17A release|biological activity PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific interleukin-17A production by T cells biological activity 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. CCL21/SLC release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells biological activity 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 IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells 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 IEDB IEDB biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells 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. CCL22/MDC release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells biological activity 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. CXCL16 release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells biological activity 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. CXCL13/BLC release|biological activity IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific 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 assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISPOT assay. CCL3/MIP-1a release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a cytometric bead array assay. CCL9/MIP-1g release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL9/MIP-1g release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an intracellular cytokine staining assay. CCL2/MCP-1 release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISPOT assay. CCL2/MCP-1 release|ELISPOT ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an intracellular cytokine staining assay. CCL9/MIP-1g release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISPOT assay. CCL9/MIP-1g release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses a cytometric bead array assay. IEDB IEDB VEGF release|cytometric bead array cytometric bead array assay measuring epitope specific 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 An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB TNF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells intracellular cytokine staining assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an intracellular cytokine staining assay. CCL5/RANTES release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific RANTES production by T cells ELISPOT assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an ELISPOT assay. CCL5/RANTES release|ELISPOT ELISPOT assay measuring epitope specific RANTES production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific lymphotoxin A production by T cells IEDB IEDB lymphotoxin A/TNFb release|ELISPOT detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL3/MIP-1a release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses a cytometric bead array assay. IEDB IEDB cytometric bead array assay measuring epitope specific 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 An assay of epitope specific lymphotoxin A production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 assay of epitope specific IP-10 production by T cells that uses an ELISPOT assay. CXCL10/IP-10 release|ELISPOT ELISPOT assay measuring epitope specific IP-10 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an intracellular cytokine staining assay. CXCL10/IP-10 release|ICS IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells ELISPOT assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-9 production by T cells IEDB IEDB IL-9 release|ELISPOT intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-9 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-9 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells ELISPOT assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-8 production by T cells IEDB IEDB IL-8 release|ELISPOT detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB IL-8 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells ELISPOT assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-3 production by T cells IEDB IL-3 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-7 production by T cells IEDB IL-7 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-7 production by T cells IEDB IEDB IL-7 release|ELISPOT intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an intracellular cytokine staining assay. IEDB IEDB IL-7 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-27 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells cytometric bead array assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a cytometric bead array assay. IEDB IL-3 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-3 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-3 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells biological activity 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. IEDB IEDB biological activity assay measuring epitope specific granzyme A release by T cells granzyme A release|biological activity biological activity 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. IEDB IEDB biological activity assay measuring epitope specific granulysin release by T cells granulysin release|biological activity cytometric bead array assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses a cytometric bead array assay. IEDB IL-27 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-27 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-23 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells ELISPOT assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-27 production by T cells IEDB IL-27 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-27 production by T cells IEDB IL-27 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-18 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-X-C motif) ligand 13 production by T cells ELISPOT assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-18 production by T cells IEDB IL-18 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-X-C motif) ligand 12 production by T cells 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. Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-C motif) ligand 22 production by T cells 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. Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-X-C motif) ligand 16 production by T cells ELISPOT assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-22 production by T cells IEDB IL-22 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-23 production by T cells IEDB IL-23 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters 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. Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-C motif) ligand 21 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-18 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific 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. Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope specific chemokine (C-C motif) ligand 19 production by T cells ELISPOT assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-21 production by T cells IEDB IL-21 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL1/TCA-3 release|RNA/DNA detection IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a cytometric bead array assay. CCL1/TCA-3 release|cytometric bead array IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISPOT assay. CCL1/TCA-3 release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses an ELISPOT. ELISPOT assay measuring epitope specific interleukin-17F production by T cells IEDB IL-17F release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses an ELISA. ELISA measuring epitope specific interleukin-17F production by T cells IEDB IL-17F release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-17F release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells ELISPOT assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses an ELISPOT. ELISPOT assay measuring epitope specific interleukin-17A production by T cells IEDB IL-17A release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters drawing a conclusion A planned process in which new information is inferred from existing information. drawing a conclusion 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. cytometric bead array assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses a cytometric bead array assay. IEDB IL-18 release|cytometric bead array PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters cytometric bead array assay measuring epitope specific interleukin-18 production by T cells detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-16 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells ELISA measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-16 production by T cells IEDB IL-16 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-16 production by T cells IEDB IL-16 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-16 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific 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 T cell epitope specific interleukin-17A production assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-17A release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an intracellular cytokine staining assay. IEDB IL-1b release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells IEDB IEDB IL-1b release|ELISPOT detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. IEDB IL-15 release|RNA/DNA detection PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells ELISPOT assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-12 production by T cells IEDB IL-12 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-15 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells ELISPOT assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-15 production by T cells IEDB IL-15 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters chromatin interaction analysis by paired-end tag sequencing Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIA-PET assay ENCODE project ChIA-PET Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] http://en.wikipedia.org/wiki/ChIA-PET 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. chromatin interaction analysis by paired-end tag sequencing structural analysis by paired-end tag sequencing An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. DNA-PET Person: Venkat Malladi, Chris Stoeckert, Jie Zheng 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] 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] DNA-PET assay ENCODE project structural analysis by paired-end tag sequencing transcript analysis by paired-end tag sequencing An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions. 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] 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] Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ENCODE project RNA-PET assay RNA-PET transcript analysis by paired-end tag sequencing transcription start site identification objective Person: Chris Stoeckert, Jie Zheng A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Penn Group transcription start site identification objective paired-end library preparation Person: Venkat Malladi, Jie Zheng ENCODE project 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. Venkat Malladi, Jie Zheng paired-end library preparation 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] DNase-seq http://en.wikipedia.org/wiki/DNase-Seq ENCODE project An assay to identify the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. DNase I hypersensitive sites sequencing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng DNase-seq assay protein and RNA interaction identification objective Jie Zheng JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. A sequence feature identification objective that aims to characterize the interactions between protein and RNA. Person: Jie Zheng protein and RNA interaction identification objective RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay RIP-seq assay ENCODE project An assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] RIP-seq Person: Venkat Malladi, Chris Stoeckert, Jie Zheng 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] cross-linking immunoprecipitation high-throughput sequencing assay ENCODE project Licatalosi et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27 456: 464-469 [PMID:18978773] HITS-CLIP An assay that employs UV-crosslinking between RNA and the protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput used for screening for RNA sequences that interact with a particular RNA-binding protein. CLIP-seq 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] CLIP-seq Person: Venkat Malladi, Chris Stoeckert, Jie Zheng cross-linking immunoprecipitation high-throughput sequencing assay formaldehyde-assisted isolation of regulatory elements assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. FAIRE-seq 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] ENCODE project http://en.wikipedia.org/wiki/FAIRE-Seq FAIRE-seq assay formaldehyde-assisted isolation of regulatory elements assay 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] 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 by use of methylation sensitive restriction enzymes to fragment DNA. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng MRE-seq ENCODE project MRE-seq assay methylation-sensitive restriction enzyme sequencing assay 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] RRBS assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol that enriches CG-rich parts of the genome. Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174] RRBS ENCODE project reduced representation bisulfite sequencing assay reduced representation bisulfite-seq shotgun bisulfite-seq assay Shotgun bisulfite sequencing whole-genome shotgun bisulfite sequencing WGSBS ENCODE project Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030] Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng WGBS A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. shotgun bisulfite-seq assay whole genome bisulfite sequencing RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay An assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. 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] 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] ENCODE project RAMPAGE Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay assay array A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group assay array secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in 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. PERSON: Matthew Brush 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. secondary cultured cell Person: Matthew Brush establishing cell line Person: Matthew Brush 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. establishing cell line PERSON:Matthew Brush 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). genetic material genomic material 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. 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). hereditary genetic material 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). genetic material OBI developer calls, March 4 2013 and March 11 2013 Illumina BeadChip An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://www.illumina.com/technology/beadarray_technology.ilmn Illumina BeadChip PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi Illumina methylation BeadChip Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg A BeadChip made for an analyte assay that generates information about DNA methylation. Illumina methylation BeadChip LSRFortessa X-20 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. Anna Maria Masci LSRFortessa X-20 http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg sequence assembly process NIAID GSCID-BRC metadata working group NIAID GSCID-BRC A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). Alejandra Gonzalez-Beltran PERSON: Jie Zheng, Chris Stoeckert PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Philippe Rocca-Serra sequence assembly process number of errors Alejandra Gonzalez-Beltran Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2 PRS, AGB Philippe Rocca-Serra a data item that is the number of times that a given process failed, as an integer number of errors random access memory size Alejandra Gonzalez-Beltran 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" PRS, AGB Philippe Rocca-Serra random access memory size 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 cultured immune cell population 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. a cultured cell population comprised of a single type of immune system cell immune cell culture sample PERSON:Matthew Brush PERSON:Matthew Brush cultured immune cell population cell culture 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. A material entity comprised of cultured cells and the media in which they are being propagated or stored. PERSON:Matthew Brush cell culture OBI-CLO Alignment Working Group (Spring 2013) random access memory Alejandra Gonzalez-Beltran Philippe Rocca-Serra RAM 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 http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02 random access memory establishing primary cell culture 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. 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. PERSON: Matthew Brush 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 establishing primary cell culture reagent PERSON:Matthew Brush PERSON:Matthew Brush 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). 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. reagent organization of specimen provider principal investigator NIAID GSCID-BRC metadata working group NIAID GSCID-BRC An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng Sample Provider PI's Institution organization of specimen provider principal investigator organization of Bioinformatics Resource Center contact person Bioinformatics Resource Center Contact's Institution NIAID GSCID-BRC PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center organization of Bioinformatics Resource Center contact person target material in specimen specification NIAID GSCID-BRC metadata working group PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC Target Material A plan specification which specifies the type of material that will be assayed in an investigation. Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. target material in specimen specification Bioinformatics Resource Center contact person PERSON: Chris Stoeckert, Jie Zheng Bioinformatics Resource Center contact person NIAID GSCID-BRC metadata working group NIAID GSCID-BRC Bioinformatics Resource Center Contact Name A person who is the contact representative of a Bioinformatics Resource Center 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. NIAID GSCID-BRC metadata working group PERSON: Chris Stoeckert, Jie Zheng Sample Scope NIAID GSCID-BRC specimen-based scope of investigation specification specimen repository organization NIAID GSCID-BRC metadata working group An organization that provides a service to store and distribute specimens NIAID GSCID-BRC Specimen Repository PERSON: Chris Stoeckert, Jie Zheng specimen repository organization email address of Bioinformatics Resource Center contact person An email address of the person who is contact representative of a Bioinformatics Resource Center NIAID GSCID-BRC metadata working group NIAID GSCID-BRC PERSON: Chris Stoeckert, Jie Zheng Bioinformatics Resource Center Contact's email email address of Bioinformatics Resource Center contact person sequencing facility contact person NIAID GSCID-BRC A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng Sequencing Facility Contact Name NIAID GSCID-BRC metadata working group sequencing facility contact person specimen provider principal investigator A person who is a principal investigator and provides the specimen NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC specimen provider principal investigator email address of specimen collector NIAID GSCID-BRC Specimen Collector's email PERSON: Chris Stoeckert, Jie Zheng An email address of the person collecting the specimen NIAID GSCID-BRC metadata working group email address of specimen collector sequencing facility organization Sequencing Facility An organization that provides sequence determination service NIAID GSCID-BRC metadata working group NIAID GSCID-BRC PERSON: Chris Stoeckert, Jie Zheng sequencing facility organization specification of data to be generated in an investigation An objective specification which indicates the type of data that will be generated and submitted to a database. Project Objectives Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC NIAID GSCID-BRC metadata working group specification of data to be generated in an investigation organization of specimen collector An organization that is the affiliation of the person collecting the specimen Specimen Collector's Institution NIAID GSCID-BRC metadata working group NIAID GSCID-BRC PERSON: Chris Stoeckert, Jie Zheng organization of specimen collector email address of sequencing facility contact person PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email NIAID GSCID-BRC An email address of the contact representative at the sequencing facility email address of sequencing facility contact person specimen collector Specimen Collector Name A person who collects the specimen NIAID GSCID-BRC metadata working group PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC specimen collector investigation assay specification A plan specification which indicates the assay type used to obtain data. Some examples of Project Method are Sequence, Array, Mass Spectrometry NIAID GSCID-BRC metadata working group Project Method NIAID GSCID-BRC PERSON: Chris Stoeckert, Jie Zheng investigation assay specification organization of sequencing facility contact person An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC Sequencing Facility Contact's Institution organization of sequencing facility contact person comment on investigation NIAID GSCID-BRC metadata working group NIAID GSCID-BRC A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng Comments comment on investigation target capture specification NIAID GSCID-BRC PERSON: Chris Stoeckert, Jie Zheng Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey NIAID GSCID-BRC metadata working group Target Capture 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. target capture specification specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID NIAID GSCID-BRC specimen identifier assigned by specimen repository specimen identifier assigned by sequencing facility Sample ID - Sequencing Facility NIAID GSCID-BRC A specimen identifier which is assigned by a sequencing facility NIAID GSCID-BRC metadata working group PERSON: Chris Stoeckert, Jie Zheng specimen identifier assigned by sequencing facility sample preparation for sequencing assay A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method NIAID GSCID-BRC sample preparation for sequencing assay email address of specimen provider principal investigator NIAID GSCID-BRC metadata working group NIAID GSCID-BRC An email address of the principal investigator providing the specimens for the investigation Sample Provider PI's email PERSON: Chris Stoeckert, Jie Zheng email address of specimen provider principal investigator sequencing service Person: Jie Zheng Adpated from 'DNA 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. NIAID GSCID-BRC sequencing service secondary cultured cell population 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. secondary cell culture sample A cultured cell population that is derived through one or more passages in culture. PERSON:Matthew Brush 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. secondary cultured cell population PERSON:Matthew Brush cancer cell line An immortal cell line derived from a transformed cell that was part of a malignant tumor. cancer cell line immortalizing cell line transformation a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture immortalizing cell line transformation testable hypothesis 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 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. hypothesis Group:2013 Philly Workshop group Group:2013 Philly Workshop group An information content entity that expresses an assertion that is intended to be tested. testable hypothesis conclusion based on data 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. Group:2013 Philly Workshop group conclusion based on data Group:2013 Philly Workshop group 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". primary cell culture A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. OBI-CLO Alignment Working Group (Spring 2013) PERSON:Matthew Brush primary cell culture cell line 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. OBI-CLO Alignment Working Group (Spring 2013) PERSON:Matthew Brush cell line culture cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. PERSON: Matthew Brush cell freezing medium computation run time Alejandra Gonzalez-Beltran Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4 PRS,AGB Philippe Rocca-Serra computation run time computation run time datum 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. multiplex ligation-mediated amplification LMA 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. MLPA Multiplex ligation-dependent probe amplification Chris Stoeckert, Jie Zheng multiplex ligation-mediated amplification web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ DNA replication timing by array assay Venkat Malladi, Chris Stoeckert, Jie Zheng An assay in which timing of DNA replication is quantified as a function of genome position using array technology. Repli-chip Repli-chip assay ENCODE project Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] DNA replication timing by array assay Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] DNA replication identification objective Group: Penn Group A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. Chris Stoeckert, Jie Zheng DNA replication identification objective chromosome conformation identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective RNA-binding protein immunoprecipitation array profiling assay ENCODE project An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] RIP-chip assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RIP-chip Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] RNA-binding protein immunoprecipitation array profiling assay Carbon-copy chromosome conformation capture assay ENCODE project Venkat Malladi, Chris Stoeckert, Jie Zheng "Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]" An assay that is used to analyze the organization of chromosomes at the genome-wide scale. 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] 5C 5C assay Carbon-copy chromosome conformation capture assay DNA replication timing by sequencing assay An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. ENCODE project 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] 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] Repli-seq Repli-seq assay DNA replication timing by sequencing assay Venkat Malladi, Chris Stoeckert, Jie Zheng RNA-binding protein immunoprecipitation tiling array profiling Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] A 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). Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RNA-binding protein immunoprecipitation tiling array profiling Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] ENCODE project microRNA profiling by high throughput sequencing assay microRNA profiling by high throughput sequencing assay microRNA-seq assay ENCODE project microRNA-seq miRNA-seq http://www.ebi.ac.uk/efo/EFO_0002896 A RNA-seq assay in which high throughput sequencing technology is used to analyse the microRNA component of the transcriptome. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng 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] protein sequencing by tandem mass spectrometry assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng 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 in which amino acid sequences of proteins is determined using multiple rounds of mass spectrometry and molecule fragmentation. protein sequencing by tandem mass spectrometry assay ENCODE project Hunt et al. Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1986;83(17): 6233–6237. [PMID:3462691] 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] micrococcal nuclease digestion followed by high throughput sequencing assay MNase-seq JZ: should be inferred as 'DNA sequencing'. Will check in the future. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Johnson et al. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006 Dec;16(12):1505-16. [PMID:17038564] MNase-seq assay ENCODE project An assay to identify nucleosome positioning by genome wide sequencing of regions senstative to digestion by micrococal nuclease chromatin immunoprecipitation with exonuclease sequencing assay chromatin immunoprecipitation with exonuclease sequencing assay ENCODE project A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing. Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] ChIP-exo assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng microRNA profiling assay A transcription profiling assay in which aims to quantify the microRNA species within a biological sample. Kolbert et al. Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues. PLoS One. 2013;8(1):e52517 [PMID: 23382819] ENCODE project microRNA profiling assay microRNA expression assay miRNA expression assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng selection A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. OBI PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. Person: Philippe Rocca-Serra selection selection process this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) mass value specification PERSON:Bjoern Peters A value specification that specifies the mass of some thing. mass value specification categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification scalar value specification 1 1 A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification comparing prediction to measurement comparing prediction to measurement A planned process in which predicted values for some thing are compared to measured values for that thing. value specification This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. value specification An information content entity that specifies a value within a classification scheme or on a quantitative scale. PERSON:Bjoern Peters The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. predicted value PERSON:Bjoern Peters predicted value 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. predicted mass value predicted mass value A predicted value where the prediction specifies the mass of some thing. PERSON:Bjoern Peters molecular-labeled material PERSON:Matthew Brush 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 OBI developer call, 3-12-12 molecular-labeled material genome coverage genome coverage 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 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%. Alejandra Gonzalez-Beltran 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%" Philippe Rocca-Serra N50 Alejandra Gonzalez-Beltran 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" N50 Philippe Rocca-Serra 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" 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 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. Alejandra Gonzalez-Beltran 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" Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html contig N50 grant agency 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization NIAID GSCID-BRC metadata working group NIAID GSCID-BRC PERSON: Jie Zheng, Chris Stoeckert funding organization An organization that provides funding support for projects such as investigations. grant agency software pipeline PERSON: Jie Zheng, Chris Stoeckert 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 NIAID GSCID-BRC software pipeline sequence annotation A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. NIAID GSCID-BRC NIAID GSCID-BRC metadata working group PERSON: Jie Zheng, Chris Stoeckert sequence annotation 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 Alejandra Gonzalez-Beltran 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" Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html scaffold N50 forward PCR primer 5' primer 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. Philippe Rocca-Serra SP6 promoter, forward primer (SP6 TTTAGGTGACACTATAG) adapted from http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p forward PCR primer forward primer sense primer sequence annotation provider NIAID GSCID-BRC metadata working group annotation provider NIAID GSCID-BRC A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert sequence annotation provider sequence assembly name NIAID GSCID-BRC A textual entity that is used to denote a sequence assembly. PERSON: Jie Zheng, Chris Stoeckert assembly name NIAID GSCID-BRC metadata working group sequence assembly name sequence annotation reporting role NIAID GSCID-BRC metadata working group NIAID GSCID-BRC 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. PERSON: Jie Zheng, Chris Stoeckert sequence annotation reporting role reverse PCR primer 3' 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. Philippe Rocca-Serra adapted from "http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p" antisense primer reverse PCR primer reverse primer flash freezing WEB: http://en.wikipedia.org/wiki/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. Person: Mathias Brochhausen, Jie Zheng flash freezing freezing Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen 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. freezing ChIP assay An assay in which protein-DNA complexes are extracted from short regions of chromatin and are reversibly cross linked, immunoprecipitated with antibodies or tags, purified, and amplified with the aim of analysis gene- and promoter-specific known targets PMID: 6379641 Gilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9. and can be found linked from here: Philippe Rocca-Serra adapted from CHS protocols, wikipedia, life tech, ChIP-seq term definition as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/ chromatin immunoprecipitation assay ChIP assay 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. Bjoern Peters Bjoern Peters, Randi Vita, James A. Overton competitive binding reference ligand role assay using chromatin immunoprecipitation PERSON: Philippe Rocca-Serra an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/ assay using chromatin immunoprecipitation http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html hardware testing design Person: Jie Zheng A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. MO_734 hardware_variation_design hardware testing design systematic review study design PERSON: Bill Hogan 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. systematic review study design Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ sequencing library multiplexing OBI PERSON:Philippe Rocca-Serra a planned process which consists in running a set of samples as a pool in one single instrument run of data acquisition process while retaining the ability to associate individual results to each of the individual input samples thanks to the use of a multiplex identifier, introduced during the ligation step of the individual library preparation and specific to a given sample. http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn sequencing library multiplexing taxonomic diversity assessment by targeted gene survey OBI PERSON:Philippe Rocca-Serra environmental gene survey http://www.ncbi.nlm.nih.gov/pubmed/20679230 http://www.ncbi.nlm.nih.gov/pubmed/25367129 is an assay which aims to provide information about taxonomic information and community diversity by mean of sequencing specific genomic regions used as marker of identity or diversity. targeted gene survey targeted gene survey DNA barcoding taxonomic diversity assessment by targeted gene survey PCR program OBI PCR program PERSON:Philippe Rocca-Serra 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. https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-standard-taq-buffer-m0273 target gene specification PERSON:Philippe Rocca-Serra PRS for OBI 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 target gene target gene specification target subfragment specification PERSON:Philippe Rocca-Serra PRS for OBI 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 target subfragment specification decision-theoretic analysis objective PERSON: Bill Hogan The best action to take is typically defined as the one that maximizes expected utility. decision analysis objective decision-theoretic analysis objective PERSON: Bill Hogan 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. decision analysis study design a study design that has a decision analysis objective specification as part PERSON: Bill Hogan PERSON: Bill Hogan decision analysis study design sequence library deconvolution PERSON: Philippe Rocca-Serra PRS for OBI is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to pull together all reads belonging to a given single sample following the sequencing of a multiplexed library which combining several samples in one sequencing event sequence library deconvolution multiplexing sequence identifier 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 OBI PERSON:Philippe Rocca-Serra 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 multiplexing sequence identifier 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. PERSON:Philippe Rocca-Serra PRS for OBI http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290/ operational taxonomic unit matrix biodiversity assessment objective PERSON:Philippe Rocca-Serra PRS for OBI 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 DNA-barcoded sequencing library PERSON:Philippe Rocca-Serra PRS for OBI 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. 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. multiplexed sequencing library Ion 316 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html 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. Ion 316 Chip Ion 316 Chip v2 Ion PGM 316 Chip Ion PGM 316 Chip v2 Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ PERSON: Sagar Jain Ion 318 Chip v2 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. Ion 318 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion 318 Chip Ion PGM 318 Chip Ion PGM 318 Chip v2 Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ PERSON: Sagar Jain ion semiconductor chip 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. http://www.thefreedictionary.com/Semiconductor+chip Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ PERSON: Sagar Jain ion chip ion integrated circuit ion semiconductor ion semiconductor chip Ion 314 Chip v2 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. Ion 314 Chip Ion 314 Chip v2 Ion PGM 314 Chip http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion PGM 314 Chip v2 Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ PERSON: Sagar Jain hydrogen/deuterium exchange assay An 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. IEDB IEDB 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. hydrogen/deuterium exchange assay cytometry assay An assay that measures properties of cells. An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. IEDB IEDB cytometry assay immunoblot assay 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. IEDB IEDB immunoblot assay fluorescence quenching binding assay 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. IEDB IEDB fluorescence quenching binding assay in vivo intervention experiment An assay in which the effect of a targeted process (the intervention) on an organism is tested. 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. IEDB IEDB 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. in vivo intervention experiment disease exacerbation in vivo intervention experiment An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. IEDB IEDB 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. Should have data about disease severity as readout; could just use disease for now disease exacerbation in vivo intervention experiment protection from challenge in vivo intervention experiment An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. IEDB IEDB 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. protection from challenge in vivo intervention experiment should have challenge as intervention tolerance induction intervention experiment An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. IEDB IEDB 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. should have tolerance induction as intervention tolerance induction intervention experiment treatment intervention experiment An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. IEDB IEDB Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. should have treatment as intervention treatment intervention experiment microarray assay An analyte assay where binding of the analyte to immobilized matrix is measured. IEDB IEDB Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. microarray assay immunohistochemistry An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. IEDB IEDB Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. immunohistochemistry assay measuring the association constant [KA] of a MHC:ligand complex A MHC binding constant determination assay measuring equilibrium association constant (KA). IEDB IEDB assay measuring the association constant [KA] of a MHC:ligand complex 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). IEDB IEDB assay measuring the dissociation constant [KD] of a MHC:ligand complex dissociation constant KD|binding assay|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. IEDB IEDB dissociation constant KD|purified MHC/direct/radioactivity|nM purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection assay measuring the half life of a MHC:ligand complex A MHC binding constant determination assay measuring half life of binding. IEDB IEDB assay measuring the half life of a MHC:ligand complex half life|binding assay|min 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). IEDB IEDB assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex 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). IEDB IEDB assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex 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). IEDB IEDB assay measuring the off rate measurement [koff] of a MHC:ligand complex off rate|binding assay|1/s 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). IEDB IEDB assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex on rate|binding assay|nM^-1s^-1 chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an analytical chromatography assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters association constant KA|chromatography|1/nM chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex chromatography 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 an analytical chromatography assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex dissociation constant KD|chromatography|nM hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a hydrogen/deuterium exchange assay. IEDB IEDB hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex qualitative binding|hydrogen/deuterium exchange immunohistochemistry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunohistochemistry assay. IEDB IEDB immunohistochemistry assay measuring binding of a B cell epitope:antibody complex qualitative binding|immunohistochemistry 3D structure determining assay of a T cell epitope:MHC:TCR complex 3D structure determining assay of a T cell epitope:MHC:TCR complex 3D structure|any method A T cell epitope recognition assay that uses a 3D structure determination of bound complex assay. IEDB IEDB Genome Analyzer IIx Illumina GA IIx ENCODE group ENCODE project Illumina Genome Analyzer IIx Genome Analyzer IIx 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 Illumina HiSeq 2000 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 Illumina HiSeq 2000 HiSeq 2000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf ENCODE project Illumina HiSeq 2500 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf ENCODE project HiSeq 2500 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. Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina HiSeq 2500 MiSeq ENCODE project 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. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng MiSeq Illumina MiSeq Methylation 450K BeadChip 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 ENCODE project PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Methylation 450K BeadChip 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 http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Methylation 27K BeadChip PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg ENCODE project Methylation 27K BeadChip Illumina Infinium Human Methylation 27K BeadChip http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf 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. 1M-Duo Infinium HD BeadChip Illumina Human 1M-Duo Infinium HD BeadChip 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. 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 http://www.illumina.com/technology/infinium_hd_assay.ilmn PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg 1M-Duo Infinium HD BeadChip ENCODE project SOLiD 3 Plus System http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf Applied Biosystems SOLiD 3 Plus System 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. Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 ENCODE project PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg SOLiD 3 Plus System Mouse 385K Whole Genome CGH Tiling Array Mouse 385K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg 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 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/ ENCODE project 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 http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf 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 ENCODE project Mouse 3x720K Whole Genome CGH Tiling Array PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Human 3x720K Whole Genome CGH Tiling Array ENCODE project PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Human 3x720K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Nimblegen Human 3x720K Whole Genome CGH Tiling Array 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. Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 Human 2.1M Whole-Genome CGH Tiling Array v2.0 Human 2.1M Whole-Genome CGH Tiling Array v2.0 Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 ENCODE project 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. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf PacBio RS II ENCODE project 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. Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Pacific Biosciences RS II http://www.pacificbiosciences.com/products/ PacBio RS II nCounter Human V2 miRNA Expression array ENCODE project http://www.nanostring.com/media/pdf/PDS_nCounter_Human_v2_miRNA_Assay.pdf An 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. 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 nCounter Human V2 miRNA Expression array PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg DNA methylation profiling by ChIP-chip assay DNA methylation ChIP-chip A ChIP-chip assay that identifies sites of DNA methylation. Penn group DNA methylation profiling by ChIP-chip assay Beta Cell Biology Consoritum Person: Chris Stoeckert, Jie Zheng transcription profiling by MPSS assay expression MPSS transcription profiling by MPSS assay Beta Cell Biology Consoritum An assay in which the transcriptome of a biological sample is analysed using Massive Parallel Signature Sequencing (MPSS). Person: Chris Stoeckert, Jie Zheng http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing histone modification identification by ChIP-chip assay histone modification identification by ChIP-chip assay Penn group Person: Chris Stoeckert, Jie Zheng Beta Cell Biology Consoritum histone modification ChIP-chip A ChIP-chip assay to identify regions containing specific histones and their modifications. histone modification identification by ChIP-Seq assay Penn group Beta Cell Biology Consoritum A ChIP-seq assay to identify regions containing specific histones and their modifications. histone modification identification by ChIP-Seq assay histone modification ChIP-Seq Person: Chris Stoeckert, Jie Zheng transcription factor binding site identification by ChIP-chip assay Person: Chris Stoeckert, Jie Zheng transcription factor binding site identification by ChIP-chip assay Penn group A ChIP-chip assay to identify binding sites for transcription factors. Beta Cell Biology Consoritum TF Binding ChIP-chip transcription factor binding site identification by ChIP-Seq assay TF Binding ChIP-Seq transcription factor binding site identification by ChIP-Seq assay Penn group Beta Cell Biology Consoritum A ChIP-seq assay to identify binding sites for transcription factors. Person: Chris Stoeckert, Jie Zheng epigenetic modification assay Person: Chris Stoeckert, Jie Zheng Penn group An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation. epigenetic modification assay Beta Cell Biology Consoritum NextSeq 500 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. ENCODE project NextSeq 500 Illumina NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina HiSeq 1000 Person: Venkat Malladi, Chris Stoeckert, Jie Zheng A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Illumina HiSeq 1000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf ENCODE project HiSeq 1000 Human Genome U133 Plus 2.0 tiling array Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix HT Human Genome U133 Plus 2 Array Plate Set 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. HG-U133 Plus 2 ENCODE project Human Genome U133 Plus 2.0 tiling array HG-U133 Plus 2 array http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 SOLiD 4 System http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 SOLiD 4 System ENCODE project 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. Applied Biosystems SOLiD 4 System Person: Venkat Malladi, Chris Stoeckert, Jie Zheng SOLiD 4 Human Exon 1.0 ST tilling array Human Exon 1.0 ST tilling array Human Exon 1.0 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 http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix Human Exon 1.0 St Array Human Exon 1.0 ST Array ENCODE project Human Genome U133 tiling array Human Genome U133 tiling array ENCODE project Person: Venkat Malladi, Chris Stoeckert, Jie Zheng 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. HG-U133 array Affymetrix HT Human Genome U133 Array Plate Set HG-U133 http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 Genome Analyzer IIe Genome Analyzer IIe Illumina GA IIe Person: Venkat Malladi, Chris Stoeckert, Jie Zheng http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf ENCODE project Illumina Genome Analyzer IIe 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 Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ PMID:15905473 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. Person:Chris Stoeckert SAGE ditag library preparation serial analysis of gene expression Person:Janos Demeter, Chris Stoeckert, Jie Zheng PMID:15905473 SAGE Details see tracker: https://sourceforge.net/p/obi/obi-terms/720/ A transcription profiling assay which aims to quantify RNA through creating short signature tags of the messages and ligating them into a larger molecule that is than sequenced. Saccharomyces Genome Database (SGD) PMID:7570003 serial analysis of gene expression genotyping by tiling array Details see tracker: https://sourceforge.net/p/obi/obi-terms/720/ PMID:19521816 Person:Janos Demeter, Chris Stoeckert, Jie Zheng A genotyping by array assay that aims to detect variation in (mostly) genomic DNA of an organism, strain, etc relative to some reference sequence employing tiling array technology. PMID:19521816 Saccharomyces Genome Database (SGD) DNA sequence variation detection by tiling array genotyping by tiling array genotyping by SNP array Person:Janos Demeter, Chris Stoeckert, Jie Zheng A genotyping by array assay that aims to detect variation in (mostly) genomic DNA of an organism, strain, etc relative to some reference sequence employing snp array technology. Details see tracker: https://sourceforge.net/p/obi/obi-terms/720/ PMID:20393561 Saccharomyces Genome Database (SGD) DNA sequence variation detection by snp array PMID:20080586 genotyping by SNP array parallel analysis of RNA structure Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ pmid:20811459 pmid:20811459 parallel analysis of RNA structure Janos Demeter, Chris Stoeckert Saccharomyces Genome Database (SGD) A single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. PARS translation-associated transcript leader sequencing TATL-seq An RNA-seq assay that combines TL-seq with polysome fractionation Saccharomyces Genome Database (SGD) pmid:23580730 translation-associated transcript leader sequencing Janos Demeter, Chris Stoeckert Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ pmid:23580730 transcript leader sequencing Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ TL-seq pmid:23580730 transcript leader sequencing Saccharomyces Genome Database (SGD) pmid:23580730 Janos Demeter, Chris Stoeckert An RNA-seq assay combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. peptide mass fingerprinting Saccharomyces Genome Database (SGD) Janos Demeter, Chris Stoeckert A mass spectrometry assay in which an unknown protein of interest is cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer. These masses are then compared to values in a database containing known protein sequences. ERO:0001668 (http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting) PMF Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ peptide mass fingerprinting protein fingerprinting array based nucleic acid structure mapping assay array based nucleic acid structure mapping assay Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Saccharomyces Genome Database (SGD) An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. OBI:0000870 pmid:23580730 Janos Demeter, Chris Stoeckert micrococcal nuclease digestion followed by tiling array assay An array based nucleic acid structure mapping assay to identify nucleosome positions, genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling arrays. Janos Demeter, Chris Stoeckert pmid:17873876 micrococcal nuclease digestion followed by tiling array assay Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/ Saccharomyces Genome Database (SGD) ribosomal profiling by sequencing assay Ingolia, Nicholas T. (28 January 2014). "Ribosome profiling: new views of translation, from single codons to genome scale". Nature Reviews Genetics 15 (3): 205-213. doi:10.1038/nrg3645. PMID 24468696. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Ribo-seq Ribo-seq assay ribosomal profiling ENCODE project Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 ribosomal profiling by sequencing assay A RNA-seq assay to sequence 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. ENCODE project Buenrostro JD, Giresi PG, Zaba LC, Chang HY, and Greenleaf WJ. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods ATAC-seq assay An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. assay for transposase-accessible chromatin using sequencing Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ATAC-seq chromatin isolation by RNA purification sequencing assay ChIRP-seq Chromatin Isolation by RNA purification 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. ENCODE project A detection of specific nucleic acids with complementary probes to discover 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. Chu et al. (31 August 2011). "Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions". Molecular Cell. chromatin isolation by RNA purification sequencing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIRP-seq assay self-transcribing active regulatory region sequencing assay Arnold et al. (January 2013). "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq". Science 339 (6123): 1074-7. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng A RNA-seq assay to identify 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 STARR-seq assay STARR-seq ENCODE project 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. self-transcribing active regulatory region sequencing assay carbon-copy chromosome conformation capture assay followed by sequencing assay HiC assay HiC Person: Venkat Malladi, Chris Stoeckert, Jie Zheng 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. 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. Carbon-copy chromosome conformation capture assay followed by sequencing ENCODE project carbon-copy chromosome conformation capture assay followed by sequencing assay Lieberman-Aiden E, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293. individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay ENCODE project individual-nucleotide resolution cross-linking and immunoprecipitation Huppertz et al., (February 2014). "iCLIP: protein-RNA interactions at nucleotide resolution.". Methods (San Diego, Calif.) 65 (3): 274-87. doi:10.1016/j.ymeth.2013.10.011 iCLIP individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay iCLIP assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng A cross-linking immunoprecipitation high-throughput sequencing assay to identify protein-RNA interactions by using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. König et al., (18 January 2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 RNA Bind-n-Seq assay RBNS RNBS assay RNA Bind-n-Seq assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng RNA Bind-n-Seq A RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs) ENCODE project Lambert et al., (June 2014). "RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins." Mol Cell. 2014 Jun 5;54(5):887-900. doi: 10.1016/j.molcel.2014.04.016 poly(A)-site sequencing assay 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 for quantitatively profiling RNA polyadenylation at the transcriptome level. ENCODE project PAS-seq assay Shepard et al., (April 2011). "Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq." RNA. 2011 Apr;17(4):761-72. doi: 10.1261/rna.2581711 PAS-seq Poly(A)-site sequencing poly(A)-site sequencing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng surface plasmon resonance sensor chip SPR sensor chip surface plasmon resonance sensor chip OBI 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 ProteOn GLC Sensor Chip #176-5011 sensor chip biosensor chip Anna Maria Masci enzyme-linked antibody Bjoern Peters, Randi Vita, James A. Overton 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. enzyme-linked antibody 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). OBI Illumina HiSeq 3000 PERSON: Sagar Jain, Richard Scheuermann Illumina HiSeq 3000 http://www.illumina.com/systems/hiseq-3000-4000.html HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. Illumina HiSeq 4000 HiSeq 4000 PERSON: Sagar Jain, Richard Scheuermann http://www.illumina.com/systems/hiseq-3000-4000.html A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. Illumina HiSeq 4000 3D structure determining assay of a MHC:ligand complex 3D structure determining assay of a MHC:ligand complex 3D structure|any method A MHC:ligand binding assay that uses a 3D structure determination of bound complex assay. IEDB IEDB in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on pathogen burden. IEDB IEDB in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden pathogen burden after challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from tumor challenge A B cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on tumor burden. IEDB IEDB in vivo assay measuring B cell epitope specific protection from tumor challenge tumor burden after challenge|in vivo assay microarray assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a microarray. IEDB IEDB microarray assay measuring binding of a B cell epitope:antibody complex qualitative binding|microarray 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. IEDB IEDB NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex dissociation constant KD|nuclear magnetic resonance (NMR)|nM assay measuring T cell epitope specific biological activity A T cell epitope recognition assay that detects biological activity. IEDB IEDB assay measuring T cell epitope specific biological activity biological activity|any method biological activity 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. CCL17/TARC release|biological activity IEDB IEDB biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells biological activity 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. IEDB IEDB MIF release|biological activity biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells biological activity 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. IEDB IEDB biological activity assay measuring epitope specific 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. IEDB IEDB assay measuring a binding constant of a T cell epitope:MHC:TCR complex binding constant|binding assay detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. CCL17/TARC release|RNA/DNA detection IEDB IEDB detection of specific nucleic acids with complementary probes assay measuring epitope specific 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 An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a cytometric bead array assay. CCL22/MDC release|cytometric bead array IEDB IEDB cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells in vitro assay measuring epitope specific T cell killing A T cell epitope specific killing assay that uses an in vitro cell killing assay. IEDB IEDB cytotoxicity|in vitro assay in vitro assay measuring epitope specific T cell killing cytometric bead array assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay. IEDB IEDB cytometric bead array assay measuring 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 T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells granzyme A release|RNA/DNA detection cytometric bead array assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay. IEDB IEDB cytometric bead array assay measuring 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 T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay. IEDB IEDB detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells granzyme B release|RNA/DNA detection cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells An assay of epitope specific macrophage migration inhibitory factor (MIF) production by T cells that uses a cytometric bead array assay. IEDB IEDB MIF release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells cytometric bead array assay measuring epitope specific oncostatin M production by T cells An assay of epitope specific oncostatin M production by T cells that uses a cytometric bead array assay. IEDB IEDB cytometric bead array assay measuring epitope specific oncostatin M production by T cells oncostatin M release|cytometric bead array ELISPOT assay measuring epitope specific perforin release by T cells A T cell epitope specific perforin release assay that uses an ELISPOT assay. ELISPOT assay measuring epitope specific perforin release by T cells IEDB IEDB perforin release|ELISPOT in vivo assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay that is performed in vivo. IEDB IEDB in vivo assay measuring epitope specific proliferation of T cells proliferation|in vivo assay in vitro assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay that is performed on cells in vitro. IEDB IEDB in vitro assay measuring epitope specific proliferation of T cells proliferation|in vitro assay assay measuring qualitiative binding of a MHC:ligand complex A MHC:ligand binding assay that detects qualitative binding. IEDB IEDB assay measuring qualitiative binding of a MHC:ligand complex qualitative binding|binding assay in vivo assay measuring T cell epitope specific protection from challenge An efficacy of T cell epitope intervention experiment that uses a protection from challenge in vivo intervention experiment. IEDB IEDB in vivo assay measuring T cell epitope specific protection from challenge protection from challenge|in vivo assay in vitro assay measuring T cell epitope specific suppression IEDB PERSON:Randi Vita, James Overton, Bjoern Peters T cell epitope dependent biological activity assay that detects suppression of an in vitro response. in vitro assay measuring T cell epitope specific suppression suppression|in vitro assay MHC ligand assay An immune epitope assay that detects either the processing and presentation of a ligand by an antigen presenting cell or the binding of a ligand to an MHC molecule. IEDB IEDB MHC ligand assay ligand presentation/binding|binding assay collection of specimens Biobank A material entity that has two or more specimens as its parts. Blood cells collected from multiple donors over the course of a study. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ OBIB, OBI Person: Chris Stoeckert, Jie Zheng collection of specimens specimens derived from shared ancestor Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ A collection of specimens derived from one common specimen via one or more material processing process(es). 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. Biobank Chris Stoeckert, Jie Zheng Duke Biobank, OBIB, OBI specimen family specimens derived from shared ancestor specimen set collection process 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. Chris Stoeckert, Jie Zheng Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy. OBIB, OBI specimen set collection process specimens collected in one encounter 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. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Biobank Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy. OBIB, OBI Person: Chris Stoeckert, Jie Zheng specimen set specimens collected in one encounter human specimen set Biobank 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. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Duke Biobank, OBIB, OBI Person: Chris Stoeckert, Jie Zheng human specimen set specimens collected longitudinally Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ 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 Person: Chris Stoeckert specimens collected longitudinally reporter gene assay An assay in which expression of a reporter gene is detected that was inserted under the control of a regulatory sequence of interest. Chris Stoeckert, Paul D. Thomas Paul D. Thomas, Yang Chai; FaceBase reporter gene assay reporter gene detection assay tracker item: 781 enhancer activity detection by reporter gene assay A reporter gene assay in which expression of a reporter gene is detected that was inserted under the control of an enhancer of interest. FaceBase, PMID 24614317 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" Paul D. Thomas, Yang Chai Tracker item: 781 enhancer activity detection by reporter gene assay enhancer reporter gene assay transcription cofactor activity region identification by ChIP-Seq assay A ChIP-seq assay to identify regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. FaceBase, PMID 19212405 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" Paul D. Thomas, Yang Chai Tracker item: 782 chromatin modifier binding site identification by ChIP-Seq assay transcription cofactor activity region identification by ChIP-Seq assay transcript expression location detection by hybridization chain reaction An in situ hybridization 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. PMID 21037591 See tracker #783 PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" Paul D. Thomas, Yang Chai transcript expression location detection by fluorescent HCR. transcript expression location detection by hybridization chain reaction Tet-assisted bisulfite sequencing assay 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. Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group Tet-assisted bisulfite sequencing TAB-seq Term request: http://sourceforge.net/p/obi/obi-terms/789/ Tet-assisted bisulfite sequencing assay http://www.ncbi.nlm.nih.gov/pubmed/23196972 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. Biobank Chris Stoeckert Duke Biobank, OBIB For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ containing a specimen function specimen container A container with the function of containing a specimen. Biobank COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube Chris Stoeckert Duke Biobank, OBIB For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ Specimen containers are typically constructed or treated in a particular manner in order to perform their containing a specimen function. This will be a defined class so that any container (e.g., cryotube, vacutainer, conical test tube) with the function of containing a specimen will be inferred to be a specimen container. specimen container physical store A container with an environmental control function. Biobank Chris Stoeckert Duke Biobank, OBIB For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ a freezer. a humidity controlled box. physical store rapid amplification of cDNA ends RACE 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. ENCODE For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/RACE_Rapid_Amplification_of_cDNA_Ends/5_Prime_RACE_and_3_Prime_RACE rapid amplification of cDNA ends 5' rapid amplification of cDNA ends 5' RACE 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. ENCODE For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/5-race-system-for-rapid-amplification-of-cdna-ends.html 3' rapid amplification of cDNA ends 3' 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. ENCODE For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/3-race-system-for-rapid-amplification-of-cdna-ends.html 5' RNA ligase mediated rapid amplification of cDNA ends 5' RLM 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. ENCODE For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert https://tools.thermofisher.com/content/sfs/manuals/cms_056070.pdf MethylC-Capture sequencing assay 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. Allum et al., Nature Commun. 2015 (PMID: 26021296) Capture Methylome David Bujold, Chris Stoeckert For details see tracker: https://sourceforge.net/p/obi/obi-terms/773/ MCC-Seq MethylC-Capture Sequencing 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. MethylC-Capture sequencing assay specimen family creation Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum. Biobank For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Mathias Brochhausen, Chris Stoeckert, Jie Zheng OBI, OBIB specimen family creation carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay. IEDB IEDB carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells proliferation|CFSE 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex dissociation constant KD|binding assay|nM 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex on rate|binding assay|M^-1s^-1 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex off rate|binding assay|1/s 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. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex association constant KA|binding assay|1/nM small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex 3D structure|small-angle scattering assay A B cell epitope 3D structure determination assay that uses a small-angle scattering assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope assay that measures the on rate using a bio-layer interferometry assay. IEDB IEDB bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex 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 B cell epitope assay that measures the off rate using a bio-layer interferometry assay. IEDB IEDB bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex off rate|bio-layer interferometry assay|1/s bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a bio-layer interferometry assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex qualitative binding|bio-layer interferometry assay bio-layer interferometry 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 bio-layer interferometry assay. IEDB IEDB bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex dissociation constant KD|bio-layer interferometry assay|nM carboxyfluorescein succinimidyl ester staining assay CFSE assay IEDB IEDB Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. a detection of molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection. carboxyfluorescein succinimidyl ester staining assay bio-layer interferometry assay 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. 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. IEDB IEDB bio-layer interferometry assay biolayer interferometry, BLI small-angle scattering assay A 3D 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. IEDB IEDB SAXS Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein small-angle scattering assay Human 6x630K CGH Whole Genome Tiling Array http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 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. NimbleGen Human 6x630K CGH Whole Genome Tiling Array Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group Term request: https://sourceforge.net/p/obi/obi-terms/791/ digital object identifier Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/ The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/ DOI OBI developers 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. digital object identifier enhanced cross-linking immunoprecipitation high-throughput sequencing assay eCLIP https://www.ncbi.nlm.nih.gov/pubmed/27018577 Jason Hilton Chris Stoeckert An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. enhanced cross-linking immunoprecipitation high-throughput sequencing assay small RNA-seq http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html Chris Stoeckert Jason Hilton An RNA-seq assay which is targeting small RNA (17-35 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. small RNA-seq bromouridine labeling and sequencing An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. Jason Hilton Bru-seq http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009065/ Chris Stoeckert bromouridine labeling and sequencing bromouridine pulse-chase and sequencing BruChase-seq Jason Hilton http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009065/ Chris Stoeckert 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. bromouridine pulse-chase and sequencing cytometry time of flight assay 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. CyTOF ImmPort 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 refelctive of the level of expression of those surface receptors. cytometry time of flight assay http://www.ncbi.nlm.nih.gov/pubmed/26190063 high performance liquid chromotography assay An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. HPLC ImmPort 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. high performance liquid chromotography assay http://www.ncbi.nlm.nih.gov/pubmed/9491555 whole genome sequencing assay 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. ImmPort WGS permits comprehensive sequencing of introns and exons, whereas 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/WES. WGS/WES http://www.ncbi.nlm.nih.gov/pubmed/25827230, http://www.ncbi.nlm.nih.gov/pubmed/23095910 whole genome sequencing assay exome sequencing assay A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). 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. ImmPort WES exome sequencing assay http://www.ncbi.nlm.nih.gov/pubmed/25827230 microscopy assay An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. ImmPort 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. http://www.ncbi.nlm.nih.gov/pubmed/21685355 microscopy assay mixed lymphocyte reaction assay 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). ImmPort MLR 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. http://www.ncbi.nlm.nih.gov/pubmed/14969764 mixed lymphocyte reaction assay killer cell immunoglobulin-like receptor typing assay A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. 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. 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. ImmPort KIR typing http://www.ncbi.nlm.nih.gov/pubmed/21239231 killer cell immunoglobulin-like receptor typing assay major histocompatibility typing assay A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules 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. 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. IEDB MHC typing, HLA typing http://www.ncbi.nlm.nih.gov/pubmed/27516207, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628004/ major histocompatibility typing assay IHC slide staining A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues. Chris Stoeckert, Ned Haubein IHC slide staining http://www.agilent.com/cs/library/technicaloverviews/public/08002_ihc_staining_methods.pdf H&E slide staining A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink. Chris Stoeckert, Ned Haubein H&E slide staining http://www.histalim.com/accueil/activities/our-services/histology/hematoxylin-eosin-2/ H&E-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of H&E slide staining. Chris Stoeckert, Ned Haubein H&E-stained fixed tissue slide specimen OBIB, OBI IHC-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. Chris Stoeckert, Ned Haubein IHC-stained fixed tissue slide specimen OBIB, OBI immunohistochemistry slide specimen single cell specimen Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ PERSON: Jie Zheng, Alexander Diehl A cell specimen that contains only one cell. PERSON: Jie Zheng, Alexander Diehl single cell specimen Illumina Genome Analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. ENCODE project Illumina Genome Analyzer Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. ENCODE project HiSeq X Ten Illumina HiSeq X Ten Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Illumina Infinium Omni5Exome-4 Kit An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. ENCODE project Illumina Infinium Omni5Exome-4 Kit Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html Illumina Infinium MethylationEPIC BeadChip An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. ENCODE project Illumina Infinium MethylationEPIC BeadChip Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf pulse stable isotope labeling by amino acids in cell culture pulsed SILAC 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. pulse stable isotope labeling by amino acids in cell culture dynamic SILAC Rob Nash pulse SILAC Schwanhausser et al., 2009 (PMID: 19053139); Frolich et al. 2009 (PMID: 18954100) amniotic fluid specimen A specimen that is derived from amniotic fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank amniotic fluid specimen bile specimen A specimen that is derived from bile. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bile specimen cerebrospinal fluid specimen A specimen that is derived from cerbrospinal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank cerebrospinal fluid specimen feces specimen A specimen that is derived from feces. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank feces specimen stool specimen digestive system fluid or secretion specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank digestive system fluid or secretion specimen gastric fluid specimen milk specimen A specimen that is derived from milk. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank milk specimen pericardial fluid specimen A specimen that is derived from pericardial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pericardial fluid specimen saliva specimen A specimen that is derived from saliva. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank saliva specimen sputum specimen A specimen that is derived from sputum. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sputum specimen sweat specimen A specimen that is derived from sweat. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sweat specimen synovial fluid specimen A specimen that is derived from synovial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank synovial fluid specimen vitreous humor specimen A specimen that is derived from vireous humor. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank vitreous fluid specimen vitreous humor specimen bone marrow specimen A specimen that is derived from bone marrow. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bone marrow specimen placenta specimen A specimen that is derived from placenta. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank placenta specimen peritoneal fluid specimen A specimen that is derived from peritoneal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank peritoneal fluid specimen pleural fluid specimen A specimen that is derived from pleural fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pleural fluid specimen brain specimen A specimen that is derived from brain. Chris Stoeckert Chris Stoeckert, NCI BBRB brain specimen hair specimen A specimen that is derived from hair. Chris Stoeckert Chris Stoeckert, NCI BBRB hair specimen prostate gland specimen A specimen that is derived from prostate gland. Chris Stoeckert Chris Stoeckert, NCI BBRB prostate gland specimen skeletal muscle tissue specimen A specimen that is derived from skeletal muscle. Chris Stoeckert Chris Stoeckert, NCI BBRB skeletal muscle tissue specimen heart specimen A specimen that is derived from heart. Chris Stoeckert Chris Stoeckert, NCI BBRB heart specimen renal medulla specimen A specimen that is derived from renal medulla. Chris Stoeckert Chris Stoeckert, NCI BBRB kidney medulla specimen renal medulla specimen adrenal gland specimen A specimen that is derived from adrenal gland. Chris Stoeckert Chris Stoeckert, NCI BBRB adrenal gland specimen breast specimen A specimen that is derived from breast. Chris Stoeckert Chris Stoeckert, NCI BBRB breast specimen mammary tissue specimen urinary bladder specimen A specimen that is derived from urinary bladder. Chris Stoeckert Chris Stoeckert, NCI BBRB urinary bladder specimen tibial artery specimen A specimen that is derived from tibial artery. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial artery specimen skin of body specimen A specimen that is derived from skin. Chris Stoeckert Chris Stoeckert, NCI BBRB skin of body specimen skin specimen pancreas specimen A specimen that is derived from pancreas. Chris Stoeckert Chris Stoeckert, NCI BBRB pancreas specimen stomach specimen A specimen that is derived from stomach. Chris Stoeckert Chris Stoeckert, NCI BBRB stomach specimen pituitary gland specimen A specimen that is derived from pituitary gland. Chris Stoeckert Chris Stoeckert, NCI BBRB pituitary gland specimen adipose tissue specimen A specimen that is derived from adipose tissue. Chris Stoeckert Chris Stoeckert, NCI BBRB adipose tissue specimen cortex of kidney specimen A specimen that is derived from cortex of kidney. Chris Stoeckert Chris Stoeckert, NCI BBRB cortex of kidney specimen kidney cortex specimen esophagus mucosa specimen A specimen that is derived from esophagus mucosa. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagus mucosa specimen colon specimen A specimen that is derived from colon. Chris Stoeckert Chris Stoeckert, NCI BBRB colon specimen lung specimen A specimen that is derived from lung. Chris Stoeckert Chris Stoeckert, NCI BBRB lung specimen esophagus muscularis mucosa specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagus muscularis mucosa specimen esophagus muscularis specimen cerebral cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert Chris Stoeckert, NCI BBRB brain cortex specimen cerebral cortex specimen thyroid gland specimen A specimen that is derived from thyroid gland. Chris Stoeckert Chris Stoeckert, NCI BBRB thyroid gland specimen cerebellum specimen A specimen that is derived from cerebellum. Chris Stoeckert Chris Stoeckert, NCI BBRB brain cerebellum specimen cerebellum specimen tibial nerve specimen A specimen that is derived from tibial nerve. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial nerve specimen coronary artery specimen A specimen that is derived from coronary artery. Chris Stoeckert Chris Stoeckert, NCI BBRB coronary artery specimen spleen specimen A specimen that is derived from spleen. Chris Stoeckert Chris Stoeckert, NCI BBRB spleen specimen aorta specimen A specimen that is derived from aorta. Chris Stoeckert Chris Stoeckert, NCI BBRB aorta specimen injection function PERSON: Alan Ruttenberg PERSON: Melanie Courtot 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 injection function Epstein Barr virus transformed B cell GROUP: OBI Biomaterial Branch PERSON: Susanna Sansone A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity 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. chimera An organism which contains cells or tissues with a different genotype GROUP: OBI PERSON: Helen Parkinson chimera obsolete_anatomical entity 13-02-2009: Biomaterial branch: change of label and definition following discussions at the OBI winter meeting 2009. It was felt that 'macroscopic part of multicellular organism' introduce an impractical delineation. IMPORTANT NOTE: OBI 'anatomical entity' would essentially correspond to FMA 'material anatomical entity' rather than FMA 'physical anatomical entity'. OBI does not include 'immaterial anatomical entity' as it would clash with the parent class 'material entity' DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes cell and biological molecules. Biom call - January 2009 - Issues: parasites are not macroscopic part or organism. fetus is_a macroscopic part (but this is up for discussion) Bjoern Peters Philippe Rocca-Serra equivalent classes 'portion of tissue' or 'multi-tissue structure' or 'portion of organism substance' Superclasses material_entity part_of some organism true 10/20/09: This class and all subclasses are currently problematic. They should all be imported from other OBO foundry ontologies. (FMA / CARO / UBERON). Currently two problems exist: There is no cross species anatomy that covers all the entities we need. Secondly: there is not good boundary between anatomical entities and smaller parts in FMA. Currently we will use anatomical entities as if they are valid across species. 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' MO Tina Boussard Tissue, organ, system, sperm, blood or body location (arm). not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure. obsolete_anatomical entity blood plasma specimen PERSON: Philippe Rocca-Serra 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. PERSON: Maura Gasparetto PERSON: Melanie Courtot PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. WEB: http://en.wikipedia.org/wiki/Blood_plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. blood plasma specimen plasma blood serum specimen PERSON: Philippe Rocca-Serra A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. PERSON: Maura Gasparetto PERSON: Melanie Courtot PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen organism 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus obsolete_immortal cell true GROUP: OBI Biomaterial Branch PERSON: Bjoern Peters a cell derived from a multicellular organism that has the potential to replicate indefinitely a single Hela cell obsolete_immortal cell obsolete_fragment derived from protein BP:03/21/2010:obsoleted as the class is no longer necessary, and we would otherwise need all kinds of 'fragment derived from' classes. Instead, use composite terms with the relationship 'derived from' some protein OR derived from some part_of protein. true A material entity which is derived from a protein GROUP: IEDB PERSON: Bjoern Peters PRS:22022008. result from protocol_application where input=protein and output=polypeptide or peptide (to capture: derives_from protein) obsolete_fragment derived from protein original term: protein fragment split into synthetic polypeptide and fragment derived from protein THE DEFINITION OF THIS SUGGESTS WE COVER THIS ALREADY IN PEPTIDE/POLYPETIDE. DO WE NEED THIS AND CAN WE DEAL WITH IT IN SOME OTHER WAY? JAMES the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme phosphate buffered saline solution PERSON: Philippe Rocca-Serra PBS buffer PERSON: Melanie Courtot PERSON: Tina Boussard 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). WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline phosphate buffered saline solution specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra A material entity that has the specimen role. GROUP: OBI Biomaterial Branch specimen obsolete_cell line cell PERSON: Susanna Sansone had superclass axiom: is_specified_output_of some 'establishing cell culture' true A material entity that represents generations of a primary culture. GROUP: OBI Biomaterial Branch obsolete_cell line cell obsolete_immortal cell line culture A cell line that is expected to be capable of indefinite propagation in an vitro culture. PERSON:Matthew Brush PERSON:Matthew Brush permanent cell line true http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line sample 2013-08-09 MHB: Replaced with cell line class from CLO, follwoing outcome of Spring 2013 CLO alignment work. Subclass axioms were: 'has grain' some 'immortal cell line cell' and 'has grain' only 'immortalcell line cell' MHB 3-5-13: This OBI class was formerly called 'immortalized cell line culture', but label changed and definition updated following CLO alignment work in spring of 2013. obsolete_immortal cell line culture xenograft PERSON: Philippe Rocca-Serra 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. 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 PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Xenograft xenograft xenotransplant cultured cell population A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. PERSON:Matthew Brush PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. 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). cell culture sample primary cultured cell population 0 A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. PERSON:Matthew Brush PERSON:Matthew Brush 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) primary cell culture primary cell culture sample 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. 0 obsolete_cell line 1. The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, 'lines' are capable of being characterized and stably propagated over a period of time. A *new* cell line can be "established" not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quescent state for future use. 2. The definitional criteria provided here for the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.? 3. Definitinal criteria are intended to be sufficiently clear to specify what are and what are not instances of 'cell lines' in the real world. A 'HeLa cell line' would be a subset of all HeLa cells in the world - specifically any subset that has been derived through a shared continuous lineage wherein the cells have always been passaged together and thereby evolved together through the selective pressures imposed by this common history. Accordingly, 'HeLa cell line' would not be used to refer to the collection of all HeLa cells in a given lab, or all HeLa cells in the ATCC repository, as cells in these collections will likely not all share a common culture history. Rather, 'HeLa cell line' could refer to the collection of cells I am culturing at a given moment, or that I apply in an experiment (as such collections typically meet the criteria of having a shared propagation history). As noted above, it is such collections that are typically referred to in scientific discourse and publications. 4. Notably, the term 'line' has been alternately used by other terminologies and communities to refer to cultures that have been immortalized - ie has attained the capacity for indefinite propagation in vitro. In this ontology, we refer to such cell lines as 'immortal cell lines', and use the term 'cell line' to indicate any culture that has been passaged. 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). OBI-CLO Alignment Working Group (Spring 2013) PERSON:Matthew Brush true 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. cell line sample 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'. 2013-08-09 MHB: Replaced with cell line class from CLO, follwoing outcome of Spring 2013 CLO alignment work. Subclass axioms were: 'has grain' some 'cell line cell' and 'has grain' only 'cell line cell' 2013-6-5 MHB: There is considerable ambiguity and inconsistent usage surrounding the term 'cell line' across biomedical communities. For exmaple, it can refer to the maximal collection of all cells in a cultured lineage (e.g. the colelction of all HeLa cells that exist), or to discrete portions of this maximal collection that are stored, exchanged, and applied experimentally (e.g. the dish of HeLa cells I am using in my experiment). A working group of representatives from OBI, CLO, and CL was assembled in spring of 2013 to harmonize modeling and terminology surrounding experimentally cultured cells across Open Biomedical Ontologies, following OBO Foundry principles of orthogonality and re-use. A consensus was reached to apply the term 'cell line' to refer not to a maximal collection of cells of a given type, but to discrete populations of cultured cells that share a common propagation history which has conferred a certain a genetic stability and compositional homogeneity to the population. This meaning reflects its most common usage in domain discourse, and will best support data annotation requirements. This view means that a 'HeLa cell line' would be a subset of all HeLa cells in the world - specifically any subset that has been derived through a shared continuous lineage wherein the cells have always been passaged together and thereby evolved together through the selective pressures imposed by this specific history. Accordingly, 'HeLa cell line' would not be used to refer to collections such as all HeLa cells in a given lab, or all HeLa cells in the ATCC repository, as all cells in these collections do not necessarily share a common culture history. Rather, it could be used to refer to the collection of cells I am culturing at a given moment, or that I apply in an experiment (as such collections typically meet the criteria of having a shared propagation history). This approach seems to accomplish several desirable goals: 1) It allows us to define the term 'cell line' for the community in a precise way that also reflects how the term is most commonly used in the literature and scientific discourse. (2) It gives a definition that provides clear criteria to help specify what are and what are not instances of 'cell lines' in the real world (3) The criteria it provides demarcate populations that represent what 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. (4) The definition seems to be true to the meaning of the word 'line' - which is suggests a specific lineage of derivation. http://purl.obolibrary.org/obo/CLO_0000031 obsolete_cell line cultured clonal cell population GROUP: OBI Biomaterial Branch PERSON: Susanna Sansone PERSON:Matthew Brush 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. cell cut Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 clonal cell culture sample cultured clonal cell population screening library 7/13/09: Need to clarify if this meets reagent role definition GROUP: IEDB PERSON: Bjoern Peters 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] 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 a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? screening library synthetic peptide Bjoern Peters IEDB PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application 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). original term: protein fragment split into synthetic polypeptide and fragment derived from protein DS: Is this synthetic an oxymoron to the biomaterial? synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme organ section GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra 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 PERSON: Helen Parkinson organ section bronchial alveolar lavage BAL GROUP: IEDB 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. PERSON: Bjoern Peters bronchial alveolar lavage solution containing lung derived T cells, eosinophils, and TNFa. obsolete_polymer MC, 20100316: Replaced by Chebi polymer and usage polymerization also fixed. true 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. James Malone Philippe Rocca-Serra TERM: CHEBI:33839 obsolete_polymer glucose in solution A scattered aggregate of glucose molecules in a liquid Glucose present in blood PERSON: Jie Zheng glucose in solution glucose molecules data transformation Philippe Rocca-Serra The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Branch editors Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing data transformation geometric mean calculation 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). Mathias Brochhausen PERSON: Mathias Brochhausen geometric mean calculation logistic-log curve fitting 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 Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman 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. logistic-log curve fitting logit-log curve fitting 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. ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman 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. 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. logit-log curve fitting log-log curve fitting 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 Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. log-log curve fitting feature extraction objective Elisabetta Manduchi 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. James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective biexponential transformation 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf biexponential transformation 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. Ryan Brinkman box-cox transformation 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." Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry http://flowcyt.sourceforge.net/gating/latest.pdf hyperlog transformation loess scale group transformation one-channel 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. Elisabetta Manduchi Loess scale group normalization applied to data from two one-channel expression microarray assays. OTHER: Editor's adjustment based on MGED Ontology term loess scale group transformation one-channel 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf logical transformation loess scale group transformation two-channel 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. Elisabetta Manduchi Loess scale group normalization applied to data from a two-channel expression microarray assay. OTHER: Adjusted from MGED Ontology loess scale group transformation two-channel loess global transformation one-channel 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. Elisabetta Manduchi 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. OTHER: Editor's generalization based on MGED Ontology term loess global transformation one-channel 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry WEB: http://flowcyt.sourceforge.net/gating/latest.pdf split-scale transformation loess global transformation two-channel 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. Elisabetta Manduchi 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. OTHER: Editor's generalization based on MGED Ontology term loess global transformation two-channel sine transformation 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. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Sine.html 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. cosine transformation Philippe Rocca-Serra 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. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Cosine.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. 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. 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. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation one-channel 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. 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. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation two-channel homogeneous polynomial transformation A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html 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. homogeneous polynomial transformation linlog transformation Philippe Rocca-Serra 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. Elisabetta Manduchi PMID: 16646782 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. linlog transformation variance stabilizing transformation 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. Elisabetta Manduchi James Malone Melanie Courtot PMID: 12169536 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. variance stabilising transformation variance stabilizing transformation loess global transformation Philippe Rocca-Serra 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. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess global transformation loess group transformation Philippe Rocca-Serra 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. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess group transformation 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. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess scale group transformation total intensity transformation single Philippe Rocca-Serra 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. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. OTHER: Adjusted from MGED Ontology 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)). total intensity transformation single total intensity transformation paired Philippe Rocca-Serra 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). Elisabetta Manduchi Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. OTHER: Adjusted from MGED Ontology 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. total intensity transformation paired quantile transformation 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. quantile transformation mean centering Philippe Rocca-Serra 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. mean centering mean centring median centering Philippe Rocca-Serra 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. median centering median centring differential expression analysis objective 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. 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 Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective 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 Person:Helen Parkinson Tina Boussard K-fold cross validation method leave one out cross validation method 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson 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 leave one out cross validation method jackknifing method Helen Parkinson Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method http://en.wikipedia.org/wiki/Resampling_%28statistics%29 simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure 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 data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points Helen Parkinson 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 boostrapping Benjamini and Hochberg false discovery rate correction method 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 Helen Parkinson Helen Parkinson 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) 2011-03-31: [PRS]. specified input and output of dt which were missing Benjamini and Hochberg false discovery rate correction method Philippe Rocca-Serra 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. Elisabetta Manduchi PMID:16762068 Philippe Rocca-Serra pareto scaling 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. Tina Hernandez-Boussard editor modular decomposition k-means clustering Elisabetta Manduchi Philippe Rocca-Serra 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). James Malone WEB: http://en.wikipedia.org/wiki/K-means k-means clustering 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). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_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. Elisabetta Manduchi PERSON: Elisabetta Manduchi average linkage hierarchical clustering complete linkage hierarchical clustering Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. complete linkage hierarchical clustering single linkage hierarchical clustering Elisabetta Manduchi 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. PERSON: Elisabetta Manduchi single linkage hierarchical clustering Benjamini and Yekutieli false discovery rate correction method A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate Helen Parkinson Helen Parkinson The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) 2011-03-31: [PRS]. specified input and output of dt which were missing Benjamini and Yekutieli false discovery rate correction method Philippe Rocca-Serra dimensionality reduction Philippe Rocca-Serra data projection 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction principal components analysis dimensionality reduction Philippe Rocca-Serra 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot pca data reduction principal components analysis dimensionality reduction probabilistic algorithm A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. James Malone PERSON: James Malone probabilistic algorithm 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. James Malone PERSON: James Malone expectation maximization 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 Richard Scheuermann global modularity calculation 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. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi PERSON: James Malone dye swap merge moving average Philippe Rocca-Serra 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. Elisabetta Manduchi Helen Parkinson PERSON: Elisabetta Manduchi PERSON: Helen Parkinson The moving average is often used to handle data from tiling arrays. moving average replicate analysis 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. Elisabetta Manduchi Helen Parkinson PERSON: Helen Parkinson PERSON:Elisabetta Manduchi Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. replicate analysis 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. Helen Parkinson PERSON: Helen Parkinson b cell epitope prediction 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. Helen Parkinson PERSON: Helen Parkinson mhc binding prediction 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. Helen Parkinson PERSON: Helen Parkinson t cell epitope prediction data imputation ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. 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. Monnie McGee data imputation continuum mass spectrum PERSON: James Malone A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. PERSON: Tina Boussard PERSON: Tina Hernandez-Boussard continuum mass spectrum characteristic path length calculation PERSON: Tina Hernandez-Boussard PERSON: Tina Hernandez-Boussard Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices characteristic path length calculation centroid mass spectrum centroid mass spectrum calculation centroiding 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 centroid mass spectrum Holm-Bonferroni family-wise error rate correction method Person:Helen Parkinson WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method 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 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 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 Holm-Bonferroni family-wise error rate correction method Philippe Rocca-Serra 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. Tina Hernandez-Boussard edge weighting editor was classified under algorithm class which is not acceptable super-class TO BE DEALT WITH STILL BY RICHARD. JAMES loess transformation Philippe Rocca-Serra 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. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess transformation 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. Elisabetta Manduchi James Malone Melanie Courtot WEB: http://en.wikipedia.org/wiki/Curve_fitting curve fitting data transformation 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. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 Monnie McGee 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt FWER correction Philippe Rocca-Serra family wise error rate correction method submatrix extraction 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.) Elisabetta Manduchi James Malone Melanie Courtot 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 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. submatrix extraction row submatrix extraction 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot 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. row submatrix extraction column submatrix extraction 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot 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. column submatrix extraction 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. James Malone Josef Spidlen Melanie Courtot PERSON: James Malone PERSON: Josef Spidlen PERSON: Richard Scheuermann PERSON: Ryan Brinkman PERSON:Melanie Courtot Richard Scheuermann Ryan Brinkman gating 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. Elisabetta Manduchi James Malone Melanie Courtot Monnie McGee PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Monnie McGee descriptive statistical calculation objective arithmetic mean calculation Philippe Rocca-Serra 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) James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee arithmetic mean calculation network analysis network topology 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. PERSON: Richard Scheuermann Richard Scheuermann network analysis sequence analysis objective James Malone PERSON: James Malone A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. sequence analysis objective longitudinal data analysis PERSON: James Malone PERSON: Tina Boussard correlation analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. longitudinal data analysis 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 Kaplan meier data transformation PERSON: James Malone PERSON: Tina Boussard http://en.wikipedia.org/wiki/Survival_analysis survival analysis survival analysis objective mass spectrometry analysis A data transformation which has the objective of spectrum analysis. mass spectrometry analysis spread calculation data transformation EDITOR A spread calculation is a data transformation that has objective spread calculation. James Malone spread calculation data transformation Kaplan Meier PERSON: James Malone PERSON: Tina Boussard 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) http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator Kaplan Meier multiple testing correction method 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 Monnie McGee 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 multiple testing procedure inter-rater reliability objective 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. Person:Alan Ruttenberg Person:Helen Parkinson a data transformation objective of determining the concordance or agreement between human judges. http://en.wikipedia.org/wiki/Inter-rater_reliability inter-rater agreement inter-rater reliability objective Westfall and Young family wise error rate correction Helen Parkinson Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing 2011-03-31: [PRS]. specified input and output of dt which were missing PRS: 2011-03-31: set specified input and specified output to the data transformation Westfall and Young FWER correction Westfall and Young family wise error rate correction polynomial transformation 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. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Polynomial.html 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 polynomial transformation 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. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Logarithm logarithmic transformation 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. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function WEB: http://en.wikipedia.org/wiki/Exponential_function exponential transformation non-negative matrix factorization 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 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. http://en.wikipedia.org/wiki/Non-negative_matrix_factorization non-negative matrix factorization soft independent modeling of class analogy analysis SIMCA 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. Tina Hernandez-Boussard WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies soft independent modeling of class analogy analysis 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. Tina Hernandez-Boussard WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant function analysis canonical variate analysis CVA Tina Hernandez-Boussard WEB: http://en.wikipedia.org/wiki/Canonical_analysis 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. 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. PERSON: Tina Hernandez-Boussard Tina Hernandez-Boussard linear discriminant functional analysis regression analysis method BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 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. Tina Hernandez-Boussard regression analysis method multiple linear regression analysis Tina Hernandez-Boussard WEB:http://en.wikipedia.org/wiki/Linear_regression 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. Tina Hernandez-Boussard WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html principal component regression partial least square regression analysis ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. PLS-RA 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. Tina Hernandez-Boussard partial least square regression analysis 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. Tina Hernandez-Boussard WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant analysis 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. WEB: http://www.camo.com/rt/Resources/pls-da.html James Malone PLS-DA partial least square discriminant analysis 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf eh transformation 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf b transformation 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf s transformation data visualization Generation of a heatmap from a microarray dataset Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data encoding as image An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Tina Boussard data visualization 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi similarity calculation 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi euclidean distance calculation 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Correlation pearson correlation coefficient calculation loess fitting Philippe Rocca-Serra 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. Monnie McGee loess fitting 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) James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee mode calculation 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. Monnie McGee WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html quantile calculation 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. From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee median calculation 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) Monnie McGee PERSON: Monnie McGee variance calculation 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) Monnie McGee PERSON: Monnie McGee standard deviation calculation interquartile-range calculation From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) Monnie McGee PERSON: Monnie McGee 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. interquartile-range calculation 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 From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) Monnie McGee WEB: http://www.riskglossary.com/link/skewness.htm skewness calculation 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 From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) Monnie McGee WEB: http://davidmlane.com/hyperstat/A53638.html kurtosis calculation data combination data pooling A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. Richard Scheuermann data combination editor 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. PERSON: Richard Scheuermann Richard Scheuermann network graph construction 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. PERSON: Richard Scheuermann Richard Scheuermann weighted network graph construction 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. PERSON: Richard Scheuermann Richard Scheuermann directed network graph construction 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. PERSON: Richard Scheuermann Richard Scheuermann node quality calculation 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. PERSON: Richard Scheuermann Richard Scheuermann node degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann quantitative node degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann node in-degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann node out-degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann node shortest path identification 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. PERSON: Richard Scheuermann Richard Scheuermann edge quality calculation 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. PERSON: Richard Scheuermann Richard Scheuermann edge betweenness calculation 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. PERSON: Richard Scheuermann Richard Scheuermann network subgraph quality calculation 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. PERSON: Richard Scheuermann Richard Scheuermann subgraph degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann quantitative subgraph degree calculation mathematical feature PERSON: James Malone James Malone This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review) feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation mathematical feature log base Elisabetta Manduchi 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. WEB: http://en.wikipedia.org/wiki/Logarithm logarithm base logarithmic base 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. PERSON: Richard Scheuermann Richard Scheuermann subgraph in-degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann subgraph out-degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann intra subgraph connectivity calculation 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. PERSON: Richard Scheuermann Richard Scheuermann subgraph modularity calculation 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. PERSON: Richard Scheuermann Richard Scheuermann network graph quality calculation 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. Elisabetta Manduchi PMID:16762068 Philippe Rocca-Serra autoscaling unit-variance scaling MA transformation 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. Elisabetta Manduchi MA transformation 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. PERSON: Elisabetta Manduchi Philippe Rocca-Serra exponential base Elisabetta Manduchi 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). WEB: http://en.wikipedia.org/wiki/Exponential_function exponential base polynomial degree Elisabetta Manduchi PERSON: Elisabetta Manduchi 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 number of variables Elisabetta Manduchi PERSON: Elisabetta Manduchi 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 Elisabetta Manduchi bottom-up 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. James Malone PERSON: Elisabetta Manduchi agglomerative hierarchical clustering divisive hierarchical clustering Elisabetta Manduchi top-down 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. James Malone PERSON: Elisabetta Manduchi divisive hierarchical clustering data partitioning Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. James Malone PERSON: Melanie Courtot PERSON: Richard Scheuermann PERSON: Ryan Brinkman data partitioning data vector reduction objective James Malone 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. PERSON: Richard H. Scheuermann Richard H. Scheuermann data vector reduction objective 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. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 Monnie McGee gFWER correction generalized family wise error rate correction method 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' Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 Monnie McGee QNFP quantile number of false positives correction method 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. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 Monnie McGee TPPFP correction method tail probability for the proportion of false positives correction method false discovery rate 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 Monnie McGee 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 Philippe Rocca-Serra false discovery rate correction method 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. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 Monnie McGee PEFP correction method proportion of expected false positives correction method 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). Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 Monnie McGee QPFP correction method quantile proportion of false positives correction method data transformation objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective normalize objective data normalization objective Elisabetta Manduchi Helen Parkinson PERSON: Elisabetta Manduchi PERSON: Helen Parkinson 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. James Malone PERSON: James Malone 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. data normalization objective correction objective PERSON: James Malone PERSON: Melanie Courtot 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 James Malone Type I error correction correction objective normalization data transformation James Malone A normalization data transformation is a data transformation that has objective normalization. PERSON: James Malone normalization data transformation averaging data transformation James Malone An averaging data transformation is a data transformation that has objective averaging. PERSON: James Malone averaging data transformation partitioning data transformation James Malone A partitioning data transformation is a data transformation that has objective partitioning. PERSON: James Malone partitioning data transformation partitioning objective Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. James Malone partitioning objective background correction objective Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. James Malone background correction objective curve fitting objective Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. James Malone curve fitting objective class discovery data transformation James Malone clustering data transformation unsupervised classification data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. PERSON: James Malone class discovery data transformation Fisher's exact test Fisher's exact test 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. James Malone WEB:http://mathworld.wolfram.com/FishersExactTest.html center calculation objective PERSON: James Malone A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. 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. James Malone center calculation objective class discovery objective PERSON: Elisabetta Manduchi PERSON: James Malone clustering 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. James Malone class discovery objective discriminant analysis objective unsupervised classification objective class prediction objective PERSON: Elisabetta Manduchi PERSON: James Malone classification 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. James Malone class prediction objective supervised classification objective spread calculation objective Person:Helen Parkinson 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 James Malone spread calculation objective center calculation data transformation James Malone A center calculation data transformation is a data transformation that has objective of center calculation. PERSON: James Malone center calculation data transformation 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. James Malone PERSON: James Malone data vector reduction data transformation scaling objective Person:Helen Parkinson 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 Awaiting English definition from Monnie McGee James Malone scaling objective 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. James Malone PERSON: James Malone descriptive statistical calculation data transformation scaling data transformation A scaling data transformation is a data transformation that has objective scaling. James Malone PERSON: James Malone scaling data transformation error correction objective Application of a multiple testing correction method PERSON: James Malone 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 error correction objective sequence analysis data transformation EDITOR 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. James Malone sequence analysis data transformation cross validation objective WEB: http://en.wikipedia.org/wiki/Cross_validation 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. James Malone cross validation objective rotation estimation objective merging objective PERSON: Data Transformation Branch 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. James Malone combining objective merging objective merging of columns from two different data sets clustered data visualization 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. James Malone clustered data visualization gene list visualization 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. James Malone gene list visualization classified data visualization 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. James Malone classified data visualization background corrected data visualization 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. James Malone Monnie McGee background corrected data visualization survival analysis data transformation A data transformation which has the objective of performing survival analysis. James Malone PERSON: James Malone survival analysis data transformation proportional hazards model estimation Cox model Cox proportional hazards model PERSON: James Malone PERSON: Tina Boussard 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 proportional hazards model estimation correlation study objective A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. PERSON: Tina Boussard correlation study objective spectrum analysis objective Calculation of characteristic path length in mass spectrometry PERSON: Tina Boussard Person:Helen Parkinson is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. spectrum analysis objective tandem mass spectrometry 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. PERSON: James Malone PERSON: Tina Boussard PERSON: Tina Boussard 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). tandem mass spectrometry gas chromatography mass spectrometry Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds. PERSON: James Malone PERSON: Tina Boussard PERSON: Tina Boussard gas chromatography mass spectrometry chi square test PERSON: James Malone PERSON: Tina Boussard 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. chi square test ANOVA ANOVA ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal. James Malone sequential design 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 MUSC PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. Philippe Rocca-Serra Provenance: OCI sequential design observation design OBI branch derived PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. Philippe Rocca-Serra observation design 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) 03/17/2010: obsoleted (on call), and replaced by 'material entity' and/or specimen. No need for the 'collection' part of this class any more after merging bfo:aggregate object into material entity, and by dealing with 'specimen' rather than with entities of organismal origin. 2009-11-04, MC: Entity of organismal origin has been deprecated a while ago. We still have collection (of entities of organismal origin). I am not sure we could replace with collection of material entity without altering the meaning (i.e. deprecating the class). In addition, if we do deprecate that class, should we just assert the children under material entity? PERSON: Susanna Sansone true PERSON: Philippe Rocca-Serra 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] PRS: How can we distinguish with 'collection' as the process of collecting entities, (eg. data collection, urine collection) a collection is a bfo:aggregate object, that is a set of material object of the same kind added during 22-02-2008 biomaterial call to distinguish library and population obsolete_collection (of entities of organismal origin) set, group, ensemble pool of specimens GROUP: CEBS PERSON: Jennifer Fostel A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish pool of specimens chemical solution GROUP: OBI Biomaterial Branch PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra 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. 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. chemical solution liquid chemical solution buffer role 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 OBI Person:Helen Parkinson Person:Philippe Rocca-Serra a role which inheres in some molecular entity realized during the process of buffering buffer buffer role solvent role Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors. solvent role 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 solute role Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) 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 solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution comet assay PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review. Philippe Rocca-Serra SCGE assay a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions. comet assay single cell gel electrophoresis assay PCR-SSCP assay PCR-SSCP assay PERSON: Philippe Rocca-Serra 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? PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases. a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure. polymerase chain reaction-single strand conformation polymorphism assay obsolete_liver GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra true PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93. PRS: Test. added for evaluation and validation of possible imports from CARO (or other anatomical resources) 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 obsolete_liver obsolete_adipose tissue GROUP: OBI Biomaterial derived PERSON: Philippe Rocca-Serra true 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. PRS: this class has been added during major biomaterial.owl cleanup for evaluation and testing of imports from CARO 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. obsolete_adipose tissue denatured polymer PERSON: Alan Ruttenberg http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 Is a polymer which has lost secondary or tertiary structure denatured polymer decapitated organism Philippe Rocca-Serra OBI Biomaterial 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 decapitated organism is an organism which has had it's head removed validated information OBI PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." Person:Philippe Rocca-Serra 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 curated information 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 A 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. OBI PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. Person:Bjoern Peters Person:Philippe Rocca-Serra curated information randomized group participant role A person enrolled in a randomized clinical trial bears a randomized group participant role Person:Helen Parkinson Philippe Rocca-Serra a role that borne by an organism and realized by some group randomization process randomized group participant role methylated polymer Philippe Rocca-Serra A methylated polymer which has artificially acquired one or more methyl groups Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 OBI Biomaterial methylated polymer genetically modified organism PERSON: Philippe Rocca-Serra 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 OBI Biomaterial an organism that is the output of a genetic transformation process genetically modified organism predicted data item 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. Philippe Rocca-Serra; Bjoern Peters A data item that was generated on the basis of a calculation or logical reasoning predicted data item mean-centered data Person:Helen Parkinson Person:Philippe Rocca-Serra 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 edited document A document which is the output of a document editing process Person:Bjoern Peters Philippe Rocca-Serra The OBI manuscript is (much) edited imformation edited document dissolved material entity A material entity that has been going through a process of being put into solution Person:Bjoern Peters Philippe Rocca-Serra Salt molecules that have been mixed into water dissolved material entity extraction A material separation in which a desired component of an input material is separated from the remainder Person:Bjoern Peters Philippe Rocca-Serra nucleic acid extraction using phenol chloroform Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. extraction filtration OBI-Branch: adapted from wikipedia and wordnet Philippe Rocca-Serra PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. filtration filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device centrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation staining Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. staining washing OBI-Branch Philippe Rocca-Serra PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing 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. irradiation Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) 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. irradiation irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves polymerization OBI-Branch Philippe Rocca-Serra 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. PRS:22102008: need to import catalyst from CHEBI 35223 polymerization 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 trypsination OBI PA Philippe Rocca-Serra 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 trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity enzymatic ligation OBI-Branch Philippe Rocca-Serra 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 PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. enzymatic ligation storage OBI-Branch Philippe Rocca-Serra A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. storage cell lysis 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. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] 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 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. electrocution OBI branch Philippe Rocca-Serra PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376. electrocution electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process. cervical dislocation OBI branch Philippe Rocca-Serra 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 PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax) cervical dislocation 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 asphyxiation OBI branch Philippe Rocca-Serra 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 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. intentional overdosing OBI Biomaterial Philippe Rocca-Serra 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 intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death lethal injection decapitation OBI-Branch Philippe Rocca-Serra 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- decapitation 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..) group randomization Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. group randomization obsolete_activation Alan Ruttenberg 2010/11/22: After OBI call, this is too broad a term, and in any case would be in the scope of GO OBI-Branch Philippe Rocca-Serra See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178 true 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!) obsolete_activation immobilization OBI-Branch Philippe Rocca-Serra 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 nucleic acid hybridization Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] hybridization assay 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. nucleic acid hybridization elution Philippe Rocca-Serra wordnet.princeton.edu/perl/webwn 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. elution 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) DNA Subtraction OBI-Branch Philippe Rocca-Serra 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. document editing Philippe Rocca-Serra and OBI consortium adapted from wikipedia Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292 document editing is a planned process with specified input original document and specified output edited document prediction OBI Philippe Rocca-Serra 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 validation Philippe Rocca-Serra adapted from wordnet (wkipedia) 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 electroporation Philippe Rocca-Serra WEB:http://en.wikipedia.org/wiki/Electroporation electropermeabilization 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 digital curation Philippe Rocca-Serra wikipedia Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. digital curation A10-Analyzer 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. A10-Analyzer John Quinn http://www.apogeeflow.com/flow_cytometry_products.htm A40-MiniFCM 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. A40-MiniFCM John Quinn http://www.apogeeflow.com/flow_cytometry_products.htm analog-to-digital converter A-D A2D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. John Quinn Melanie Courtot The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. analog-to-digital converter http://en.wiktionary.org/wiki/Analog-to-Digital_Converter flow cytometer analyzer 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. FACS Calibur, Luminex 100 John Quinn flow cytometer analyzer http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm arc lamp 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. John Quinn The Jablochkoff Candle arc lamp http://en.wikipedia.org/wiki/Arc_lamp argon ion laser http://en.wikipedia.org/wiki/Laser#Gas_lasers 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. Daniel Schober John Quinn argon ion laser argon ion laser in a cytometer avalanche photodiode 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. C30644E - InGaAs Avalanche Photodiode John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 avalanche photodiode Bactiflow 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. Bactiflow John Quinn http://www.chemunex.com/products/chemframe.htm band pass filter 530/30 BP filter, 585/42 BP filter 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. Person:John Quinn band pass filter http://en.wikipedia.org/wiki/Band_pass_filter BioSorter1000 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 1000 at TSRI Flow Cytometry Core Facility BioSorter1000 John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter2000 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 2000 at TSRI Flow Cytometry Core Facility BioSorter2000 John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter250 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 250 at TSRI Flow Cytometry Core Facility BioSorter250 John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter500 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. BioSorter 500 at TSRI Flow Cytometry Core Facility BioSorter500 John Quinn http://www.unionbio.com/products/BioSorter.html Cell Lab Quanta SC 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. Cell Lab Quanta SC John Quinn http://www.beckmancoulter.com/cell-lab charge plate John Quinn LSR2 charge plate 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. Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 charge plate cell sorter collection tube John Quinn LSR2 collection tube 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. Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 cell sorter collection tube Cyan 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. Cyan John Quinn http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm CYFlow ML 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. CYFlow ML John Quinn http://www.partec.de/products/cyflow-ml.html CyFlow SL CyFlow SL John Quinn 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. http://www.partec.de/products/cyflow.html CyFlow SL3 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 SL3 John Quinn http://www.partec.de/products/cyflowsl3.html CyFlow Space 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. CyFlow Space CyFlow Space at TSRI Flow Cytometry Core Facility John Quinn http://www.partec.de/products/cyflowspace.html CytoBuoy flow cytometer analyzer 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. CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations CytoBuoy flow cytometer analyzer John Quinn, Melanie Courtot http://www.cytobuoy.com/ CytoSence 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. CytoSence John Quinn http://www.cytobuoy.com/ CytoSub 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. CytoSub John Quinn http://www.cytobuoy.com/ dichroic filter 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. Cy3 Dichroic Filter John Quinn dichroic filter http://en.wikipedia.org/wiki/Dichroic_filter dichroic mirror 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. John Quinn ViewLux Alexa 594 dichroic mirror dichroic mirror http://en.wikipedia.org/wiki/Dichroic_mirror differential pressure gauge John Quinn LSR2 differential pressure gauge 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. Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 differential pressure gauge diode laser 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. Daniel Schober FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. John Quinn diode laser dye laser 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. Daniel Schober John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. dye laser FACS Calibur "FACS Calibur at TFL, BCCRC, Vancouver" "http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11" FACS Calibur John Quinn The FACS Calibur is one of the most popular cytometers in use for research. FACS Canto 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. FACS Canto John Quinn http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf FACS Canto2 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. FACS Canto2 John Quinn http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01 FACS Scan 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. FACS Scan John Quinn http://www.brc.ubc.ca/brc/facs.html FACSAria 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. FACSAria FACSAria at TSRI Flow Cytometry Core Facility John Quinn http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf FACSvantage FACSvantage FACSvantage at TSRI Flow Cytometry Core Facility John Quinn 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. http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 FC 500 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. FC 500 John Quinn http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp flow cell flow_cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. Biofilm Flow Cell Person:John Quinn flow cell http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cytometer 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. FACS Calibur John Quinn flow cytometer http://en.wikipedia.org/wiki/Flow_cytometer fluid pressure regulator LSR2 fluid pressure regulator Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. Person: John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 fluid pressure regulator gas laser http://en.wikipedia.org/wiki/Gas_laser 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. Daniel Schober John Quinn gas laser helium-neon gas laser used to erradiate cells in a flow cytometer. Guava EasyCyte Mini 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. Guava EasyCyte Mini John Quinn http://www.guavatechnologies.com/main/products/easyCyteMini.cfm Guava EasyCyte Plus 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. Guava EasyCyte Plus John Quinn http://www.guavatechnologies.com/main/products/easycyte-new.cfm Guava Personal Cell Analysis 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. Guava Personal Cell Analysis Guava_PCA John Quinn http://www.guavatechnologies.com/main/products/PCA-new.cfm Guava Personal Cell Analysis-96 Guava Personal Cell Analysis-96 Guava_PCA-96 John Quinn 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. http://www.guavatechnologies.com/main/products/PCA-96new.cfm helium cadmium ion laser 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. John Quinn KIMMON HeCd 325nm laser helium cadmium ion laser http://en.wikipedia.org/wiki/Laser#Gas_lasers helium neon ion laser http://en.wikipedia.org/wiki/Laser#Gas_lasers 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. Daniel Schober John Quinn helium neon ion laser Amnis ImageStream Amnis ImageStream It has both components, an Image cytometer and a flow cytometer. John Quinn Melanie Courtot 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. http://www.amnis.com/ inFlux Analyzer John Quinn 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. http://www.cytopeia.com/analyzer.htm inFlux Analyzer Influx Cell Sorter 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. Influx Cell Sorter Influx Cell Sorter at TSRI Flow Cytometry Core Facility John Quinn http://www.cytopeia.com/sorter.htm interrogation_point Interrogation point in BD FACS Calibur John Quinn 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. http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11 interrogation_point ion laser http://en.wikipedia.org/wiki/Ion_laser 2 Watt Lexel 88 Argon Ion laser An ion laser is a gas laser which uses an ionized gas as its lasing medium. Daniel Schober John Quinn ion laser jet_in_air_flow_chamber 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. Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm jet_in_air_flow_chamber krypton ion laser 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. Daniel Schober John Quinn Lexel 95L krypton laser krypton ion laser LactoScope C4 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. Josef Spidlen LactoScope C4 LactoScope C4 Automatic Economical Melanie Courtot http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm laser http://en.wikipedia.org/wiki/Laser 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. A laser is the most common way to irradiate a cell in a flow cytometer. Daniel Schober John Quinn laser light amplification by the stimulated emission of radiation light source 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. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source logarithmic voltage amplifier 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. HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 logarithmic voltage amplifier long pass filter 750 LP filter 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. John Quinn http://en.wikipedia.org/wiki/high-pass_filter long pass filter LSR2 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. John Quinn LSR2 LSR2 at TSRI Flow Cytometry Core Facility http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf Luminex 100 John Quinn Luminex 100 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. http://www.luminexcorp.com/products/luminex_100IS.html Luminex 200 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 John Quinn Luminex 200 http://www.luminexcorp.com/support/faqs.html MACS Quant 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. John Quinn MACS Quant http://www.miltenyi.com 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. Gold vapor laser, Helium-cadmium metal-vapor laser John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 metal vapor laser mixed argon-krypton gas laser 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. John Quinn argon-krypton laser in a cytometer http://www.eio.com/repairfaq/sam/laserarg.htm mixed argon-krypton gas laser MoFlo 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. John Quinn MoFlo MoFlo at TSRI Flow Cytometry Core Facility http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16 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 John Quinn http://www.nuncbrand.com/page.aspx?ID=301 multi-well plate neodymium-YAG laser 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. Daniel Schober John Quinn Neodymium-YAG Laser in DURIP99 System neodymium-YAG laser obscuration bar Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 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. Daniel Schober John Quinn obscuration bar obscuration bar in a flow cytometer optical filter 720 LP filter, 580/30 BP filter 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. John Quinn http://en.wikipedia.org/wiki/Optical_filter optical filter optical subsystem 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. John Quinn Person: Daniel Schober 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. optical subsystem optical subsystem of a cytometer particle delivery vessel FC 500 particle delivery vessel FG: this should be delted - particle delivery is a role that an object can play John Quinn 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. Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 particle delivery vessel photodetector 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 photomultiplier tube, a photo diode John Quinn http://einstein.stanford.edu/content/glossary/glossary.html photodetector photodiode 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. Avalanche photodiode John Quinn http://cyto.mednet.ucla.edu/Protocols/flow.htm photodiode photomultiplier tube 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. John Quinn R9647 by manufactured by Hamamatsu http://cyto.mednet.ucla.edu/Protocols/flow.htm photomultiplier tube piezo electric crystal think this is natural thing, not a device HP/JF 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. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm piezo electric crystal quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar plate loader 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. FC 500 plate loader John Quinn 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. http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf plate loader preamplifier 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. Built in preamplifier in a Hamamatsu H9656 PMT John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 preamplifier quartz cuvette 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. CVF-Q-10 flow chamber, CV-Q-10 flow chamber John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm quartz cuvette flow chamber Reflection 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. John Quinn Reflection Reflection at TSRI Flow Cytometry Core Facility http://www.i-cyt.com/reflection.htm cytometer sample tube 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. John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 cytometer sample tube sample tube in a cytometer sheath tank John Quinn LSR2 sheath tank 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. Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 sheath tank short pass filter 620 SP filter 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. John Quinn http://en.wikipedia.org/wiki/Low-pass_filter short pass filter solid state laser 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. Daniel Schober Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command http://en.wikipedia.org/wiki/Solid-state_laser solid state laser Somacount 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. John Quinn Somacount http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575 SomaScope "http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10" Josef Spidlen SomaScope SomaScope Mark II Automatic Economical The SomaScope is an instrument to quantify somatic cells in milk. flow cytometer sorter 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. BioSorter2000, LSR2 John Quinn Melanie Courtot flow cytometer sorter http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm syringe pump NE-1000 Single Syringe Pump 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. Person:John Quinn http://www.answers.com/topic/syringe, 2007-05-11 syringe pump voltage amplifier Frank Gibson A voltage amplifier is a device that amplifies the voltage signal. John Quinn Linear amplifier, log amplifier, microwave amplifier http://en.wiktionary.org/wiki/amplifier voltage amplifier waste tank LSR2 waste tank 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. Person:John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 waste tank DNA sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. ABI 377 DNA Sequencer, ABI 310 DNA Sequencer DNA sequencer MO Trish Whetzel array scanner GROUP: MGED Ontology An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip GenePix 4200A, GenePix4000B Trish Whetzel array scanner arrayer BioRobotics Microgrid II TAS, Affymetrix GMS 417 MO_697 arrayer Trish Whetzel a device which deposits biological material onto a substrate in a defined pattern. arrayer centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Person: Jennifer Fostel Melanie Courtot Trish Whetzel centrifuge http://en.wikipedia.org/wiki/Centrifuge computer A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Apple PowerBook, Dell OptiPlex Melanie Courtot Trish Whetzel computer http://en.wikipedia.org/wiki/Computer heating block 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 An instrument used to heat and/or maintain material at a set temperature. Daniel Schober MO heating block homogenizer A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Melanie Courtot Trish Whetzel homogenizer http://en.wikipedia.org/wiki/Homogenizer mortar, blender hybridization chamber A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. Glass Array Hybridization Cassette MO_563 hybridization_chamber Trish Whetzel hybridization chamber hybridization station A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. Labnet Problot12 MO_497 hybridization station Trish Whetzel hybridization station liquid handler Beckman BioMek 2000 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. MO_868 liquid_handler a device that is used for automated liquid transfer and handling. liquid handler liquid_handling_instrument oligonucleotide synthesizer An instrument used to chemically synthesize oligonucleotides. Automated Multiplex Oligonucleotide Synthesizer MO Trish Whetzel oligonucleotide synthesizer sonicator 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. MO Sonicator 3000 Trish Whetzel sonicator spectrophotometer 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. Helios Gamma Spectrophotometer MO Melanie Courtot Trish Whetzel spectrophotometer thermal cycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. DNA_amplifier MO Melanie Courtot PCR_machine Piko(tm) 96-well Thermal Cycler Polymerase_Chain_Reaction_ machine Trish Whetzel thermal cycler thermocycler vacuum dryer An instrument which removes liquid by the application of negative pressure, i.e. vacuum. MO Model 777 Microarray Oven Trish Whetzel vacuum dryer vortexer 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. Melanie Courtot Trish Whetzel VWR Genie 2 http://en.wikipedia.org/wiki/Vortex_mixer vortex_mixer vortexer microarray wash station ArrayIt(r) Microarray Wash Station MO_626 wash_station Trish Whetzel a device that is used to wash Affymetrix-type arrays. microarray wash station temperature control bath Alan Ruttenburg Daniel Schober Frank Gibson OBI Instrument branch 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). 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. temperature control bath molecular crosslinker 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. MO ?? cannot be found in MO Stratalinker Trish Whetzel a device that is able to chemically join two or more molecules. molecular crosslinker molecular crosslinker image cytometer An image_cytometer is an instrument for image-based study or measurement of cells. Melanie Courtot The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. http://web.mit.edu/solab/Research/ImageCytometry.html image cytometer cytometer A cytometer is an instrument for counting and measuring cells. Melanie Courtot cytometer http://medical.merriam-webster.com/medical/cytometer gel tank Person:Frank Gibson CHEF gel box, slab gel box, capillary electrophoresis Person:Kevin Clancy 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. electrophoresis box electrophoresis unit gel tank sep:00095 power supply Frank Gibson sep:00093 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. Daniel Schober PERSON: Daniel Schober PSU electrical power supply power pack power supply power supply unit was power_pack, maps to SEP electrical_power_supply fluorometer 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. Allyson Lister Kevin Lister OBI fluorometer laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 multispectral imaging flow cytometer 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. MIFC Melanie Courtot http://www.amnis.com/ multispectral imaging flow cytometer microarray An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. PERSON: Chris Stoeckert A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. Daniel Schober microarray DNA microarray PERSON: Frank Gibson Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 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. DNA Chip DNA microarray DNA-array 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 PERSON: Daniel Schober protein microarray PERSON: Daniel Schober 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. Daniel Schober 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. protein microarray droplet sorter OBI Instrument branch OBI Instrument branch 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. droplet sorter water bath Daniel Schober PERSON: Daniel Schober 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). A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. water bath oil bath Daniel Schober PERSON: Daniel Schober 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). An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period. oil bath digital-to-analog converter Daniel Schober PERSON: Daniel Schober A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal. A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound. digital-to-analog converter microtome PERSON: Daniel Schober PERSON: Phillippe Rocca-Serra A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. microtome microscope PERSON: Phillippe Rocca-Serra wikipedia 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:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6 microscope microscope slide OBI biomaterial branch PERSON: Phillippe Rocca-Serra 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 microscope slide animal cage OBI biomaterial branch PERSON: Phillippe Rocca-Serra 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. animal cage laboratory cage study design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design clinical study design Clinical Research Glossary Version 4.0 CDICS glossary group 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] PlanAndPlannedProcess Branch The definition needs to be extended to other things than simply patients clinical study design repeated measure design 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. PlanAndPlannedProcess Branch 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 http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design cross over design (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) 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. Philippe Rocca-Serra 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 cross over design n-to-1 design Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) 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). Philippe Rocca-Serra n-to-1 design matched pairs design 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: 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. Philippe Rocca-Serra http://www.holah.karoo.net/experimentaldesigns.htm matched pairs design parallel group design 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 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. Philippe Rocca-Serra http://www.holah.karoo.net/experimentaldesigns.htm independent measure design parallel group design randomized complete block design 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. Philippe Rocca-Serra 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)) http://www.tufts.edu/~gdallal/ranblock.htm randomized complete block design balanced incomplete block design PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. Philippe Rocca-Serra balanced incomplete block design 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 loop design A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design MO_912 PMID: 12933549 Philippe Rocca-Serra on behalf of MO loop design reference design A reference experiment design type is where all samples are compared to a common reference. MO_699 PMID: 12933549 Philippe Rocca-Serra on behalf of MO reference design latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and 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. 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. Philippe Rocca-Serra latin square design graeco latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and Greco-Latin square design is a study design which relates to Latin square design 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. Philippe Rocca-Serra graeco latin square design only 2 articles in pubmed ->probably irrelevant hyper graeco latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and PRS to do Philippe Rocca-Serra hyper graeco latin square design no example found in pubmed->not in use in the community factorial design 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. Philippe Rocca-Serra factorial design 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) 2x2 factorial design 2x2 factorial design PMID: 17561240 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. Philippe Rocca-Serra a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors fractional factorial design 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 Philippe Rocca-Serra fractional factorial design http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control dye swap design An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip MO_858 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. Philippe Rocca-Serra on behalf of MO dye swap design replicate design 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. MO_885 Philippe Rocca-Serra on behalf of MO replicate design self vs self design A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. MO_490 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. Philippe Rocca-Serra on behalf of MO self vs self design time series design Groups of assays that are related as part of a time series. MO_887 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. Philippe Rocca-Serra on behalf of MO time series design 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. PRS PRS a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen stopping rule compliance rule PRS PRS a compliance rule is a rule which ensures a compliance process occurs compliance rule standard compliance rule PRS PRS a standard compliance rule is a compliance rule which defines conformity to a representation standard standard compliance rule ethical standard compliance rule PRS PRS an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur ethical standard compliance rule eligibility criterion Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. Person: Philippe Rocca-Serra an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. eligibility criterion eligibility rule inclusion criteria Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . Person: Philippe Rocca-Serra an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. inclusion condition inclusion criteria inclusion rule exclusion criterion Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. Person: Philippe Rocca-Serra an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study exclusion criterion adding substance to cell culture renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms Bjoern Peters IEDB adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient adding substance to cell culture is process in which a material substance is added to a cell culture tumor grading Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney Determination of 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. OBI branch derived; submitted by MO grading of tumor tumor grading performing a clinical assessment clinical diagnosis (maybe CIO) OBI branch derived PlanAndPlannedProcess Branch a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. performing a clinical assessment human subject enrollment As with group assignment, should the specified output here be an organism which bears a role A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. Bjoern Peters IEDB criteria come from plan / clinical trial branch enlisting familiy members of HIV patients into a study human subject enrollment collecting specimen from organism IEDB PERSON:Bjoern Peters a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient killing Philippe Rocca-Serra A protocol application in which an organism is intentionally put to death CEBS, Biomaterial_branch Jennifer Fostel Terminal sacrifice of animals by cervical dislocation at the end of an investigation. death status type 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. euthanisia killing life termination sacrifice administering substance in vivo 1 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells Person:Bjoern Peters Bjoern Peters Different routes and means of administration should go as children underneath this IEDB Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/ administering substance in vivo injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally 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 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. Bjoern Peters 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' IEDB This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition acquisition the planned process of gaining possession of a continuant exposure of material to environment Alan says there will be problmes, e.g. with selection by survival Bjoern Peters IEDB 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. exposure of material to environment material acquisition 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 material procurement 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. This excludes processes that create or change materials, such as material transformations. An acquisition in which possession of a material entity is gained. Bjoern Peters, Alan Ruttenberg, Helen Parkinson IEDB material acquisition acclimatization 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. CEBS, Biomaterial_branch Jennifer Fostel acclimatization placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress environmental material collection process 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 IEDB Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas environmental material collection process the researcher is very interested in the location information acquisition data collection An acquisition in which possession of information is gained. Bjoern Peters Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC OBI branch derived This excludes processes that create or change information, such as assays and data transformations. information acquisition material component separation Bjoern Peters IEDB Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space material component separation group assignment cohort assignment study 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 OBI Plan Philippe Rocca-Serra group assignment group assignment is a process which has an organism as specified input and during which a role is assigned pooling specimens 2 OBI branch derived PlanAndPlannedProcess Branch http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. physical combination of several instances of like material pooling specimens sample pooling detection of molecular label 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 OBI developer call, 3-12-12 PERSON:Matthew Brush 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 detection of molecular label material portioning OBI branch derived PERSON:Bjoern Peters a material processing in which the input substance is partitioned into a number of portions that are similar in composition. aliquoting apportioning material portioning pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock non-specific labeling OBI branch derived PlanAndPlannedProcess Branch The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. definition blessed by Allyson, Bjoern, Jay & Randi non-specific labeling histology PRS:20090901: addition of alternative term = histopathology histopathology OBI branch derived PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney histology need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement cell fixation OBI branch derived PERSON:Bjoern Peters a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time 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&amp;list_uids=16080188&dopt=AbstractPlus should include capturing what qualities are being preserved we could generalize this for other input materials excision Alan Ruttenberg, Kevin Clancy Cutting out the portion of a gel which contains a DNA fragment excision the use physical means to remove a portion of a substance from the rest www.crohnsresource.com/glossary.jsp (via google define:resection) non specific enzymatic cleavage OBI branch derived PERSON:Kevin Clancy The use of agarase to digest an agar gel a protocol application to digest the fraction of input material that is susceptible to that enzyme non specific enzymatic cleavage maintaining cell culture OBI branch derived PlanAndPlannedProcess Branch When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing maintaining cell culture substance detection OBI branch derived PERSON:Kevin Clancy any protocol which results in the detection of a specified substance substance detection the detection of phycoerytherin by means of flow cytometry longitudinal mass measurement assay A process in which the mass of a material is measured at two or more time points Helen Parkinson OBI branch derived The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection longitudinal mass measurement assay artificially induced cell membrane lysis ---\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. OBI branch derived PlanAndPlannedProcess Branch a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate artificially induced cell membrane lysis http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent. artificially induced reverse transcription 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. OBI branch derived PERSON:Kevin Clancy The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA 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 a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) artificially induced reverse transcription isolation of cell culture supernatant OBI branch derived PlanAndPlannedProcess Branch 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. This does not apply to the case where the cells are lysed a protocol which results in the separation of supernatant material from a cell culture isolation of cell culture supernatant experimental disease induction OBI branch derived PlanAndPlannedProcess Branch a protocol application to induce a specific disease in an organism could be defined class experimental disease induction the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. enzyme-linked immunospot assay 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. 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. ELISPOT assay IEDB IEDB enzyme-linked immunospot assay artificially induced DNA repair ---\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 OBI branch derived PlanAndPlannedProcess Branch a protocol application to repair damaged DNA molecules artificially induced DNA repair the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands cell permeabilization A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application Electroporation of HeLa cells to allow transfection with pUC19. OBI branch derived PERSON:Bjoern Peters cell permeabilization definition blessed by Jay, Alan, Randi need to add output cell has_quality permeable precipitation OBI branch derived PERSON:Kevin Clancy 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) precipitation establishing cell culture PERSON:Matthew Brush 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. establishing cell culture 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). PERSON:Matthew Brush cell culture splitting cell culture passaging 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. OBI branch derived PlanAndPlannedProcess Branch 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 cell culture splitting addition of molecular label labeling OBI developer call, 3-12-12 PERSON:Matthew Brush The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay addition of molecular label artificially induced methylation A planned process of adding methyl groups to polymers OBI branch derived PERSON:Kevin Clancy artificially induced methylation the use of enzymes to add methyl groups to DNA molecules synthesis OBI branch derived PERSON:Kevin Clancy This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription making cDNA from nucleotides using RNA as a template synthesis synthesize the construction of a biomaterial from simpler biomaterials concentrate Evaporation of the solution containing DNA to increase the concentration of the DNA molecules OBI branch derived PERSON:Kevin Clancy 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 concentrate recombinant plasmid cloning OBI branch derived PERSON:Kevin Clancy 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. recombinant plasmid cloning the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial genetic transformation OBI branch derived PERSON:Kevin Clancy The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 genetic modification genetic transformation the introduction. alteration or integration of genetic material into a cell or organism lavage A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid OBI branch derived PlanAndPlannedProcess Branch This is not washing, in which case the material of interest is not the resulting fluid lavage the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present 3D structure determination assay 3D structure determination assay An assay that determines the 3-dimensional configuration of an input material. IEDB IEDB The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. preparative chromatography OBI branch derived PERSON:Kevin Clancy; Bjoern Peters The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides. preparative chromatography 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 sequencing assay OBI branch derived PlanAndPlannedProcess Branch The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template has_output should be sequence of input; we don't have sequence well defined yet sequencing assay the use of a chemical or biochemical means to infer the sequence of a biomaterial vector mediated amplification E coli expressing the gene for M avium p35 were cultured in order to produce p35. OBI branch derived PERSON:Kevin Clancy The process of creating a copy of some biological entity in cell culture vector mediated amplification DNA polymerase amplification Philippe Rocca-Serra DNA polymerase amplification DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input OBI branch derived PERSON:Kevin Clancy The use of taq polymerase to amplify a DNA fragment during a PCR. specific enzymatic cleavage OBI branch derived PERSON:Kevin Clancy The use of a protease to digest a protein into peptides a protocol application to digest the fraction of input material that is susceptible to that enzyme specific enzymatic cleavage gradient separation OBI branch derived PERSON:Kevin Clancy 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 gradient separation the use of a sucrose gradient to isolate mitochondria dialysis OBI branch derived PERSON:Kevin Clancy a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition dialysis the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage 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. 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. OBI branch derived PERSON:Kevin Clancy 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 electrophoresis selection by survival OBI branch derived PERSON:Kevin Clancy 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 selection by survival the use of environmental conditions to select for the organism or cells that have a certain trait DNA cleavage, restriction analysis DNA cleavage, restriction analysis PERSON:Kevin Clancy restriction enzyme assay the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components protease cleavage OBI branch derived PlanAndPlannedProcess Branch enzymatic digestion protease cleavage protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). the use of trypsin to cleave pepsin into peptide fragments enzymatic DNA replication OBI branch derived PERSON:Kevin Clancy enzymatic DNA replication the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial the use of enzymes to duplicate DNA molecules enzymatic amplification OBI branch derived PERSON:Kevin Clancy 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 DNA transduction OBI branch derived PERSON:Kevin Clancy 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 DNA transfection OBI branch derived PERSON:Kevin Clancy 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. OBI branch derived PlanAndPlannedProcess Branch needs defined relationship to cell culture vector mediated expression 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 recombinant vector cloning molecular cloning OBI branch derived 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) recombinant vector cloning obsolete_defined processes true OBI branch derived Place holder class, see editor note PlanAndPlannedProcess Branch Remove to simplify OBI release Discussed on 2012 Ann Arbor OBI wokshop obsolete_defined processes specific labeling OBI branch derived PlanAndPlannedProcess Branch 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 definition blessed by Allyson, Bjoern, Jay & Randi specific labeling RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA OBI branch derived PlanAndPlannedProcess Branch RNA extraction requested by Helen Parkinson for MO nucleic acid extraction OBI branch derived Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. PlanAndPlannedProcess Branch a material separation to recover the nucleic acid fraction of an input material nucleic acid extraction requested by Helen Parkinson for MO. Could be defined class cell culture supernatant GROUP: IEDB PERSON: Bjoern Peters 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 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 cell pellet GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214 GROUP: CEBS PERSON: Helen Parkinson cell pellet phage display library PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra 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] PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction WEB: http://www.immuneepitope.org/home.do 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 phage display library 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 lysed material GROUP: PSI PERSON: Susanna Sansone 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 a cell lysate is a material entity which is output of a cell lysis process cell lysate lysate peptide construct IEDB 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 PERSON: Bjoern Peters a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion peptide construct transgenic organism PERSON: Philippe Rocca-Serra GROUP:IEDB 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 PERSON: Bjoern Peters PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it transgenic organism whole mount tissue PERSON: Philippe Rocca-Serra 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 GROUP: OBI PERSON: Helen Parkinson 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 whole mount sample whole mount tissue assay bead 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. Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. OBI assay bead bead epitope IEDB IEDB a material entity bearing the epitope role epitope obsolete_occurrence of disease true An occurrence of disease is a process involving pathologic changes within an organism IEDB IEDB obsolete_occurrence of disease replaced by http://purl.obolibrary.org/obo/OGMS_0000063 'disease course' Details see https://sourceforge.net/tracker/?func=detail&aid=3515228&group_id=177891&atid=886178 host exposure to infectious agent IEDB IEDB 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 IEDB IEDB administration in vivo with infectious agent is an administration of an infectious agent to a host organism occurrence of infectious disease IEDB IEDB Is an occurrence of a disease caused by an infection occurrence of infectious disease disposition to cause an allergic reaction allergenic disposition IEDB IEDB 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. disposition to cause an allergic reaction allergic reaction IEDB IEDB allergic reaction an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) occurrence of allergy IEDB IEDB 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 assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-2 production by T cells IEDB IL-2 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters epitope binding by adaptive immune receptor IEDB IEDB 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. Immunization in vivo IEDB IEDB Immunization in vivo Process of administering an object playing the role of immunogen to a living organism adaptive immune effector function 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. IEDB IEDB adaptive immune effector function living with infected household contact 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 IEDB IEDB living with infected household contact living in endemic area 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 IEDB IEDB living in endemic area pathogen release in laboratory accident 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 IEDB IEDB pathogen release in laboratory accident Immunization in vitro IEDB IEDB Immunization in vitro Process of administering an object playing the role of immunogen to a cell culture infection process IEDB IEDB infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment adaptive immune receptor IEDB IEDB adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. immunogen IEDB IEDB a material entity bearing the immunogen role immunogen environmental exposure to infectious agent IEDB IEDB 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 environmental exposure to infectious agent host of immune response 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. 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. An organism in which an immune response process occurs. IEDB IEDB host of immune response 293-T cell line 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 IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5008.html C1R 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 IEDB IEDB experimental infection of cell culture IEDB IEDB experimental infection of cell culture is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture EL-4 cell line A cell line derived from mouse (C57BL/6N) lymphoma cells. EL-4 cell line IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1160.html HeLa cell line A cell line derived from human cervical cancer cells. HeLa cell line IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1597.html JAWS II cell line A cell line derived from mouse dendritic cells. IEDB IEDB JAWS II cell line http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology antigen IEDB IEDB antigen is a material entity that has the antigen role Jurkat cell line A cell line derived from human T cells. IEDB IEDB Jurkat cell line http://www.biotech.ist.unige.it/cldb/cl5296.html JY cell line The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) IEDB IEDB JY cell line assay measuring binding of a T cell epitope:MHC:TCR complex An immune epitope assay that detects T cell epitope recognition. IEDB IEDB T cell binding|any method assay measuring binding of a T cell epitope:MHC:TCR complex RMA cell line 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. IEDB IEDB RMA cell line T2 cell line A human T-B lymphoblastoid hybrid cell line IEDB IEDB T2 cell line http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology infectious disease IEDB IEDB infectious disease is a disease caused by an infectious agent lymph node cell specimen 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. IEDB IEDB lymph node cell specimen cultured adherent cell populaiton 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. IEDB 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. IEDB adherent cell culture sample cultured adherent cell populaiton cultured PBMC cell population 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). IEDB IEDB PBMC cell culture sample cultured PBMC cell population disposition to be bound by an adaptive immune receptor epitope disposition IEDB IEDB Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. disposition to be bound by an adaptive immune receptor organ harvesting IEDB IEDB The process of removing an organ from its source organism organ harvesting cultured CD3+ T cell population A T cell population characterized by expressing the CD3 molecule on its surface. CD3+ T cell culture sample IEDB IEDB cultured CD3+ T cell population cultured CD3- T cell population A T cell population characterized by not expressing the CD3 molecule on its surface. CD3- T cell culture sample IEDB IEDB cultured CD3- T cell population allergy IEDB IEDB allergy 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 cultured CD4- T cell population A T cell population characterized by not expressing the CD4 molecule on its surface. CD4- T cell culture sample IEDB IEDB cultured CD4- T cell population cultured CD8- T cell population A T cell population characterized by not expressing the CD8 molecule on its surface. CD8- T cell culture sample IEDB IEDB cultured CD8- T cell population cultured CD4-/CD8- T cell population A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. CD4-/CD8- T cell culture sample IEDB IEDB cultured CD4-/CD8- T cell population cancer A disease characterized by abnormal and uncontrolled cell division IEDB IEDB cancer autoimmune disease IEDB IEDB Is a disease characterized by an immune response of an organism against parts of itself autoimmune disease obsolete_disease true http://purl.obolibrary.org/obo/OGMS_0000031 IEDB IEDB obsolete_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. IEDB IEDB epitope specific IL-2 release by T cells MHC:epitope complex binding to TCR IEDB IEDB MHC:epitope complex binding to TCR 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. ELISPOT assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interferon-gamma production by T cells IEDB IFNg release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters exposure resulting in immune reactivity a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity IEDB IEDB exposure resulting in immune reactivity immunogen role IEDB IEDB any entity capable of eliciting an immune response when introduced to components of the immune system immunogen role host of immune response role 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. IEDB IEDB host of immune response 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. effector T cell function IEDB IEDB 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 antigen presentation function should add a reference to the antigen processing and presentation process. APC IEDB IEDB 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. antigen presentation function restricting MHC role IEDB IEDB 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 donor A T cell line from a PPD(+) donor. Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. donor role A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. IEDB IEDB donor immune epitope carrier role 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. A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity. IEDB IEDB immune epitope carrier role adjuvant role adjuvent role Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response. IEDB IEDB adjuvant role disposition to infect an organism IEDB IEDB Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease disposition to infect an organism immunization Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). IEDB IEDB 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 blood harvesting A material separation where blood is taken from an organism. IEDB IEDB blood harvesting L cell line A cell line derived from mouse fibroblasts. IEDB IEDB L cell line http://www.biotech.ist.unige.it/cldb/cl3075.html cultured antigen presenting cell population A culture of PBMCs. A culture of Hela cells. IEDB a cell culture including cells that have an antigen presentation function cultured antigen presenting cell population antigen presenting cell culture sample cultured effector T cell population A cell culture including cells that have an effector T cell function A culture of cytotoxic CD8+ T cells. IEDB cultured effector T cell population culture of effector T cells effector T cell culture sample material to be added 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 mixture of peptides that is being added into a cell culture. IEDB a material that is added to another one in a material combination process material to be added target of material addition 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. A cell culture into which a mixture of peptides is being added. A material entity into which another is being added in a material combinatino process IEDB target of material addition environmental proximity to infectious agent IEDB IEDB Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result environmental proximity to infectious agent 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 IEDB IEDB contact to pathogen carrying biological vector splenocyte specimen 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. IEDB IEDB splenocyte specimen P815 cell line A cell line derived from mouse mastocytoma. IEDB IEDB P815 cell line http://www.biotech.ist.unige.it/cldb/cl5244.html assay antigen role Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with 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. see OBI_1110120 below IEDB IEDB assay antigen role pathologic process IEDB IEDB abnormal, harmful processes caused by or associated with a disease pathologic process assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex qualitative binding|binding assay 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. IEDB IEDB assay measuring MHC ligand processing and presentation ligand presentation|any method assay measuring binding of a MHC:ligand complex A MHC ligand assay that detects the binding of a ligand to an MHC molecule. IEDB IEDB MHC binding|binding assay assay measuring binding of a MHC:ligand complex assay measuring binding of a B cell epitope:antibody complex An immune epitope assay that detects B cell epitope recognition. IEDB IEDB antibody binding|any method assay measuring binding of a B cell epitope:antibody complex immune epitope assay An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event IEDB IEDB immune epitope assay immune epitope assay biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope dependent biological activity assay that detects cytokine production. IEDB IEDB biological activity assay measuring epitope specific cytokine production by T cells cytokine release|biological activity biological activity 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. IEDB IEDB biological activity assay measuring epitope specific T cell killing cytotoxicity|biological activity biological activity assay measuring epitope specific proliferation of T cells A T cell epitope dependent biological activity assay that detects T cell proliferation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters biological activity assay measuring epitope specific proliferation of T cells proliferation|biological activity CD8 receptor A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. CD8 CD8 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. WEB: http://en.wikipedia.org/wiki/CD8 51 chromium assay measuring epitope specific T cell killing 51 chromium assay measuring epitope specific T cell killing A T cell epitope specific killing assay performed in vitro that uses a chromium release assay. IEDB IEDB cytotoxicity|51 chromium ELISA measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. ELISA measuring epitope specific interferon-gamma production by T cells IEDB IFNg release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-2 production by T cells IEDB IL-2 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-4 production by T cells IEDB IL-4 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-5 production by T cells IEDB IL-5 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. ELISA measuring epitope specific tumor necrosis factor production by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNFa release|ELISA ELISA measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-10 production by T cells IEDB IL-10 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells GM-CSF release|ELISA IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-6 production by T cells IEDB IL-6 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-13 production by T cells IEDB IL-13 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-12 production by T cells IEDB IL-12 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-1 beta production by T cells IEDB IL-1b release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-17 production by T cells IEDB IL-17 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISA measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an ELISA. ELISA measuring epitope specific interleukin-18 production by T cells IEDB IL-18 release|ELISA PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-4 production by T cells IEDB IL-4 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells IEDB IEDB TNFa release|ELISPOT ELISPOT assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-10 production by T cells IEDB IL-10 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters ELISPOT assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. ELISPOT assay measuring epitope specific interleukin-13 production by T cells IEDB IL-13 release|ELISPOT PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. IEDB IFNg release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-2 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters TNFa release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-4 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-10 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. IEDB IL-17 release|ICS PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex A T cell epitope qualitative binding assay that uses an MHC multimer staining assay. IEDB MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters qualitative binding|multimer/tetramer 3H-thymidine assay measuring epitope specific proliferation of T cells 3H-thymidine assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay. IEDB IEDB proliferation|3H-thymidine BrdU assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay. BrdU assay measuring epitope specific proliferation of T cells IEDB IEDB proliferation|BrdU epitope specific T cell proliferation A biological process where T cells proliferate resulting from the recognition of a T cell epitope. IEDB IEDB 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. IEDB IEDB epitope specific GM-CSF release by T cells 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. IEDB IEDB epitope specific IFN-g release by T cells 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. IEDB IEDB epitope specific IL-10 release by T cells 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. IEDB IEDB epitope specific IL-12 release by T cells 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. IEDB IEDB epitope specific IL-13 release by T cells 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. IEDB IEDB epitope specific IL-17 release by T cells 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. IEDB IEDB epitope specific IL-18 release by T cells 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. IEDB IEDB epitope specific IL-1b release by T cells 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. IEDB IEDB epitope specific IL-4 release by T cells allergen A material entity bearing the disposition to cause an allergic reaction Birch pollen is an allergen IEDB IEDB allergen 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. IEDB IEDB epitope specific IL-5 release by T cells 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. IEDB IEDB epitope specific IL-6 release by T cells epitope specific killing by T cells 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. IEDB IEDB epitope specific killing by T cells epitope specific TNF release by T cells A biological process where T cells produce TNF resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific TNF release by T cells assay detecting IFN-gamma production An IFN-g ELISPOT is an assay detecting ifn-gamma production IEDB IFNg release PERSON: Bjoern Peters an assay that determines information about the production of the cytokine interferon gamma assay detecting IFN-gamma production direct submission to IEDB A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB) IEDB PERSON: Bjoern Peters 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 direct submission to IEDB chromium release assay 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. 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. IEDB PlanAndPlannedProcess Branch, IEDB chromium release assay clinical history clinical history A series of statements representing health-relevant qualities of a patient and of a patient's family. phenotype phenotype A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease disease course 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' disease course The totality of all processes through which a given disease instance is realized. treatment treatment A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder fixed tissue specimen A processed specimen that is the output of a fixation process. fixed tissue specimen fixed tissue slide specimen A fixed tissue specimen that is placed in a slide. fixed tissue slide specimen age A time quality inhering in a bearer by virtue of how long the bearer has existed. age fluorescence 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. fluorescence biological sex An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. biological sex length A 1-D extent quality which is equal to the distance between two points. length mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass temperature A physical quality of the thermal energy of a system. temperature behavioral quality 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. behavioral quality female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. volume pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. pressure diluted A concentration which relatively low. diluted damaged A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. damaged lateral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. lateral to ventral to 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. ventral to dorsal to 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. dorsal to quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity quality of related physical entities A physical entity quality which exists in relation towards some other entity. quality of related physical entities mixed sex A biological sex quality inhering in a population of multiple sexes. mixed sex biomaterial purity A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. biomaterial purity hermaphrodite A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. hermaphrodite a mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. a mating type (yeast) alpha mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. alpha mating type (yeast) h minus A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. h minus h plus A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. h plus F mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. F mating type F minus mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. F minus mating type ploidy 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. ploidy haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. haploid polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. polyploid aneuploid 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. aneuploid diploid 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. diploid cellular quality A monadic quality of continuant that exists at the cellular level of organisation. cellular quality alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. alive dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. dead quality of a solid 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. quality of a solid quality of a gas 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. quality of a gas quality of a liquid 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. quality of a liquid relational spatial quality A quality of related physical entities inhering in a bearer by virtue of the bearer's pertaining to or involving or having the nature of space in relation to another entity. relational spatial quality anterior to 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. anterior to frontal radioactive A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. radioactive left side of A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. left side of right side of A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. right side of frozen A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. frozen organismal quality A quality that inheres in an entire organism or part of an organism. organismal quality handedness 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 left handedness 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. left handedness right handedness 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. right handedness ambidextrous handedness 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. ambidextrous handedness fluid flow rate 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. fluid flow rate protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. antithrombin III is a protein protein CD4 molecule 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. CD4 molecule CD3 subunit with immunoglobulin domain 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. CD3 subunit with immunoglobulin domain antithrombin-III A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof. antithrombin-III double-stranded RNA-specific adenosine deaminase A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof. double-stranded RNA-specific adenosine deaminase deoxyribonuclease-1 A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof. deoxyribonuclease-1 glial cell line-derived neurotrophic factor A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof. glial cell line-derived neurotrophic factor ribonuclease T2 A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof. ribonuclease T2 DNA ligase A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. DNA ligase Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule ligase T cell receptor co-receptor CD8 A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. T cell receptor co-receptor CD8 guanyl-specific ribonuclease T1 A protein that is a translation product of the Aspergillus oryzae rntA gene or a 1:1 ortholog thereof. guanyl-specific ribonuclease T1 nuclease S1 A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof. nuclease S1 ribonuclease U2 A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof. ribonuclease U2 ribonuclease V1 A protein with ribonuclease activity that is a constituent of cobra venom. ribonuclease V1 ribonuclease CL3 A protein with ribonuclease activity that is purified from chicken liver. ribonuclease CL3 molecular label role MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role) a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. OBI developer call, 3-12-12 molecular label role molecular tracer role molecular label 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 molecular tracer OBI developer call, 3-12-12 molecular label region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule region sequence polypeptide A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. polypeptide polypeptide sequence supercontig One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. supercontig contig A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. contig miRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. miRNA sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. sequence_assembly circular A quality of a nucleotide polymer that has no terminal nucleotide residues. circular assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. assembly pituitary gland The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. pituitary gland lymph node 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. lymph node life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage mouth 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). mouth amniotic fluid Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. amniotic fluid blood A fluid that is composed of blood plasma and erythrocytes. blood breast The upper ventral region of an animal's torso. breast renal medulla renal medulla the inner portion of the kidney consisting of the renal pyramids organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. organism substance material anatomical entity Anatomical entity that has mass. material anatomical entity anatomical cluster Anatomical group that has its parts adjacent to one another. anatomical cluster tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. tissue multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. multi-tissue structure epithelium 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]. epithelium stomach An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. stomach aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation aorta heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. heart brain The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. brain cerebral cortex The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. cerebral cortex adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue adipose tissue strand of hair A filament, mostly protein, that grows from follicles found in the dermis[WP]. strand of hair pleural fluid Transudate contained in the pleural cavity. pleural fluid urine Excretion that is the output of a kidney urine sweat Secretion produced by a sweat gland. sweat synovial fluid Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae. synovial fluid skeletal muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. skeletal muscle tissue colon Last portion of the large intestine before it becomes the rectum. colon cortex of kidney Outer cortical portion of the kidney, between the renal capsule and the renal medulla. cortex of kidney urinary bladder distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. urinary bladder pancreas An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. pancreas peritoneal fluid Transudate contained in the peritoneal cavity. peritoneal fluid tibial nerve The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. tibial nerve cerebrospinal fluid A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. cerebrospinal fluid coronary artery An artery that supplies the myocardium. coronary artery vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. vein vitreous humor A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina vitreous humor saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. saliva caudate nucleus 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. caudate nucleus putamen 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. putamen milk An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. milk bile bile vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. placenta organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. placenta feces Portion of semisolid bodily waste discharged through the anus[MW,modified] feces cerebellum Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. cerebellum thyroid gland A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. thyroid gland lung Respiration organ that develops as an oupocketing of the esophagus. lung dermis 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]. dermis hypodermis 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]. hypodermis skin of body The organ covering the body that consists of the dermis and epidermis. skin of body spleen spleen the organ that functions to filter blood and to store red corpuscles and platelets liver An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. liver peritoneum A serous membrane that lines the peritoneal cavity[VHOG,modified]. peritoneum prostate gland The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. prostate gland adrenal gland Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. adrenal gland bone marrow bone marrow the soft tissue that fills the cavities of bones pericardial fluid Transudate contained in the pericardial cavity.[FMA] pericardial fluid esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. esophagus mucosa left cerebral hemisphere A cerebral hemisphere that is in the left side of a brain. left cerebral hemisphere right cerebral hemisphere A cerebral hemisphere that is in the right side of a brain. right cerebral hemisphere esophagus muscularis mucosa A muscularis mucosa that is part of a esophagus. esophagus muscularis mucosa mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. mucosa of nasopharynx mucosa of oropharynx A mucosa that is part of a oropharynx [Automatically generated definition]. mucosa of oropharynx digestive system fluid or secretion digestive system fluid or secretion sputum Matter ejected from the lungs, bronchi, and trachea, through the mouth. sputum tibial artery The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. tibial artery length unit A unit which is a standard measure of the distance between two points. length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit substance unit A unit which is a standardised quantity of an element or compound with uniform composition. substance unit concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. volume unit frequency unit A unit which is a standard measure of the number of repetitive actions in a particular time. frequency unit pressure unit A unit which is a standard measure of the force applied to a given area. pressure unit volumetric flow rate unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . volumetric flow rate unit rate unit A unit which represents a standard measurement occurrence of a process per unit time. rate unit vaccine vaccine 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. vaccination vaccination 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. Obsolete Class Obsolete Class example to be eventually removed example to be eventually removed failed exploratory term Person:Alan Ruttenberg The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term PERSON:Alan Ruttenberg organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting core Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split other true 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. other universal A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf Alan Ruttenberg Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. universal defined class "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. Alan Ruttenberg named class expression named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions to be replaced with external ontology term Alan Ruttenberg Terms with this status should eventually replaced with a term from another ontology. group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Transformation-ML web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf 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) person:Jennifer Fostel ACS web-page:http://www.isac-net.org/content/view/607/150/ ACS 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/) d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. person:Jennifer Fostel XML web-page:http://www.w3.org/XML/ RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document XML XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel RDF web-page:http://www.w3.org/RDF/ A FOAF file, a SKOS file, an OWL file. RDF 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/) person:Jennifer Fostel zip web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ MagicDraw MDZIP archive, Java JAR file. person:Jennifer Fostel zip 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 web-page:http://www.gnu.org/software/tar/manual/ Example.tar file. person:Jennifer Fostel tar 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 web-page:http://www.fcspress.com/ FCS FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. person:Jennifer Fostel Compensation-ML web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML 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) compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment person:Jennifer Fostel Gating-ML web-page:http://www.flowcyt.org/gating/ Gating-ML Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) foogate.xml, Gating-ML file describing gates used in a GvHD experiment. person:Jennifer Fostel OWL web-page:http://www.w3.org/2004/OWL/ OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. OWL 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/) person:Jennifer Fostel obsolete_the supplier role of Affymetrix obsolete_the supplier role of Affymetrix true Affymetrix Affymetrix supplied microarray An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Philippe Rocca-Serra Thermo Waters Philippe Rocca-Serra Waters BIO-RAD BIO-RAD Philippe Rocca-Serra GenePattern hierarchical clustering GenePattern hierarchical clustering James Malone Ambion Ambion Philippe Rocca-Serra Helicos Helicos Philippe Rocca-Serra Roche Philippe Rocca-Serra Roche Illumina Illumina Philippe Rocca-Serra GenePattern PCA GenePattern PCA GenePattern module SVM GenePattern module SVM GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern k-nearest neighbors GenePattern k-nearest neighbors James Malone GenePattern LOOCV GenePattern LOOCV GenePattern k-means clustering GenePattern k-means clustering James Malone Agilent Agilent Philippe Rocca-Serra GenePattern module KMeansClustering GenePattern module KMeansClustering GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern CART GenePattern CART James Malone GenePattern module CARTXValidation GenePattern module CARTXValidation GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. Li-Cor Li-Cor Philippe Rocca-Serra Bruker Corporation Bruker Corporation Philippe Rocca-Serra GenePattern module KNNXValidation GenePattern module KNNXValidation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module PeakMatch GenePattern module PeakMatch GenePattern module KNN GenePattern module KNN GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern SVM GenePattern SVM James Malone Applied Biosystems Applied Biosystems Philippe Rocca-Serra GenePattern module PCA GenePattern module PCA GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern peak matching GenePattern peak matching James Malone Ryan Brinkman Bruker Daltonics Bruker Daltonics Philippe Rocca-Serra GenePattern HeatMapViewer data visualization GenePattern HeatMapViewer data visualization James Malone The GenePattern process of generating Heat Maps from clustered data. GenePattern HierarchicalClusteringViewer data visualization GenePattern HierarchicalClusteringViewer data visualization James Malone The GenePattern process of generating hierarchical clustering visualization from clustered data. GenePattern module HeatMapViewer A GenePattern software module which is used to generate a heatmap view of data. GenePattern module HeatMapViewer James Malone GenePattern module HierarchicalClusteringViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. GenePattern module HierarchicalClusteringViewer James Malone Sysmex Corporation, Kobe, Japan 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 obsolete_the manufacturer role of Agilent obsolete_the manufacturer role of Agilent true obsolete_manufacturer role of Bruker Daltonics obsolete_manufacturer role of Bruker Daltonics true obsolete_the manufacturer role of Thermo obsolete_the manufacturer role of Thermo true obsolete_the manufacturer role of Li-Cor obsolete_the manufacturer role of Li-Cor true obsolete_the manufacturer role of Roche obsolete_the manufacturer role of Roche true obsolete_the manufacturer role of Ambion obsolete_the manufacturer role of Ambion true obsolete_the manufacturer role of BIO-RAD obsolete_the manufacturer role of BIO-RAD true obsolete_the regulator role of the FDA obsolete_the regulator role of the FDA true obsolete_the manufacturer role of Illumina obsolete_the manufacturer role of Illumina true obsolete_the manufacturer role of Helicos obsolete_the manufacturer role of Helicos true obsolete_manufacturer role of Bruker Corporation obsolete_manufacturer role of Bruker Corporation true obsolete_the manufacturer role of Waters obsolete_the manufacturer role of Waters true obsolete_manufacturer role of applied biosystems obsolete_manufacturer role of applied biosystems true U.S. Food and Drug Administration FDA U.S. Food and Drug Administration right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory Edingburgh handedness inventory PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html 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. eBioscience A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience Cytopeia A supplier of flow cytometry analyzers Cytopeia Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Exalpha Biological A supplier of flow cytometry analyzers Exalpha Biological Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Apogee Flow Systems A supplier of flow cytometry analyzers Apogee Flow Systems Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Exbio Antibodies A supplier of flow cytometry analyzers Exbio Antibodies Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Becton Dickinson (BD Biosciences) A supplier of flow cytometry analyzers Becton Dickinson (BD Biosciences) Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Dako Cytomation A supplier of flow cytometry analyzers Dako Cytomation Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Millipore A supplier of flow cytometry analyzers Karin Breuer Millipore WEB:http://www.guavatechnologies.com/@2011/04/11 Antigenix A supplier of flow cytometry analyzers Antigenix Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Partec A supplier of flow cytometry analyzers Karin Breuer Partec WEB:http://www.partec.de/@2011/04/11 Beckman Coulter A supplier of flow cytometry analyzers Beckman Coulter Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) A supplier of flow cytometry analyzers Advanced Instruments Inc. (AI Companies) Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Miltenyi Biotec A supplier of flow cytometry analyzers Karin Breuer Miltenyi Biotec WEB:http://www.miltenyibiotec.com/@2011/04/11 AES Chemunex A supplier of flow cytometry analyzers AES Chemunex Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 Bentley Instruments A supplier of flow cytometry analyzers Bentley Instruments Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Invitrogen A supplier of flow cytometry analyzers Invitrogen Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Luminex A supplier of flow cytometry analyzers Karin Breuer Luminex WEB:http://www.luminexcorp.com/@2011/04/11 CytoBuoy A supplier of flow cytometry analyzers CytoBuoy Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Nimblegen Person: Jie Zheng Pacific Biosciences 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. Pacific Biosciences Person: Jie Zheng NanoString Technologies 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. NanoString Technologies axiom holds for all times ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times relation has no temporal argument ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) relation has no temporal argument meter 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. m meter kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kg kilogram second 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. s sec second centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. centimeter cm millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. millimeter mm micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. micrometer um nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nanometer nm angstrom A length unit which is equal to 10 [-10] m. angstrom gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. g gram milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. microgram ug nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. nanogram ng picogram A mass unit which is equal to 10^[-12] g. pg picogram degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C degree C degree Celsius minute A time unit which is equal to 60 seconds. min minute hour A time unit which is equal to 3600 seconds or 60 minutes. h hour hr day A time unit which is equal to 24 hours. day week A time unit which is equal to 7 days. week month 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. month year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. micromole umol nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nanomole nmol picomole A substance unit equal to 10^[-12] mol. picomole pmol molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). M molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. micromolar uM nanomolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nM nanomolar picomolar A unit of molarity which is equal to 10^[-12] M. pM picomolar cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cc cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. milliliter ml liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. L liter cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. microliter ul nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nanoliter nl picoliter A volume unit which is equal to 10^[-12] L. picoliter pl hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage % w/w A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. mass percentage percent weight pr weight mass volume percentage % w/v A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. mass volume percentage percent vol per vol volume percentage % v/v A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. percent vol per vol volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. g per L g/L gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. mg per ml mg/ml milligram per milliliter pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. milliliter per liter ml per L ml/l gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. g/dl gram per deciliter colony forming unit per volume A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute count per nanomolar second A rate unit which is equal to one over one nanomolar second. count per nanomolar second count per molar second A rate unit which is equal to one over one molar second. count per molar second count per nanomolar A rate unit which is equal to one over one nanomolar. count per nanomolar count per molar A rate unit which is equal to one over one molar. count per molar microgram per liter A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. microgram per liter ng/ml ug/L IAO Release 2015-02-23 IAO Release 2015-02-23 SVN $Revision: 717 $ OBI Release 2017-02-22 SVN Revision: Unversioned directory 2 Person:Alan Ruttenberg To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) IAO_0021000-IAO_0021999 IAO_0020000-IAO_0020999