Ontology for Biomedical Investigations
type: Ontology
version IRI: obi-base.owl
default language: en
IAO_0000589: Ontology for Biomedical Investigations
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Alan Ruttenberg
creator: Allyson Lister
creator: Barry Smith
creator: Bill Bug
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Mungall
creator: Chris Stoeckert
creator: Chris Taylor
creator: Christian Bolling
creator: Cristian Cocos
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Elisabetta Manduchi
creator: Eric Deutsch
creator: Frank Gibson
creator: Gilberto Fragoso
creator: Helen C. Causton
creator: Helen Parkinson
creator: Holger Stenzhorn
creator: James A. Overton
creator: James Malone
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jessica Turner
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Brush
creator: Matthew Pocock
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
creator: Philippe Rocca-Serra
creator: Phillip Lord
creator: Pierre Grenon
creator: Richard Bruskiewich
creator: Richard Scheuermann
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
date: 2009-07-31
description: An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.
Format: OWL-DL
subject: An ontology for the annotation of biomedical and functional genomics experiments.
license: http://creativecommons.org/licenses/by/4.0/
comment: 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.
version info: 2025-12-18

ISA alternative term
type: AnnotationProperty
IAO_0000114: IAO_0000122
IAO_0000115: An alternative term used by the ISA tools project (http://isa-tools.org).
IAO_0000116: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
IAO_0000117: Person: Alejandra Gonzalez-Beltran
IAO_0000117: Person: Philippe Rocca-Serra
IAO_0000119: ISA tools project (http://isa-tools.org)
sub property of: IAO_0000118

NIAID GSCID-BRC alternative term
type: AnnotationProperty
IAO_0000114: IAO_0000122
IAO_0000115: 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).
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: NIAID GSCID-BRC metadata working group
sub property of: IAO_0000118

IEDB alternative term
type: AnnotationProperty
IAO_0000114: IAO_0000122
IAO_0000115: An alternative term used by the IEDB.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
sub property of: IAO_0000118

FGED alternative term
type: AnnotationProperty
IAO_0000114: IAO_0000122
IAO_0000115: An alternative term used by the Functional Genomics Data (FGED) Society.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: Penn Group
sub property of: IAO_0000118

Contributor
type: AnnotationProperty

Coverage
type: AnnotationProperty

Creator
type: AnnotationProperty

Date
type: AnnotationProperty

Description
type: AnnotationProperty

Format
type: AnnotationProperty

Resource Identifier
type: AnnotationProperty

Language
type: AnnotationProperty

Publisher
type: AnnotationProperty

Relation
type: AnnotationProperty

Rights Management
type: AnnotationProperty

Source
type: AnnotationProperty

Subject and Keywords
type: AnnotationProperty

Title
type: AnnotationProperty

Resource Type
type: AnnotationProperty

license
type: AnnotationProperty
IAO_0000117: Mark Miller
date: 2018-05-11T13:47:29Z

label
type: AnnotationProperty

provides_service_consumer_with
type: ObjectProperty
sub property of: BFO_0000051
domain: service
IAO_0000112: 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.
IAO_0000115: A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.

is_supported_by_data
type: ObjectProperty
domain: OBI_0001909
range: IAO_0000027
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: OBI
IAO_0000119: OBI
IAO_0000119: Philly 2011 workshop

has specified input
type: ObjectProperty
sub property of: RO_0000057
inverse of: is specified input of
domain: COB_0000035
IAO_0000111: has specified input
IAO_0000112: see is_input_of example_of_usage
IAO_0000114: IAO_0000122
IAO_0000115: The inverse property of is specified input of
IAO_0000116: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Larry Hunter
IAO_0000117: PERSON: Melanie Coutot

obsolete_is_concretization_of
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: is_concretization_of
IAO_0000115: 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.
IAO_0000116: replaced by: http://purl.obolibrary.org/obo/BFO_0000058
IAO_0000117: PERSON: Alan Ruttenburg
IAO_0000117: PERSON: Barry Smith
IAO_0000231: IAO_0000228
deprecated: true

is specified input of
type: ObjectProperty
sub property of: RO_0000056
range: COB_0000035
IAO_0000111: is specified input of
IAO_0000112: 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
IAO_0000114: IAO_0000122
IAO_0000115: A relation between a completely executed 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.
IAO_0000117: Alan Ruttenberg
IAO_0000117: PERSON:Bjoern Peters

obsolete_is_concretized_as
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: is_concretized_as
IAO_0000115: 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.
IAO_0000116: replaced by: http://purl.obolibrary.org/obo/BFO_0000059
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Barry Smith
IAO_0000231: IAO_0000228
deprecated: true

obsolete_has_quality
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: has_quality
IAO_0000114: IAO_0000122
IAO_0000115: 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]
IAO_0000116: replaced by: http://purl.obolibrary.org/obo/BFO_0000086
IAO_0000117: GROUP:OBI:<http://obi.sourceforge.net>
IAO_0000117: PERSON: Chris Mungall
IAO_0000231: IAO_0000228
deprecated: true

has specified output
type: ObjectProperty
sub property of: RO_0000057
inverse of: is specified output of
domain: COB_0000035
IAO_0000111: has specified output
IAO_0000114: IAO_0000122
IAO_0000115: The inverse property of is specified output of
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Larry Hunter
IAO_0000117: PERSON: Melanie Courtot

obsolete_is_realized_by
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: is_realized_by
IAO_0000114: IAO_0000122
IAO_0000115: Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
IAO_0000116: replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
IAO_0000117: GROUP:OBI:<http://obi.sourceforge.net>
IAO_0000117: PERSON: Chris Mungall
IAO_0000118: executed_during
IAO_0000118: has_realization
IAO_0000118: is_realized_as
IAO_0000231: IAO_0000228
deprecated: true

obsoleted_has_specified_output_information
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: obsoleted_has_specified_output_information
IAO_0000115: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Frank Gibson
IAO_0000231: IAO_0000103
deprecated: true

is_manufactured_by
type: ObjectProperty
domain: BFO_0000040
range: manufacturer
IAO_0000111: is_manufactured_by
IAO_0000112: 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)
IAO_0000115: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000117: Liju Fan
IAO_0000118: has_make
IAO_0000118: has_manufacturer

obsolete_has_function
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: has_function
IAO_0000112: heart has_function to-pump-blood
IAO_0000114: IAO_0000122
IAO_0000115: Relation between an independent continuant and a function.
IAO_0000116: replaced by: http://purl.obolibrary.org/obo/BFO_0000085
IAO_0000117: GROUP:OBI:<http://obi.sourceforge.net>
IAO_0000117: PERSON: Chris Mungall
IAO_0000231: IAO_0000228
deprecated: true

obsoleted_is_reagent_in
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: obsoleted_is_reagent_in
IAO_0000112: 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
IAO_0000115: Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
IAO_0000117: Alan Ruttenberg
IAO_0000231: IAO_0000103
deprecated: true

obsolete_realizes
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: realizes
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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]
IAO_0000116: replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'
IAO_0000117: GROUP:OBI:<http://obi.sourceforge.net>
IAO_0000117: PERSON: Chris Mungal
IAO_0000118: executes
IAO_0000118: has_function_part
IAO_0000118: involves_execution_of
IAO_0000118: is_realization_of
IAO_0000231: IAO_0000228
deprecated: true

obsoleted_utilizes_reagent
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: obsoleted_utilizes_reagent
IAO_0000112: see example_of_usage for is_reagent_in
IAO_0000115: Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
IAO_0000117: Alan Ruttenberg
IAO_0000231: IAO_0000103
deprecated: true

obsoleted_is_device_for
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: obsoleted_is_device_for
IAO_0000112: 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
IAO_0000115: Relationship between a device and a protocol application in which it participates
IAO_0000117: Alan Ruttenberg
IAO_0000231: IAO_0000103
deprecated: true

is specified output of
type: ObjectProperty
sub property of: RO_0000056
range: COB_0000035
IAO_0000111: is specified output of
IAO_0000114: IAO_0000122
IAO_0000115: A relation between a completely executed 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.
IAO_0000117: Alan Ruttenberg
IAO_0000117: PERSON:Bjoern Peters

obsoleted_utilizes_device
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: obsoleted_utilizes_device
IAO_0000112: see example_of_usage for is_device_for
IAO_0000115: Relationship between protocol application and an intrument in which it participates
IAO_0000117: Alan Ruttenberg
IAO_0000231: IAO_0000103
deprecated: true

is_proxy_for
type: ObjectProperty
IAO_0000111: is_proxy_for
IAO_0000112: 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
IAO_0000115: 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.
IAO_0000116: 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)
IAO_0000117: Alan Ruttenberg

obsoleted_has_specified_input_information
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: has specified input information
IAO_0000115: 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.
IAO_0000117: PERSON: Frank Gibson
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000118: consumes data
IAO_0000231: IAO_0000103
deprecated: true

obsolete_has_role
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: has_role
IAO_0000114: IAO_0000122
IAO_0000115: A relation between a continuant C and a role R. The reciprocal relation of role_of.
IAO_0000116: replaced by: http://purl.obolibrary.org/obo/BFO_0000087
IAO_0000117: GROUP:OBI:<http://obi.sourceforge.net>
IAO_0000117: PERSON:Chris Mungal
IAO_0000231: IAO_0000228
deprecated: true

obsolete_results_from
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: obsolete_results_from
IAO_0000116: 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
IAO_0000231: IAO_0000103
deprecated: true

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: COB_0000035
range: IAO_0000005
IAO_0000111: achieves_planned_objective
IAO_0000112: A cell sorting process achieves the objective specification 'material separation objective'
IAO_0000115: 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.
IAO_0000117: BP, AR, PPPB branch
IAO_0000119: PPPB branch derived
IAO_0000232: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

obsoleted_is_specified_information_output_of
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: is_specified_information_output_of
IAO_0000115: A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
IAO_0000116: is replaced by has_specified_output_of
IAO_0000117: PERSON: James Malone
IAO_0000119: Editor
IAO_0000231: IAO_0000103
deprecated: true

has grain
type: ObjectProperty
sub property of: BFO_0000051
IAO_0000111: has grain
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000119: 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

obsoleted_is_specified_information_intput_of
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: obsoleted_is_specified_information_intput_of
IAO_0000115: Is the inverse relation of has_specfied_input_information
IAO_0000116: is replaced by is_specified_intput_of
IAO_0000231: IAO_0000103
deprecated: true

is grain of
type: ObjectProperty
sub property of: BFO_0000050
IAO_0000111: is grain of
IAO_0000115: 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.
IAO_0000116: JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000119: 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

provisions
type: ObjectProperty
inverse of: has_supplier
IAO_0000111: provisions
IAO_0000115: A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use
IAO_0000116: 5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship.
IAO_0000117: GROUP: Relations branch
IAO_0000118: supplies

has_supplier
type: ObjectProperty
domain: BFO_0000040
range: Class
  union of: NCBITaxon 9606
  union of: organization
IAO_0000111: has_supplier
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Alan Rutternberg
IAO_0000117: PERSON: Cristian Cocos
IAO_0000117: PERSON: Frank Gibson
IAO_0000117: PERSON: Melanie Courtot

objective_achieved_by
type: ObjectProperty
domain: IAO_0000005
range: COB_0000035
IAO_0000111: objective_achieved_by
IAO_0000114: IAO_0000122
IAO_0000115: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
IAO_0000117: OBI
IAO_0000119: OBI

is member of organization
type: ObjectProperty
inverse of: has organization member
domain: Class
  union of: NCBITaxon 9606
  union of: organization
range: organization
IAO_0000111: is member of organization
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000116: 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.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000117: Person:Helen Parkinson
IAO_0000119: Person:Alan Ruttenberg
IAO_0000119: Person:Helen Parkinson
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

has category label
type: ObjectProperty
sub property of: BFO_0000051
domain: categorical measurement datum
range: categorical label
IAO_0000111: has category label
IAO_0000115: 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
type: ObjectProperty
type: SymmetricProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000111: has disposition to bind
IAO_0000115: A relationship between two material entitites that each have disposition to form a complex with the other.
IAO_0000116: 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
IAO_0000119: IEDB

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: NCBITaxon 9606
  union of: organization
IAO_0000115: Relating an organization to a legal person or organization.
IAO_0000116: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
IAO_0000117: Person: Jie Zheng

specifies value of
type: ObjectProperty
sub property of: IAO_0000136
domain: OBI_0001933
IAO_0000115: A relation between a value specification and an entity which the specification is about.

has value specification
type: ObjectProperty
sub property of: BFO_0000051
domain: IAO_0000030
range: OBI_0001933
IAO_0000114: IAO_0000120
IAO_0000115: A relation between an information content entity and a value specification that specifies its value.
IAO_0000117: PERSON: James A. Overton
IAO_0000119: OBI

has performer
type: ObjectProperty
sub property of: RO_0000057
domain: COB_0000035
range: Class
  intersection of: Class
    union of: COB_0001300
    union of: NCBITaxon 9606
    union of: organization
  intersection of: Restriction
    on property: RO_0000087
    some values from: investigation agent role
IAO_0000114: IAO_0000428
IAO_0000115: A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process.
IAO_0000117: OBI
IAO_0000119: OBI
comment: The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system).

has assay target context
type: ObjectProperty
range: BFO_0000040
IAO_0000115: A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc.
IAO_0000117: Hector Guzman-Orozco
IAO_0000119: OBI
IAO_0000233: https://github.com/obi-ontology/obi/issues/1516

has study design
type: ObjectProperty
inverse of: is study design of
domain: investigation
range: OBI_0500000
IAO_0000111: has study design
IAO_0000115: A relation between an investigation and a study design in which part of the investigation is a study design execution that carries out the study design.
IAO_0000117: Sebastian Duesing
IAO_0000233: https://github.com/obi-ontology/obi/issues/1831
IAO_0000234: Charlie Hoyt

is study design of
type: ObjectProperty
domain: OBI_0500000
range: investigation
IAO_0000111: is study design of
IAO_0000115: A relation between a study design and an investigation when part of the investigation is a study design execution that carries out the study design.
IAO_0000117: Sebastian Duesing
IAO_0000233: https://github.com/obi-ontology/obi/issues/1831
IAO_0000234: Charlie Hoyt

process is result of
type: ObjectProperty
sub property of: RO_0002087
IAO_0000111: process is result of
IAO_0000112: The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
IAO_0000115: is a relationship between a process and a preceding occurrent that directly caused the later one to occur
IAO_0000117: IEDB
IAO_0000117: PERSON:Bjoern Peters

obsolete_is_described_by
type: ObjectProperty
sub property of: ObsoleteProperty
IAO_0000111: is_described_by
IAO_0000231: IAO_0000103
deprecated: true

bound_to
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
IAO_0000111: bound_to
IAO_0000115: A relationship between two material entities that form a complex based on a selective, non-covalent interaction.
IAO_0000116: 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.

adjacent to
type: ObjectProperty

has_feature_value
type: DatatypeProperty
domain: OBI_0200140
IAO_0000111: has_feature_value
IAO_0000115: 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.
IAO_0000117: James Malone

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: OBI_0001933
range: real
IAO_0000114: IAO_0000120
IAO_0000115: A relation between a value specification and a number that quantifies it.
IAO_0000116: 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.
IAO_0000117: PERSON: James A. Overton
IAO_0000119: OBI

has specified value
type: DatatypeProperty
domain: OBI_0001933
IAO_0000115: A relation between a value specification and a literal.
IAO_0000116: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
IAO_0000119: OBI

has representation
type: DatatypeProperty
IAO_0000112: 12th arrondissement of Paris
IAO_0000112: 20g
IAO_0000112: I feel sick to my stomach every Tuesday
IAO_0000114: IAO_0000122
IAO_0000115: 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text.
IAO_0000116: Further processing may enable the value to be represented in a component data structure such as an OBI value specification.
IAO_0000117: Damion Dooley
IAO_0000117: Mark Miller
date: 2019-07-14T07:05:50Z

CHEBI_33839
type: Class
IAO_0000118: polymer

fluorescence microscopy assay
type: Class
subclass of: light microscopy assay
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0000053
      some values from: PATO_0000018
IAO_0000115: Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.
IAO_0000118: FM
IAO_0000118: fluorescence imaging
IAO_0000118: fluorescence microscopic imaging
IAO_0000119: CHMO

confocal fluorescence microscopy assay
type: Class
subclass of: OBI_0002119
IAO_0000115: 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.
IAO_0000118: CLSM
IAO_0000118: LSCM
IAO_0000118: confocal fluorescence imaging
IAO_0000118: confocal laser scanning fluorescence microscopy
IAO_0000118: confocal laser scanning microscopy
IAO_0000118: confocal-laser scanning microscopy
IAO_0000118: fluorescence confocal microscopy
IAO_0000118: fluorescence confocal scanning laser microscopy
IAO_0000118: scanning confocal fluorescence microscopy
IAO_0000119: CHMO

light microscopy assay
type: Class
subclass of: OBI_0002119
IAO_0000115: Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
IAO_0000118: OM
IAO_0000118: light microscopy
IAO_0000118: optical microscopy
IAO_0000119: CHMO

liquid chromatography-tandem mass spectrometry
type: Class
subclass of: OBI_0003540
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0003547
IAO_0000115: 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.
IAO_0000118: LC-MS-MS
IAO_0000118: LC-MS/MS
IAO_0000118: LC-MS2
IAO_0000118: LC-MSMS
IAO_0000118: LC/MS/MS
IAO_0000118: LCMSMS
IAO_0000118: liquid chromatography tandem mass spectrometry
IAO_0000118: liquid chromatography tandem mass spectroscopy
IAO_0000118: liquid chromatography-tandem mass spectroscopy
IAO_0000119: CHMO

CLO_0000001
type: Class
subclass of: Class
  union of: Restriction
    on property: is specified output of
    some values from: OBI_0001867
  union of: Restriction
    on property: RO_0001000
    some values from: Restriction
      on property: is specified output of
      some values from: OBI_0001867
subclass of: Restriction
  on property: RO_0001000
  some values from: CL_0000001
comment: '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.

CLO_0009829
type: Class
subclass of: Restriction
  on property: has grain
  some values from: CLO_0000018
subclass of: Restriction
  on property: has grain
  all values from: CLO_0000018
subclass of: Restriction
  on property: is specified output of
  qualified cardinality: 0
  on class: cell line immortalization

CL_0000000
type: Class
IAO_0000112: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."

GO_0032640
type: Class
IAO_0000118: TNF alpha production

GO_0032641
type: Class
IAO_0000118: TNF beta production

GO_0032991
type: Class
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000000001
IAO_0000112: A ribosome is a protein complex.
IAO_0000118: protein complex

GO_0042571
type: Class
IAO_0000118: antibody
IEDB alternative term: antibody

NCBITaxon 9606
type: Class
IAO_0000118: human being

role of being consumer safety officer
type: Class
subclass of: role of regulator of consumables and medical devices
IAO_0000111: role of being consumer safety officer
IAO_0000112: Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
IAO_0000112: Person charged with serving as CSO, FDA official who coordinates the review
IAO_0000114: IAO_0000120
IAO_0000115: the role of a human being that is realized by enforcing regulations to ensure consumer safety
IAO_0000117: Jennifer Fostel
IAO_0000117: Person:Helen Parkinson
IAO_0000119: OBI, CDISC

fluorescent reporter intensity
type: Class
subclass of: IAO_0000109
IAO_0000111: fluorescent reporter intensity
IAO_0000114: IAO_0000125
IAO_0000115: A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:OBI
IAO_0000232: 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.

obsolete planned process
type: Class
subclass of: ObsoleteClass
IAO_0000112: Injecting mice with a vaccine in order to test its efficacy
IAO_0000114: IAO_0000122
IAO_0000115: A process that realizes a plan which is the concretization of a plan specification.
IAO_0000116: '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.)
IAO_0000116: 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.
IAO_0000117: Bjoern Peters
IAO_0000119: branch derived
IAO_0000231: IAO_0000228
IAO_0000232: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
IAO_0000232: 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)
IAO_0100001: COB_0000035
deprecated: true

regulator role
type: Class
subclass of: regulatory role
IAO_0000111: regulator role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: regulator
IAO_0000119: OBI

biological feature identification objective
type: Class
subclass of: IAO_0000005
IAO_0000111: biological feature identification objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

regulation-assigned role
type: Class
subclass of: regulatory role
IAO_0000111: regulation-assigned role
IAO_0000112: Approval letter
IAO_0000114: IAO_0000123
IAO_0000115: Regulation-assigned role is a regulatory role defined by legislation or governmental orders
IAO_0000117: Person: Jennifer Fostel

regulatory role
type: Class
subclass of: BFO_0000023
IAO_0000111: regulatory role
IAO_0000112: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: GROUP: Role branch
IAO_0000119: OBI, CDISC
IAO_0000232: 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

material supplier role
type: Class
subclass of: service provider role
IAO_0000111: material supplier role
IAO_0000112: Jackson Labs is an organization which provide mice as experimental material
IAO_0000114: IAO_0000120
IAO_0000115: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
IAO_0000116: Supplier role is a special kind of service, e.g. biobank
IAO_0000117: PERSON:Jennifer Fostel
IAO_0000118: material provider role
IAO_0000118: supplier

contract research organization role
type: Class
subclass of: worker role
IAO_0000111: contract research organization role
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: contract research organization

list-mode data file
type: Class
subclass of: IAO_0000030
IAO_0000111: list-mode data file
IAO_0000112: 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.
IAO_0000114: IAO_0000125
IAO_0000115: A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
IAO_0000116: 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.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:Flow Cytometry community

classified data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: class prediction data transformation
subclass of: IAO_0000100
IAO_0000111: classified data set
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee
IAO_0000118: data set with assigned class labels

reference substance role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: BFO_0000040
IAO_0000111: reference substance role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: reference substance
IAO_0000119: OBI

cytological stain role
type: Class
subclass of: dye role
IAO_0000111: cytological stain role
IAO_0000112: haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
IAO_0000114: IAO_0000120
IAO_0000115: A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization
IAO_0000117: Person:Helen Parkinson
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: cytological stain

centrifuge pellet role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: BFO_0000040
subclass of: Restriction
  on property: BFO_0000054
  all values from: OBI_0302886
IAO_0000111: centrifuge pellet role
IAO_0000112: Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
IAO_0000114: IAO_0000125
IAO_0000115: 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..
IAO_0000117: GROUP: Role branch
IAO_0000119: OBI
IAO_0000232: 9Mar09 after discussion with process branch changed definition to include use of centrifuge;

clinical research coordinator role
type: Class
subclass of: worker role
IAO_0000111: clinical research coordinator role
IAO_0000114: IAO_0000123
IAO_0000115: a worker role comprised of handling the administrative duties of a trial or study.
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: clinical research coordinator

supernatant role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: BFO_0000040
subclass of: Restriction
  on property: BFO_0000054
  all values from: OBI_0600014
IAO_0000111: supernatant role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: GROUP: Role branch
IAO_0000119: OBI

chromatography column
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: BFO_0000051
  some values from: container
subclass of: Restriction
  on property: RO_0000085
  some values from: Class
    intersection of: material separation function
    intersection of: Restriction
      on property: BFO_0000054
      all values from: OBI_0600046
IAO_0000111: chromatography column
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Frank Gibson
IAO_0000119: http://en.wikipedia.org/wiki/Column_chromatography
IAO_0000232: open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178

drug role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: COB_0000013
IAO_0000111: drug role
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Role Branch
IAO_0000118: drug
IAO_0000119: OBI, CDISC

pump valve switch
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: pump valve switch
IAO_0000114: IAO_0000123
IAO_0000115: A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
IAO_0000116: FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument
IAO_0000117: OBI Instrument branch
IAO_0000119: OBI

xenotransplantation
type: Class
subclass of: transplantation
IAO_0000111: xenotransplantation
IAO_0000114: IAO_0000125
IAO_0000115: is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

physical document
type: Class
subclass of: COB_0000026
IAO_0000111: physical document
IAO_0000112: a book is a physical document
IAO_0000114: IAO_0000120
IAO_0000115: A physical document is an object serving as a record of information by means of symbolic marks.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: GROUP: OBI

waiting
type: Class
subclass of: OBI_0600009
IAO_0000111: waiting
IAO_0000114: IAO_0000125
IAO_0000115: A planned process where an agent does not take any new actions towards a particular objective for a period of time until a set of conditions is met.
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000119: OBI branch derived
IAO_0000232: BP: I have doubts about the utility of this.
IAO_0000232: We need a better handling/modeling of time (January 2008)

obsolete processed material
type: Class
subclass of: ObsoleteClass
IAO_0000112: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
IAO_0000114: IAO_0000122
IAO_0000115: Is a material entity that is created or changed during material processing.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000231: IAO_0000228
IAO_0100001: COB_0000026
deprecated: true

chromatography device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: chromatography device
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Frank Gibson
IAO_0000118: chromatography instrument
IAO_0000119: http://en.wikipedia.org/wiki/Chromatography
IAO_0000232: open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178

mass spectrometer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: BFO_0000051
  some values from: mass analyzer
subclass of: Restriction
  on property: BFO_0000051
  some values from: ion source
subclass of: Restriction
  on property: BFO_0000051
  some values from: ion detector
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: mass spectrometer
IAO_0000112: LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Frank Gibson
IAO_0000119: http://en.wikipedia.org/wiki/Mass_spectrometry

obsolete_platform
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
IAO_0000117: OBI Instrument branch
IAO_0000119: OBI Instrument branch
IAO_0000231: IAO_0000103
deprecated: true

liquid chromatography mass spectrometry platform
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: BFO_0000051
  some values from: chromatography device
subclass of: Restriction
  on property: BFO_0000051
  some values from: mass spectrometer
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: liquid chromatography mass spectrometry platform
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: OBI instrument branch
IAO_0000119: OBI Instrument branch

microarray platform
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0400147
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: microarray platform
IAO_0000114: IAO_0000123
IAO_0000115: A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
IAO_0000117: OBI Instrument branch
IAO_0000119: OBI Instrument branch

ratio of collected to emitted light
type: Class
subclass of: IAO_0000109
IAO_0000111: ratio of collected to emitted light
IAO_0000112: 10%
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: person:Chris Stoeckert
IAO_0000117: person:Kevin Clancy
IAO_0000119: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

software optimization objective
type: Class
subclass of: software testing objective
IAO_0000111: software optimization objective
IAO_0000114: IAO_0000123
IAO_0000115: Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
IAO_0000117: Jennifer Fostel

notified body role
type: Class
subclass of: role of regulator of consumables and medical devices
IAO_0000111: notified body role
IAO_0000112: The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000116: 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.
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: notified body
IAO_0000119: OBI, CDISC

allotransplantation
type: Class
subclass of: transplantation
IAO_0000111: allotransplantation
IAO_0000114: IAO_0000125
IAO_0000115: is the transplantation of organs between members of the same species.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

gamma counter
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: gamma counter
IAO_0000112: A Geiger counter
IAO_0000114: IAO_0000122
IAO_0000115: A processed material which measures gamma radiation
IAO_0000117: Frank Gibson
IAO_0000119: http://en.wikipedia.org/wiki/Gamma_counter

trial monitor role
type: Class
subclass of: responsible party role
IAO_0000111: trial monitor role
IAO_0000114: IAO_0000123
IAO_0000115: a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: trial monitor
IAO_0000232: 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.

positive reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: BFO_0000054
  all values from: assay
IAO_0000111: positive reference substance role
IAO_0000112: MMS mutagen
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: positive reference substance

polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
type: Class
subclass of: COB_0000013
IAO_0000111: polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
IAO_0000112: PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: adapted from Wikipedia before possible import from CHEBI

investigation
type: Class
subclass of: COB_0000082
subclass of: Restriction
  on property: BFO_0000051
  some values from: IAO_0000572
subclass of: Restriction
  on property: BFO_0000051
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: BFO_0000051
  some values from: study design execution
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has specified output
      some values from: OBI_0500000
IAO_0000111: investigation
IAO_0000112: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
IAO_0000114: IAO_0000122
IAO_0000115: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
IAO_0000117: Bjoern Peters
IAO_0000119: OBI branch derived
IAO_0000232: Could add specific objective specification
IAO_0000232: 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
ISA alternative term: study

evaluant role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: BFO_0000040
subclass of: Restriction
  on property: BFO_0000054
  all values from: assay
IAO_0000111: evaluant role
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000116: 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)
IAO_0000116: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI
IAO_0000232: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.

reporting party role
type: Class
subclass of: investigation agent role
IAO_0000111: reporting party role
IAO_0000112: Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: a study personnel role played by a party who reports the outcome of a study component
IAO_0000116: MO:submitter mapped to this term. So, alternative term 'submitter' was added.
IAO_0000117: Jennifer Fostel
IAO_0000118: reporting party
IAO_0000118: submitter
IAO_0000119: OBI

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: COB_0000035
subclass of: Restriction
  on property: BFO_0000055
  some values from: evaluant role
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0000087
      some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: IAO_0000027
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: BFO_0000040
        intersection of: Restriction
disjoint with: planning
disjoint with: OBI_0200000
disjoint with: OBI_0600013
IAO_0000111: assay
IAO_0000112: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
IAO_0000114: IAO_0000122
IAO_0000115: A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
IAO_0000116: 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.
IAO_0000116: Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000118: measuring
IAO_0000118: scientific observation
IAO_0000119: OBI branch derived
ISA alternative term: study assay
IEDB alternative term: any method

quantitative confidence value
type: Class
subclass of: IAO_0000027
IAO_0000111: quantitative confidence value
IAO_0000114: IAO_0000125
IAO_0000115: A data item which is used to indicate the degree of uncertainty about a measurement.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:OBI

sample preparation for assay
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: sample preparation for assay
IAO_0000114: IAO_0000125
IAO_0000115: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000118: study
IAO_0000119: OBI branch derived

diagnosis textual entity
type: Class
subclass of: IAO_0000300
IAO_0000111: diagnosis textual entity
IAO_0000114: IAO_0000123
IAO_0000115: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
IAO_0000117: Jennifer Fostel

unplanned occurrence effecting an investigation
type: Class
subclass of: BFO_0000015
IAO_0000111: unplanned occurrence effecting an investigation
IAO_0000112: Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
IAO_0000114: IAO_0000120
IAO_0000115: a process which is external in origin to the investigation that has an impact on the outcome.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: OBI

eMedical record
type: Class
subclass of: IAO_0000030
IAO_0000111: eMedical record
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: person:Jennifer Fostel
IAO_0000119: article-without-pmid-or-doi:CDISCglossary

culture medium
type: Class
subclass of: COB_0000026
IAO_0000111: culture medium
IAO_0000112: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
IAO_0000114: IAO_0000122
IAO_0000115: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
IAO_0000116: 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.
IAO_0000117: Person: Jennifer Fostel, Jie Zheng
IAO_0000119: OBI

electronic case report tabulation
type: Class
subclass of: IAO_0000030
IAO_0000111: electronic case report tabulation
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: person:Jennifer Fostel
IAO_0000119: CDISC glossary

polystyrene tube
type: Class
subclass of: test tube
IAO_0000111: polystyrene tube
IAO_0000112: Polystyrene tubes can be used to contain tissue culture cells during centrifgation
IAO_0000114: IAO_0000122
IAO_0000115: A polystyrene tube is a test tube made of polystyrene
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000119: PERSON: Chris Stoeckert

reagent role
type: Class
subclass of: OBI_0003610
IAO_0000111: reagent role
IAO_0000112: Buffer, dye, a catalyst, a solvating agent.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Matthew Brush
IAO_0000118: reagent
IAO_0000119: PERSON:Matthew Brush
IAO_0000232: 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.
comment: (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 t…

role of regulator of chemical manufacturer
type: Class
subclass of: regulator role
IAO_0000111: role of regulator of chemical manufacturer
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: regulator of chemical manufacture
IAO_0000119: OBI

detector reagent role
type: Class
subclass of: BFO_0000023
IAO_0000111: detector reagent role
IAO_0000114: IAO_0000123
IAO_0000115: a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
IAO_0000116: 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances
IAO_0000119: 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

role of certified IRB professional
type: Class
subclass of: regulation-assigned role
IAO_0000111: role of certified IRB professional
IAO_0000112: CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person:Helen Parkinson
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: certified IRB professional
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional

patient role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: NCBITaxon 9606
IAO_0000111: patient role
IAO_0000112: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000116: See also OMRSE:00000011 'patient role'
IAO_0000117: GROUP:Role Branch
IAO_0000118: patient
IAO_0000119: OBI, CDISC
IAO_0000232: 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

obsolete material processing
type: Class
subclass of: ObsoleteClass
IAO_0000112: A cell lysis, production of a cloning vector, creating a buffer.
IAO_0000114: IAO_0000122
IAO_0000115: A planned process which results in physical changes in a specified input material
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Frank Gibson
IAO_0000117: PERSON: Jennifer Fostel
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Philippe Rocca Serra
IAO_0000119: OBI branch derived
IAO_0000231: IAO_0000228
IAO_0100001: COB_0000110
deprecated: true

protocol testing objective
type: Class
subclass of: methodology testing objective
IAO_0000111: protocol testing objective
IAO_0000114: IAO_0000123
IAO_0000115: Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
IAO_0000117: Jennifer Fostel

participant under investigation role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: BFO_0000054
  all values from: study design execution
IAO_0000111: study subject role
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI
IAO_0000232: 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

obsolete_role of being first subject treated
type: Class
subclass of: ObsoleteClass
IAO_0000112: Rat 1A; first enrolled patient to receive treatment
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Role Branch
IAO_0000119: OBI
IAO_0000231: IAO_0000103
deprecated: true

measured expression level
type: Class
subclass of: IAO_0000109
IAO_0000111: measured expression level
IAO_0000112: Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI Data Transformation branch

responsible party role
type: Class
subclass of: investigation agent role
IAO_0000111: responsible party role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: responsible party
IAO_0000119: OBI

principal investigator role
type: Class
subclass of: responsible party role
IAO_0000111: principal investigator role
IAO_0000114: IAO_0000123
IAO_0000115: a responsible party role played by a person responsible for the overall conduct of a study
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: principal investigator
IAO_0000232: 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)

transplantation
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: transplantation
IAO_0000114: IAO_0000125
IAO_0000115: a protocol application to replace an organ or tissue of an organism
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

obsolete biological vector role
type: Class
subclass of: ObsoleteClass
IAO_0000112: 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI and Wikipedia
IAO_0000231: IAO_0000103
deprecated: true

pH indicator dye role
type: Class
subclass of: dye role
IAO_0000111: pH indicator dye role
IAO_0000112: bromophenol blue has a pH indicator dye role
IAO_0000112: phenol red in RPMI; pH=4 indicator dye (also carries reference role)
IAO_0000114: IAO_0000120
IAO_0000115: the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity
IAO_0000117: Person: Jennifer Fostel
IAO_0000117: Person:Helen Parkinson
IAO_0000118: pH indicator dye

specimen role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
IAO_0000111: specimen role
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI
IAO_0000233: https://github.com/obi-ontology/obi/issues/1013

sequence feature identification objective
type: Class
subclass of: biological feature identification objective
IAO_0000111: sequence feature identification objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

intervention design
type: Class
equivalent class: Class
  intersection of: OBI_0500000
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: study design independent variable
      intersection of: Restriction
        on property: IAO_0000136
        some values from: study intervention
IAO_0000111: intervention design
IAO_0000112: 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.
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: Philppe Rocca-Serra
IAO_0000119: OBI branch derived

worker role
type: Class
subclass of: investigation agent role
IAO_0000111: worker role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000116: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: worker
IAO_0000119: OBI

Bernoulli trial
type: Class
subclass of: assay
IAO_0000114: IAO_0000125
IAO_0000115: An assay where the output data is a datum with one of two values denoting success and failure.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

gene list
type: Class
subclass of: IAO_0000100
IAO_0000111: gene list
IAO_0000112: 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.
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:OBI
IAO_0000232: kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.

number of particles in subset
type: Class
subclass of: IAO_0000109
IAO_0000111: number of particles in subset
IAO_0000112: 500, 200, 0
IAO_0000114: IAO_0000120
IAO_0000115: A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
IAO_0000117: person:Kevin Clancy
IAO_0000119: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

number of lost events electronic
type: Class
subclass of: IAO_0000109
IAO_0000111: number of lost events electronic
IAO_0000112: 74, 0, 14 events lost due to data acquisition electronic coincidence.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: person:Kevin Clancy
IAO_0000119: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

calibration substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: BFO_0000054
  all values from: calibration
IAO_0000111: calibration substance role
IAO_0000112: pH buffer used to calibrate a pH meter bears a calibration substance role
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Jennifer Fostel

molecular feature identification objective
type: Class
subclass of: biological feature identification objective
IAO_0000111: molecular feature identification objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

hardware testing objective
type: Class
subclass of: methodology testing objective
IAO_0000111: hardware testing objective
IAO_0000114: IAO_0000123
IAO_0000115: Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
IAO_0000117: Jennifer Fostel

incubator
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: incubator
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
IAO_0000117: Frank Gibson
IAO_0000119: http://www.medterms.com/script/main/art.asp

obsolete_label role
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000428
IAO_0000115: Label role is a role which inheres in a material entity and which is realized in a detection of label assay
IAO_0000117: Role Branch
IAO_0000118: label
IAO_0000119: OBI
IAO_0000231: IAO_0000228
IAO_0100001: OBI_0002743
deprecated: true

baseline participant role
type: Class
subclass of: reference subject role
IAO_0000111: baseline participant role
IAO_0000112: Subject at time = 0; subject before a stress test.
IAO_0000114: IAO_0000123
IAO_0000115: a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: baseline participant

role of independent data monitoring committee
type: Class
subclass of: trial monitor role
IAO_0000111: role of independent data monitoring committee
IAO_0000114: IAO_0000120
IAO_0000115: a trial monitor role charged recommending whether to continue, modify, or end the trial
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: independent data monitoring committee

pathologist role
type: Class
subclass of: worker role
IAO_0000111: pathologist role
IAO_0000114: IAO_0000123
IAO_0000115: a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: Pathologist

supernatant collection system harvesting frame
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
IAO_0000111: supernatant collection system harvesting frame
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Daniel Schober
IAO_0000119: google

filter paper
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: filter function
IAO_0000111: filter paper
IAO_0000114: IAO_0000120
IAO_0000115: A device manufacture with the intent to provide a porous unsized paper used for filtering.
IAO_0000117: Frank Gibson
IAO_0000119: sep:00107

cell co-culturing
type: Class
subclass of: BFO_0000015
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: CL_0000000
  intersection of: Restriction
    on property: has specified input
    min cardinality: 2
subclass of: Restriction
  on property: has specified input
  some values from: culture medium
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: cell co-culturing
IAO_0000112: Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
IAO_0000114: IAO_0000125
IAO_0000115: A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

role of Institutional Review Board
type: Class
subclass of: regulator role
IAO_0000111: role of Institutional Review Board
IAO_0000112: 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
IAO_0000112: Animal protocol review board
IAO_0000114: IAO_0000120
IAO_0000115: the role of a organization that is realized by members reviewing study designs for their agreement with regulations
IAO_0000117: Person:Helen Parkinson
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: Internal Review Board
IAO_0000119: OBI, CDISC
IAO_0000232: 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.

eSource document
type: Class
subclass of: IAO_0000030
IAO_0000111: eSource document
IAO_0000114: IAO_0000125
IAO_0000115: 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
IAO_0000117: person:Jennifer Fostel
IAO_0000119: article-without-pmid-or-doi:CDISCglossary

crossover population role
type: Class
subclass of: reference subject role
IAO_0000111: crossover population role
IAO_0000114: IAO_0000123
IAO_0000115: a role realized when a participant serves as reference to itself
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: crossover population

complete nutrient role
type: Class
subclass of: nutrient role
IAO_0000111: complete nutrient role
IAO_0000112: 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
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: complete nutrient

radiolabel role
type: Class
subclass of: OBI_0002743
IAO_0000111: radiolabel role
IAO_0000114: IAO_0000120
IAO_0000115: a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection
IAO_0000117: Jennifer Fostel
IAO_0000118: radiolabel

clonal cDNA library
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600064
subclass of: Restriction
  on property: has grain
  some values from: recombinant vector
IAO_0000111: cDNA library
IAO_0000112: PMID:6110205. collection of cDNA derived from mouse splenocytes.
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: PERSON: Luisa Montecchi
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: GROUP: PSI
IAO_0000232: PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction

electronic case report form
type: Class
subclass of: IAO_0000030
IAO_0000111: electronic case report form
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: person:Jennifer Fostel
IAO_0000119: CDISC glossary

placebo role
type: Class
subclass of: negative reference substance role
IAO_0000111: placebo role
IAO_0000112: Pill consisting of inert materials
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: placebo
IAO_0000232: 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.

autotransplantation
type: Class
subclass of: transplantation
IAO_0000111: autotransplantation
IAO_0000114: IAO_0000125
IAO_0000115: is the transplantation of tissue from one part of \nthe body to another in the same individual. )
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

parameter threshold
type: Class
subclass of: IAO_0000109
IAO_0000111: parameter threshold
IAO_0000112: 0.01, 0.03
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: person:Kevin Clancy
IAO_0000119: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

study group role
type: Class
subclass of: BFO_0000023
IAO_0000111: study group role
IAO_0000112: The group of randomized participants that are assigned to a treatment arm of the trial
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Jennifer Fostel
IAO_0000118: study group population

p-value
type: Class
subclass of: quantitative confidence value
IAO_0000111: p-value
IAO_0000112: 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).
IAO_0000114: IAO_0000121
IAO_0000115: 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.
IAO_0000116: May be outside the scope of OBI long term, is needed so is retained
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000119: WEB: http://en.wikipedia.org/wiki/P-value

population
type: Class
subclass of: BFO_0000040
IAO_0000111: population
IAO_0000112: 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.
IAO_0000114: IAO_0000125
IAO_0000115: 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
IAO_0000116: 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/
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: adapted from Oxford English Dictionnary
IAO_0000232: rem1: collection somehow always involve a selection process

NMR 3D molecular structure determination assay
type: Class
equivalent class: Class
  intersection of: OBI_0003117
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: BFO_0000034
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: NMR instrument
  intersection of: Restriction
    on property: has specified output
    some values from: 3D structural organization datum
IAO_0000112: 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).
IAO_0000115: A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample.
IAO_0000117: IEDB
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: IEDB

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000101
IAO_0000114: IAO_0000125
IAO_0000115: An assay that produces a picture of an entity.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

protocol optimization objective
type: Class
subclass of: protocol testing objective
IAO_0000111: protocol optimization objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

role of pathology review board
type: Class
subclass of: worker role
IAO_0000111: role of pathology review board
IAO_0000114: IAO_0000123
IAO_0000115: a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: pathology review board

microtiter plate
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
IAO_0000111: microtiter plate
IAO_0000112: A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
IAO_0000114: IAO_0000122
IAO_0000115: A microtiter_plate is a flat plate with multiple wells used as small test tubes.
IAO_0000117: Melanie Courtot
IAO_0000118: microplate
IAO_0000119: http://en.wikipedia.org/wiki/Microtiter_plate

role of impartial witness
type: Class
subclass of: regulation-assigned role
IAO_0000111: role of impartial witness
IAO_0000112: According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000116: 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
IAO_0000117: Person: Helen Parkinson
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: impartial witness

chromatin immunoprecipitation
type: Class
subclass of: immunoprecipitation
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: Bjoern Peters, Randi Vita, James A. Overton
IAO_0000118: ChIP
IAO_0000119: OBI

biological replicate role
type: Class
subclass of: reference subject role
IAO_0000111: biological replicate role
IAO_0000112: A member of a dose-time group; a patient in a given arm of a trial
IAO_0000114: IAO_0000120
IAO_0000115: a reference participant role realized by equivalent treatment of participants
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: biological replicate
IAO_0000119: OBI

radioactivity detection
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000053
        some values from: PATO_0001741
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: BFO_0000040
        intersection of: Restriction
IAO_0000112: 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.
IAO_0000115: An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.
IAO_0000117: IEDB
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: IEDB

investigation agent role
type: Class
equivalent class: Class
  intersection of: BFO_0000023
  intersection of: Restriction
    on property: RO_0000052
    some values from: Restriction
      on property: RO_0000053
      some values from: Restriction
        on property: RO_0000059
        some values from: Restriction
subclass of: Restriction
  on property: BFO_0000054
  all values from: investigation
IAO_0000111: investigation agent role
IAO_0000112: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000116: 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)
IAO_0000117: GROUP: Role Branch
IAO_0000118: investigator
IAO_0000119: OBI
IAO_0000232: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
ISA alternative term: study person role
comment: 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)

nutrient role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: BFO_0000040
IAO_0000111: nutrient role
IAO_0000112: Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: GROUP: Role branch
IAO_0000118: nutrient
IAO_0000119: Wikipedia, feb 29, 2008
IAO_0000232: 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.

obsolete_dropout role
type: Class
subclass of: ObsoleteClass
IAO_0000112: 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)
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Role Branch
IAO_0000119: OBI
IAO_0000231: IAO_0000103
deprecated: true

obsolete health care provider role
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000120
IAO_0000115: a worker role of providing medical care either within or outside the study timeline
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: health care provider
IAO_0100001: OMRSE_00000012
deprecated: true

methodology testing objective
type: Class
subclass of: IAO_0000005
IAO_0000111: methodology testing objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

analytical cytology data file
type: Class
subclass of: IAO_0000030
IAO_0000111: analytical cytology data file
IAO_0000112: FCS file, ACS file, foo.fcs, foo.asc
IAO_0000114: IAO_0000125
IAO_0000115: A digital entity intended to capture data in analytical cytology domain.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:Flow Cytometry community

proxy respondent role
type: Class
subclass of: worker role
IAO_0000111: proxy respondent role
IAO_0000114: IAO_0000120
IAO_0000115: Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
IAO_0000117: Jennifer Fostel
IAO_0000118: proxy respondent

fluorescence compensation matrix
type: Class
subclass of: IAO_0000030
IAO_0000111: fluorescence compensation matrix
IAO_0000112: ((1.053096, -0.22476), (-0.24877, 1.053096))
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:Flow Cytometry community

negative reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: BFO_0000054
  all values from: assay
IAO_0000111: negative reference substance role
IAO_0000112: Saline solution
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: negative reference substance

role of legally acceptable representative
type: Class
subclass of: regulation-assigned role
IAO_0000111: role of legally acceptable representative
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: 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]
IAO_0000117: Person: Jennifer Fostel
IAO_0000117: Person:Helen Parkinson
IAO_0000118: legally acceptable representative
IAO_0000119: OBI, CDISC

investigation results report
type: Class
subclass of: IAO_0000088
IAO_0000111: investigation results report
IAO_0000114: IAO_0000125
IAO_0000115: An investigation report is a report on the results of an investigation.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:OBI

cellular feature identification objective
type: Class
subclass of: biological feature identification objective
IAO_0000111: cellular feature identification objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

reference subject role
type: Class
subclass of: participant under investigation role
subclass of: Restriction
  on property: RO_0000052
  some values from: Class
    union of: COB_0000022
    union of: OBI_0100051
IAO_0000111: reference subject role
IAO_0000112: Saline treated rat; one of three identically-treated subjects
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Jennifer Fostel
IAO_0000118: reference participant
IAO_0000119: OBI

vital dye role
type: Class
subclass of: dye role
IAO_0000111: vital dye role
IAO_0000112: typtan blue has a vital dye
IAO_0000114: IAO_0000120
IAO_0000115: A dye role that is realized when used to detect live cells in an experiment
IAO_0000116: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178
IAO_0000117: Person: Helen Parkinson
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: vital dye

obsolete_blinded medication role
type: Class
subclass of: ObsoleteClass
IAO_0000112: 115 patients received ipilimumab and blinded medication
IAO_0000112: Inert pill shaped like aspirin tablet
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Jennifer Fostel
IAO_0000117: Person:Helen Parkinson
IAO_0000231: IAO_0000103
deprecated: true

sub-investigator role
type: Class
subclass of: worker role
IAO_0000111: sub-investigator role
IAO_0000114: IAO_0000123
IAO_0000115: a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: sub-investigator
IAO_0000232: 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

data encoding
type: Class
subclass of: IAO_0000572
IAO_0000111: data encoding
IAO_0000112: storage of measurement results from an assay into a text file, such as
IAO_0000114: IAO_0000120
IAO_0000115: a documenting process to encode an information entity into a digital document
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived
IAO_0000232: We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE

enzymatic cleavage
type: Class
subclass of: COB_0000110
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: BFO_0000034
    intersection of: Restriction
      on property: RO_0000052
      some values from: enzyme
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100051
IAO_0000111: enzymatic cleavage
IAO_0000112: 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
IAO_0000114: IAO_0000125
IAO_0000115: a material processing that digests the fraction of input material that is susceptible to that enzyme
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

hardware optimization objective
type: Class
subclass of: hardware testing objective
IAO_0000111: hardware optimization objective
IAO_0000114: IAO_0000123
IAO_0000115: Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
IAO_0000117: Jennifer Fostel

obsolete_defined_material
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000121
IAO_0000115: Place holder class, Utility class to gather the defined classes
IAO_0000117: Susanna Sansone
IAO_0000119: OBI Biomaterial derived
IAO_0000231: IAO_0000226
deprecated: true

trial statistician role
type: Class
subclass of: worker role
subclass of: Restriction
  on property: BFO_0000054
  all values from: Class
    intersection of: investigation
    intersection of: Restriction
      on property: BFO_0000051
      some values from: Restriction
        on property: BFO_0000055
        some values from: Restriction
IAO_0000111: trial statistician role
IAO_0000114: IAO_0000123
IAO_0000115: a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
IAO_0000117: Person:Jennifer Fostel
IAO_0000118: trial statistician
IAO_0000232: 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]

standard error
type: Class
subclass of: quantitative confidence value
IAO_0000111: standard error
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:OBI
IAO_0000232: see P-Value

antigen role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: BFO_0000054
  all values from: GO_0006955
IAO_0000111: antigen role
IAO_0000114: IAO_0000123
IAO_0000115: A role of a material entity that is being recognized in whole or in part by receptors of the immune system such as antibodies or T cell receptors.
IAO_0000116: 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
IAO_0000117: Role Branch
IAO_0000119: OBI
IAO_0000232: 9Mar09 waiting for discussion with immunology terms

software testing objective
type: Class
subclass of: methodology testing objective
IAO_0000111: software testing objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

sponsor role
type: Class
subclass of: responsible party role
IAO_0000111: sponsor role
IAO_0000114: IAO_0000120
IAO_0000115: a responsible party role involved with any of the following activities: initiating, managing and funding a study
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: sponsor
IAO_0000232: CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators

organization
type: Class
subclass of: BFO_0000040
IAO_0000111: organization
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000117: PERSON: Susanna Sansone
IAO_0000119: GROUP: OBI

feed role
type: Class
subclass of: complete nutrient role
IAO_0000111: feed role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: feed
IAO_0000119: OBI

technical replicate role
type: Class
subclass of: reference subject role
IAO_0000111: technical replicate role
IAO_0000112: Aliquots of a tissue subjected to parallel assays
IAO_0000114: IAO_0000123
IAO_0000115: technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: technical replicate

dye role
type: Class
subclass of: OBI_0002743
IAO_0000111: dye role
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel
IAO_0000118: dye
IAO_0000119: A substance used to color materials www.answers.com/topic/dye 19feb09

cluster
type: Class
subclass of: IAO_0000100
IAO_0000111: cluster
IAO_0000112: Cluster of the lymphocytes population.
IAO_0000114: IAO_0000125
IAO_0000115: A data set which is a subset of data that are a similar to each other in some way.
IAO_0000117: person:Allyson
IAO_0000117: person:Chris Stoeckert
IAO_0000119: group:OBI

cohort role
type: Class
subclass of: biological replicate role
IAO_0000111: cohort role
IAO_0000112: 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
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel
IAO_0000119: 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.
IAO_0000119: 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).
IAO_0000119: 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.

artificially induced nucleic acid hybridization
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: artificially induced nucleic acid hybridization
IAO_0000112: 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
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

DNA extraction
type: Class
subclass of: OBI_0666667
subclass of: Restriction
  on property: has specified output
  some values from: DNA extract
IAO_0000111: DNA extraction
IAO_0000114: IAO_0000123
IAO_0000115: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

plan
type: Class
subclass of: BFO_0000017
IAO_0000111: plan
IAO_0000112: The plan of researcher X to perform an experiment according to a protocol.
IAO_0000114: IAO_0000125
IAO_0000115: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process.
IAO_0000116: 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.
IAO_0000117: AR, BP, JM, MC, PRS
IAO_0000119: branch derived

obsolete_sample population
type: Class
subclass of: ObsoleteClass
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Jennifer Fostel
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000118: recruited population
IAO_0000119: GROUP: OBI Biomaterial Branch
IAO_0000231: IAO_0000227
deprecated: true

organism feature identification objective
type: Class
subclass of: biological feature identification objective
IAO_0000111: organism feature identification objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Jennifer Fostel

number of lost events computer
type: Class
subclass of: IAO_0000109
IAO_0000111: number of lost events computer
IAO_0000112: 0, 125, 787 events lost due to computer busy.
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: person:Kevin Clancy
IAO_0000119: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

protocol
type: Class
subclass of: IAO_0000104
IAO_0000111: protocol
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
ISA alternative term: study protocol

role of regulator of consumables and medical devices
type: Class
subclass of: regulator role
IAO_0000111: role of regulator of consumables and medical devices
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person: Jennifer Fostel
IAO_0000118: drug regulatoy authority
IAO_0000119: OBI, CDISC

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: BFO_0000015
subclass of: Restriction
  on property: BFO_0000055
  some values from: material to be added role
subclass of: Restriction
  on property: BFO_0000055
  some values from: target of material addition role
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0000087
      some values from: material to be added role
    intersection of: Restriction
      on property: RO_0001025
      some values from: Class
        intersection of: BFO_0000040
        intersection of: Restriction
IAO_0000111: adding a material entity into a target
IAO_0000112: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
IAO_0000114: IAO_0000122
IAO_0000115: 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'.
IAO_0000116: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
IAO_0000117: BP
IAO_0000119: branch derived

analyte role
type: Class
subclass of: OBI_0002444
subclass of: Restriction
  on property: RO_0000081
  some values from: Class
    union of: COB_0000011
    union of: COB_0000013
IAO_0000111: analyte role
IAO_0000112: Glucose in blood (measured in an assay to determine the concentration of glucose).
IAO_0000114: IAO_0000122
IAO_0000115: A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
IAO_0000116: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
IAO_0000116: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
IAO_0000116: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI
IAO_0000232: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.

disease stage
type: Class
subclass of: GO_0008150
subclass of: Restriction
  on property: BFO_0000050
  some values from: OGMS_0000063
IAO_0000111: disease stage
IAO_0000112: Stage II breast cancer, The timepoint of recovery from a disease
IAO_0000114: IAO_0000123
IAO_0000115: a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
IAO_0000117: PERSON: Bjoern peters

intraperitoneal injection
type: Class
equivalent class: Class
  intersection of: intraperitoneal administration
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: syringe
IAO_0000111: intraperitoneal injection
IAO_0000115: 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
IAO_0000117: BP

precipitate
type: Class
subclass of: COB_0000026
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600034
IAO_0000111: precipitate
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: a precipitate is a material entity which is output of a precipitation process
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000118: precipited material
IAO_0000119: GROUP: OBI Biomaterial Branch

protein-protein interaction detection assay
type: Class
subclass of: assay
IAO_0000114: IAO_0000123
IAO_0000115: An assay that determines interactions between proteins, such as protein-protein binding.

transcription factor binding site assay
type: Class
subclass of: binding assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000030
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: SO_0000235
IAO_0000112: Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
IAO_0000114: IAO_0000120
IAO_0000115: An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: TF binding
IAO_0000119: OBI
IAO_0000233: https://sourceforge.net/p/obi/obi-terms/767/

obsolete_enrollment
type: Class
subclass of: ObsoleteClass
IAO_0000112: 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
IAO_0000114: IAO_0000125
IAO_0000115: enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
IAO_0000117: Bjoern Peters
IAO_0000119: IEDB
IAO_0000231: IAO_0000227
deprecated: true

adverse event trigger
type: Class
subclass of: IAO_0000001
IAO_0000111: adverse event trigger
IAO_0000114: IAO_0000125
IAO_0000115: revisit?
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000119: OBI branch derived

eluate
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: COB_0000013
    intersection of: Restriction
      on property: RO_0000087
      some values from: OBI_0302732
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302905
IAO_0000111: eluate
IAO_0000112: Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000116: need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000118: eluted material
IAO_0000119: OBI Bionaterial

material to be added role
type: Class
subclass of: BFO_0000023
IAO_0000111: material to be added role
IAO_0000112: drug added to a buffer contained in a tube; substance injected into an animal;
IAO_0000114: IAO_0000120
IAO_0000115: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
IAO_0000117: Role Branch
IAO_0000119: OBI
IAO_0000232: 9 March 09 from discussion with PA branch

obsolete_peritoneum
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000002
IAO_0000115: is the serous membrane that forms the lining of the abdominal cavity
IAO_0000231: IAO_0000228
deprecated: true

drawing a conclusion based on data
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: has specified input
  some values from: IAO_0000027
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0001909
IAO_0000111: interpreting data
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Jennifer Fostel
IAO_0000119: Bjoern Peters

planning
type: Class
subclass of: Class
  intersection of: BFO_0000015
  intersection of: Restriction
    on property: RO_0000057
    some values from: IAO_0000104
IAO_0000111: planning
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: a process of creating or modifying a plan specification
IAO_0000116: 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'.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters
IAO_0000119: Plans and Planned Processes Branch

obsolete_documenting
type: Class
subclass of: ObsoleteClass
IAO_0000112: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
IAO_0000114: IAO_0000125
IAO_0000117: Bjoern Peters
IAO_0000119: wikipedia http://en.wikipedia.org/wiki/Documenting
IAO_0000231: IAO_0000228
IAO_0100001: IAO_0000572
deprecated: true

histological sample preparation
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100066
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
subclass of: Restriction
  on property: RO_0000057
  some values from: OBI_0400168
IAO_0000111: histological sample preparation
IAO_0000114: IAO_0000125
IAO_0000115: 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
IAO_0000117: PERSON:Bjoern Peters
IAO_0000119: OBI branch derived

inductive reasoning
type: Class
subclass of: drawing a conclusion based on data
IAO_0000111: inductive reasoning
IAO_0000112: 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.
IAO_0000114: IAO_0000428
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000117: Bjoern Peters
IAO_0000119: wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning

mass analyzer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: mass analyzer
IAO_0000112: The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Frank Gibson
IAO_0000117: PERSON: Daniel Schober
IAO_0000119: http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer

hypothesis-driven investigation
type: Class
subclass of: investigation
IAO_0000111: hypothesis-driven investigation
IAO_0000114: IAO_0000125
IAO_0000115: is an investigation with the goal to test one or more hypothesis
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

hypothesis generating investigation
type: Class
subclass of: investigation
IAO_0000111: hypothesis generating investigation
IAO_0000114: IAO_0000125
IAO_0000115: is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
IAO_0000117: PlanAndPlannedProcess Branch
IAO_0000119: OBI branch derived

ion source
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: ionization function
IAO_0000111: ion source
IAO_0000112: The ion source of a Voyager-DE??? STR Biospectrometry Workstation
IAO_0000114: IAO_0000122
IAO_0000115: 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))).
IAO_0000117: Frank Gibson
IAO_0000119: http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source

ion detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: ion detector
IAO_0000112: The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Frank Gibson
IAO_0000119: http://en.wikipedia.org/wiki/Mass_spectrometry#Detector

metabolite profiling assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100051
IAO_0000112: Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
IAO_0000114: IAO_0000120
IAO_0000115: An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: metabolite assay
IAO_0000118: metabolomic assay
IAO_0000119: OBI

light emission function
type: Class
subclass of: excitation function
IAO_0000111: light emission function
IAO_0000114: IAO_0000122
IAO_0000115: A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

record function
type: Class
subclass of: BFO_0000034
IAO_0000111: record function
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

magnify function
type: Class
subclass of: BFO_0000034
IAO_0000111: magnify function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

contain function
type: Class
subclass of: BFO_0000034
IAO_0000111: contain function
IAO_0000112: A syringe, a beaker
IAO_0000114: IAO_0000122
IAO_0000115: A contain function is a function to constrain a material entities location in space
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

heat function
type: Class
subclass of: BFO_0000034
IAO_0000111: heat function
IAO_0000114: IAO_0000122
IAO_0000115: A heat function is a function that increases the internal kinetic energy of a material
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

material separation function
type: Class
subclass of: BFO_0000034
IAO_0000111: material separation function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

ionize process
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: BFO_0000055
  some values from: ionization function
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: RO_0000057
  some values from: BFO_0000040
IAO_0000111: ionize process
IAO_0000112: Electrospray ionization in mass spectrometry
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
IAO_0000117: Person:Bjoern Peters

excitation function
type: Class
subclass of: BFO_0000034
IAO_0000111: excitation function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

freeze function
type: Class
subclass of: BFO_0000034
IAO_0000111: freeze function
IAO_0000114: IAO_0000122
IAO_0000115: A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

synthesizing function
type: Class
subclass of: BFO_0000034
IAO_0000111: synthesizing function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

perturb function
type: Class
subclass of: BFO_0000034
IAO_0000111: perturb function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot
IAO_0000119: http://en.wikipedia.org/wiki/Perturbation_biology

filter function
type: Class
subclass of: material separation function
IAO_0000111: filter function
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Frank Gibson

mechanical function
type: Class
subclass of: BFO_0000034
IAO_0000111: mechanical function
IAO_0000114: IAO_0000122
IAO_0000115: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot
IAO_0000119: http://en.wikipedia.org/wiki/Mechanical_work

gas filter function
type: Class
subclass of: filter function
IAO_0000111: gas filter function
IAO_0000114: IAO_0000122
IAO_0000115: A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture
IAO_0000117: Frank Gibson

liquid filter function
type: Class
subclass of: filter function
IAO_0000111: liquid filter function
IAO_0000114: IAO_0000122
IAO_0000115: A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture
IAO_0000117: Frank Gibson

transfer function
type: Class
subclass of: BFO_0000034
IAO_0000111: transfer function
IAO_0000114: IAO_0000122
IAO_0000115: A transfer function is a function to displace a material from one location to another.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

electricity supply function
type: Class
subclass of: energy supply function
IAO_0000111: electricity supply function
IAO_0000112: the function of supplying current during a neuroscience experiment.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot
IAO_0000118: power supply

ionization function
type: Class
subclass of: BFO_0000034
IAO_0000111: ionization function
IAO_0000112: The ion source in amass spectrometer
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot
IAO_0000119: http://en.wikipedia.org/wiki/Ionization

cool function
type: Class
subclass of: BFO_0000034
IAO_0000111: cool function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

connection function
type: Class
subclass of: BFO_0000034
IAO_0000111: connection function
IAO_0000112: An electricity cable
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

isoelectric focusing device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: transfer function
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: isoelectric focusing device
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Frank Gibson
IAO_0000118: isoelectric focusing unit
IAO_0000119: sep:00097

thermostatic circulator
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: thermostatic circulator
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Frank Gibson
IAO_0000119: sep:00098

energy supply function
type: Class
subclass of: BFO_0000034
IAO_0000111: energy supply function
IAO_0000114: IAO_0000122
IAO_0000115: An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
IAO_0000117: Frank Gibson

information processor function
type: Class
subclass of: BFO_0000034
subclass of: Restriction
  on property: BFO_0000051
  some values from: measure function
subclass of: Restriction
  on property: BFO_0000051
  some values from: consume data function
IAO_0000111: information processor function
IAO_0000114: IAO_0000122
IAO_0000115: An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
IAO_0000117: Frank Gibson
IAO_0000118: data processor function

signal conversion function
type: Class
subclass of: information processor function
IAO_0000111: signal conversion function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot
IAO_0000118: transduction function

blot module
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: transfer function
IAO_0000111: blot module
IAO_0000114: IAO_0000123
IAO_0000115: A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
IAO_0000117: Frank Gibson
IAO_0000119: sep:00092

signal amplification function
type: Class
subclass of: signal conversion function
IAO_0000111: signal amplification function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

image acquisition function
type: Class
subclass of: measure function
subclass of: Restriction
  on property: RO_0000052
  some values from: image creation device
subclass of: Restriction
  on property: BFO_0000054
  all values from: image creation
IAO_0000111: image acquisition function
IAO_0000114: IAO_0000122
IAO_0000115: An image acquisition function is a function to acquire an image of a material
IAO_0000117: Frank Gibson

image creation device
type: Class
equivalent class: Class
  intersection of: COB_0001300
  intersection of: Restriction
    on property: RO_0000085
    some values from: image acquisition function
IAO_0000111: image acquisition device
IAO_0000114: IAO_0000123
IAO_0000115: An image creation device is a device which captures a digitized image of an object
IAO_0000117: Frank Gibson
IAO_0000118: image acquisition device
IAO_0000119: sep:00096

solid support function
type: Class
subclass of: BFO_0000034
IAO_0000111: solid support function
IAO_0000112: Taped, glued, pinned, dried or molecularly bonded to a solid support
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

display function
type: Class
subclass of: information processor function
IAO_0000111: display function
IAO_0000114: IAO_0000122
IAO_0000115: A display function is a function to present information by translating that information through some lookup process into visual form.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

environment control function
type: Class
subclass of: BFO_0000034
IAO_0000111: environment control function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Bill Bug
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

sort function
type: Class
subclass of: material separation function
IAO_0000111: sort function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: Daniel Schober
IAO_0000117: Frank Gibson
IAO_0000117: Melanie Courtot

gel dryer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: gel dryer
IAO_0000114: IAO_0000120
IAO_0000115: A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
IAO_0000117: Frank Gibson
IAO_0000119: sep:00094

primer role
type: Class
subclass of: complementary nucleotide probe role
subclass of: Restriction
  on property: BFO_0000054
  all values from: polymerase chain reaction
IAO_0000111: primer role
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000119: (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

PCR product
type: Class
equivalent class: Class
  intersection of: CHEBI 4705
  intersection of: Restriction
    on property: is specified output of
    some values from: polymerase chain reaction
IAO_0000111: PCR product
IAO_0000112: PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
IAO_0000114: IAO_0000122
IAO_0000115: is double stranded DNA that is the specified output of a polymerase chain reaction
IAO_0000116: We are using PCR and not the written out words, as this is the most common used.
IAO_0000117: GROUP: OBI BIomaterial Branch
IAO_0000119: GROUP: OBI BIomaterial Branch

viral RNA extraction
type: Class
subclass of: OBI_0666666
subclass of: Restriction
  on property: has specified input
  some values from: NCBITaxon_10239
IAO_0000111: viral RNA extraction
IAO_0000112: 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
IAO_0000114: IAO_0000123
IAO_0000115: The extraction of RNA from an input material that specifically isolates viral RNA
IAO_0000117: Person:Bjoern Peters

nucleic acid template role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: RO_0000052
  some values from: CHEBI_33696
subclass of: Restriction
  on property: BFO_0000054
  all values from: polymerase chain reaction
IAO_0000111: nucleic acid template role
IAO_0000112: a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
IAO_0000114: IAO_0000123
IAO_0000115: 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.

recombinant plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600064
IAO_0000111: recombinant plasmid
IAO_0000114: IAO_0000120
IAO_0000115: a plasmid in which extraneous DNA has been inserted.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Kevin Clancy
IAO_0000117: PERSON: Melanie Courtot
IAO_0000119: GROUP: OBI Biomaterial Branch

cloning vector role
type: Class
subclass of: material to be added role
subclass of: Class
  intersection of: Restriction
    on property: RO_0000052
    some values from: CHEBI_33696
  intersection of: Restriction
    on property: BFO_0000054
    all values from: OBI_0600064
IAO_0000111: cloning vector role
IAO_0000112: pBluescript plays the role of a cloning vector
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/
IAO_0000117: PERSON: Helen Parkinson

cell cycle synchronization
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: cell cycle synchronization
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
IAO_0000117: OBI PA
IAO_0000119: Bjoern Peters and Nicole Washington

polymerase chain reaction
type: Class
subclass of: OBI_0600058
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: synthesizing function
    intersection of: Restriction
      on property: RO_0000052
      some values from: GO_0042575
subclass of: Restriction
  on property: has specified input
  some values from: CHEBI_16991
subclass of: Restriction
  on property: has specified output
  some values from: PCR product
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: polymerase chain reaction
IAO_0000112: Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: OBI Plan
IAO_0000118: PCR
IAO_0000119: adapted from wikipedai

cloning insert role
type: Class
subclass of: BFO_0000023
IAO_0000111: cloning insert role
IAO_0000114: IAO_0000121
IAO_0000115: 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.
IAO_0000116: 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"
IAO_0000117: GROUP: Role branch
IAO_0000119: OBII and Wikipedia

measuring glucose concentration in blood serum assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100017
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_17234
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_17234
IAO_0000112: Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319.
IAO_0000114: IAO_0000123
IAO_0000115: An assay that determines the concentration of glucose molecules in a blood serum sample
IAO_0000117: Bjoern Peters
IAO_0000119: OBI

reverse transcriptase
type: Class
equivalent class: Class
  intersection of: enzyme
  intersection of: Restriction
    on property: RO_0000085
    some values from: Restriction
      on property: BFO_0000054
      all values from: GO_0003964
subclass of: enzyme
IAO_0000111: reverse transcriptase
IAO_0000114: IAO_0000125
IAO_0000115: enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
IAO_0000117: person:Melanie Courtot
IAO_0000119: group:OBI

obsolete_trypsinized material
type: Class
subclass of: ObsoleteClass
IAO_0000112: A trypsinized suspension of cells
IAO_0000114: IAO_0000002
IAO_0000115: A material entity that has undergone a process of digestion with trypsin
IAO_0000117: Person:Bjoern Peters
IAO_0000231: IAO_0000103
deprecated: true

syringe
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: transfer function
IAO_0000111: syringe
IAO_0000112: 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
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: OBI Instrument adapted from Wikipedia

extract
type: Class
subclass of: COB_0000026
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302884
IAO_0000111: extract
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: an extract is a material entity which results from an extraction process
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000118: extracted material
IAO_0000119: GROUP: OBI Biomatrial Branch

transcription profiling assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: RNA extract
        intersection of: Restriction
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: analyte role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: CHEBI_33697
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100051
      intersection of: Restriction
        on property: BFO_0000051
        some values from: CHEBI_33697
  intersection of: Restriction
    on property: has specified output
    some values from: IAO_0000109
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: GO_0010467
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: transcription profiling identification objective
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity.
IAO_0000116: This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: gene expression profiling
IAO_0000118: transcription profiling
IAO_0000119: OBI

averaging objective
type: Class
subclass of: OBI_0200166
IAO_0000111: averaging objective
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
IAO_0000117: Elisabetta Manduchi
IAO_0000117: James Malone
IAO_0000119: PERSON: Elisabetta Manduchi

injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: material to be added role
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: syringe
subclass of: BFO_0000015
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
IAO_0000111: injection
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: OBI Biomaterial

enzyme
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Class
    union of: CHEBI_33697
    union of: GO_0032991
    union of: PR_000000001
    union of: Restriction
      on property: BFO_0000051
      some values from: CHEBI_33697
    union of: Restriction
      on property: BFO_0000051
      some values from: GO_0032991
    union of: Restriction
      on property: BFO_0000051
      some values from: PR_000000001
  intersection of: Restriction
    on property: RO_0000085
    some values from: Restriction
      on property: BFO_0000054
      all values from: GO_0003824
subclass of: BFO_0000040
IAO_0000111: enzyme
IAO_0000114: IAO_0000125
IAO_0000115: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
IAO_0000116: 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.
IAO_0000117: person: Melanie Courtot
IAO_0000119: GROUP:OBI

intraperitoneal administration
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: RO_0000081
        some values from: UBERON_0002358
IAO_0000111: intraperitoneal administration
IAO_0000112: 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
IAO_0000115: The administration of a substance into the peritoneum of an organism
IAO_0000117: Person:Bjoern Peters

plasmid
type: Class
equivalent class: Class
  intersection of: CHEBI 4705
  intersection of: Restriction
    on property: RO_0000085
    some values from: Restriction
      on property: BFO_0000054
      all values from: GO_0010467
  intersection of: Restriction
    on property: RO_0000086
    some values from: SO_0000988
subclass of: CHEBI 4705
IAO_0000111: plasmid
IAO_0000114: IAO_0000125
IAO_0000115: plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
IAO_0000117: person:Melanie Courtot
IAO_0000119: group:OBI

injection into organ section
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: material to be added role
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: syringe
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: RO_0000081
        some values from: OBI_0100066
subclass of: BFO_0000015
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
IAO_0000111: injection into organ section
IAO_0000112: Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
IAO_0000114: IAO_0000123
IAO_0000115: A process in which an input substance is injected into a organ section.
IAO_0000117: Person:Bjoern Peters

polyacrylamide gel
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_28619
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302890
IAO_0000111: polyacrylamide gel
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
IAO_0000117: PERSON: Jie Zheng
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: GROUP: OBI Biomaterial Branch

DNA sequence feature detection assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
IAO_0000112: genotyping using an Affymetrix chip
IAO_0000114: IAO_0000123
IAO_0000115: An assay with the objective to determine a sequence feature of DNA
IAO_0000117: Bjoern Peters
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: OBI

adding material objective
type: Class
subclass of: material combination objective
IAO_0000111: adding material objective
IAO_0000112: creating a mouse infected with LCM virus
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: BP

genotyping assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: BFO_0000051
      some values from: CHEBI_16991
subclass of: Restriction
  on property: has specified output
  some values from: genotype information
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: SNP analysis
IAO_0000118: genotype profiling
IAO_0000119: OBI Biomaterial

needle
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: transfer function
IAO_0000111: needle
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: OBI Instrument

analyte measurement objective
type: Class
subclass of: assay objective
IAO_0000111: analyte measurement objective
IAO_0000112: The objective to measure the concentration of glucose in a blood sample
IAO_0000114: IAO_0000122
IAO_0000115: an assay objective to determine the presence or concentration of an analyte in the evaluant
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: PPPB branch

DNA sequence variation detection assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: DNA extract
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
IAO_0000112: Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
IAO_0000114: IAO_0000122
IAO_0000115: An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: OBI Biomaterial

agarose gel
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302890
IAO_0000111: agarose gel
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: GROUP: OBI Biomaterial Branch

assay objective
type: Class
subclass of: IAO_0000005
IAO_0000111: assay objective
IAO_0000112: the objective to determine the weight of a mouse.
IAO_0000114: IAO_0000122
IAO_0000115: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
IAO_0000117: PPPB branch
IAO_0000119: PPPB branch

obsolete_heart
type: Class
subclass of: ObsoleteClass
IAO_0000112: Alan Ruttenberg's heart
IAO_0000114: IAO_0000002
IAO_0000115: The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions
IAO_0000117: Person:Bjoern Peters
IAO_0000119: http://en.wikipedia.org/wiki/Heart
IAO_0000231: IAO_0000230
deprecated: true

analyte assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
IAO_0000112: 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
IAO_0000114: IAO_0000122
IAO_0000115: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
IAO_0000117: Alan Ruttenberg
IAO_0000117: Bjoern Peters
IAO_0000117: Helen Parkinson
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: Alan Ruttenberg
IAO_0000119: Bjoern Peters
IAO_0000119: Helen Parkinson
IAO_0000119: OBI Planned process branch
IAO_0000119: Philippe Rocca-Serra

target of material addition role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: BFO_0000040
subclass of: Restriction
  on property: BFO_0000054
  all values from: adding a material entity into a target
IAO_0000111: target of material addition role
IAO_0000112: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
IAO_0000114: IAO_0000120
IAO_0000115: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
IAO_0000116: 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.
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI

mass measurement assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: BFO_0000040
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000414
IAO_0000112: The patients was weighed and mass was determined to be 47 kilograms
IAO_0000114: IAO_0000120
IAO_0000115: An assay that determines the mass of an evaluant
IAO_0000117: Helen Parkinson
IAO_0000119: OBI

obsolete_identification
type: Class
subclass of: ObsoleteClass
IAO_0000112: DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
IAO_0000114: IAO_0000124
IAO_0000115: a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
IAO_0000117: Philippe Rocca-Serra
IAO_0000231: IAO_0000103
deprecated: true

intracellular electrophysiology recording assay
type: Class
subclass of: OBI_0002176
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000414
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0005216
IAO_0000114: IAO_0000123
IAO_0000115: An electrophysiology assay where the recording location of the electrode is intracellular.
IAO_0000117: Frank Gibson
IAO_0000119: Frank Gibson

packed column
type: Class
subclass of: chromatography column
IAO_0000111: packed column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218

obsolete_defined_output
type: Class
subclass of: ObsoleteClass
IAO_0000112: 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.
IAO_0000114: IAO_0000121
IAO_0000115: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Melanie Courtot
IAO_0000231: IAO_0000226
deprecated: true

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: RO_0000087
    some values from: regulator role
IAO_0000111: regulatory agency
IAO_0000112: The US Environmental Protection Agency
IAO_0000114: IAO_0000122
IAO_0000115: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
IAO_0000117: GROUP: OBI Biomaterial Branch
IAO_0000119: WEB: en.wikipedia.org/wiki/Regulator

normalized data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200169
subclass of: IAO_0000100
IAO_0000111: normalized data set
IAO_0000114: IAO_0000125
IAO_0000115: A data set that is produced as the output of a normalization data transformation.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Melanie Courtot

measure function
type: Class
subclass of: BFO_0000034
subclass of: Restriction
  on property: RO_0000079
  some values from: COB_0000026
subclass of: Restriction
  on property: BFO_0000054
  all values from: Restriction
    on property: has specified output
    some values from: IAO_0000109
IAO_0000111: measure function
IAO_0000112: A glucometer measures blood glucose concentration, the glucometer has a measure function.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: PERSON: Daniel Schober
IAO_0000117: PERSON: Helen Parkinson
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON:Frank Gibson

extracellular electrophysiology recording assay
type: Class
subclass of: OBI_0002176
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000414
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0005216
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: An electrophysiology assay where the recording location of the electrode is extracellular.
IAO_0000117: Frank Gibson
IAO_0000117: Helen Parkinson
IAO_0000119: Frank Gibson

consume data function
type: Class
subclass of: BFO_0000034
subclass of: Restriction
  on property: RO_0000079
  some values from: BFO_0000040
IAO_0000111: consume data function
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: PERSON: Daniel Schober
IAO_0000117: PERSON: Frank Gibson
IAO_0000117: PERSON: Melanie Courtot

material transformation objective
type: Class
subclass of: IAO_0000005
IAO_0000111: material transformation objective
IAO_0000112: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
IAO_0000114: IAO_0000122
IAO_0000115: an objective specifiction that creates an specific output object from input materials.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Frank Gibson
IAO_0000117: PERSON: Jennifer Fostel
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000118: artifact creation objective
IAO_0000119: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: COB_0000035
subclass of: Restriction
  on property: has specified input
  some values from: BFO_0000040
subclass of: Restriction
  on property: has specified output
  some values from: COB_0000026
IAO_0000111: manufacturing
IAO_0000114: IAO_0000122
IAO_0000115: A planned process with the objective to produce a processed material which will have a function for future use.
IAO_0000116: A person or organization (having manufacturer role) is a participant in this process
IAO_0000116: Manufacturing implies reproducibility and responsibility AR
IAO_0000116: This includes a single scientist making a processed material for personal use.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Frank Gibson
IAO_0000117: PERSON: Jennifer Fostel
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
IAO_0000111: manufacturing objective
IAO_0000114: IAO_0000122
IAO_0000115: is the objective to manufacture a material of a certain function (device)
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Frank Gibson
IAO_0000117: PERSON: Jennifer Fostel
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: GROUP: OBI PlanAndPlannedProcess Branch

column chromatography detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: column chromatography detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077
IAO_0000232: chromatography detector, defined class/xps

Bruker autosampler
type: Class
subclass of: autosampler
IAO_0000111: Bruker autosampler
IAO_0000114: IAO_0000120
IAO_0000115: A Bruker autosampler is an autosampler made by Bruker.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209

organic acid column
type: Class
subclass of: chromatography column
IAO_0000111: organic acid column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099

thermal conductivity detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: thermal conductivity detector
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: TCD, hot wire detector
IAO_0000119: WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084

Bruker US 2 NMR magnet
type: Class
subclass of: Bruker NMR magnet
IAO_0000111: Bruker US 2 NMR magnet
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189
IAO_0000232: NMR instrument

protein column
type: Class
subclass of: chromatography column
IAO_0000111: protein column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
IAO_0000232: refactor as defined class

solvent mixer
type: Class
subclass of: chromatography instrument
IAO_0000111: solvent mixer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072

mass spectrometry assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: BFO_0000034
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: mass spectrometer
IAO_0000112: 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.
IAO_0000115: An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: Philippe Rocca-Serra

study design execution
type: Class
equivalent class: Class
  intersection of: COB_0000035
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Restriction
      on property: RO_0000059
      some values from: OBI_0500000
IAO_0000111: study design execution
IAO_0000112: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
IAO_0000114: IAO_0000122
IAO_0000115: a planned process that carries out a study design
IAO_0000116: 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.
IAO_0000119: branch derived
IAO_0000232: 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.

Bruker NMR Case sample changer
type: Class
subclass of: Bruker autosampler
IAO_0000111: Bruker NMR Case sample changer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/automation.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203
IAO_0000232: NMR instrument

nano pump system
type: Class
subclass of: chromatography pump system
IAO_0000111: nano pump system
IAO_0000114: IAO_0000120
IAO_0000115: A pump system optimized for nano flow chromatography.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052

Bruker AutoClean system
type: Class
subclass of: NMR tube washing system
IAO_0000111: Bruker AutoClean system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: washing system/NMR tube washing system, XPS: device has function washing
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205

manual injection system
type: Class
subclass of: sample injection system
IAO_0000111: manual injection system
IAO_0000114: IAO_0000120
IAO_0000115: The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064

Varian GEMINI spectrometer
type: Class
subclass of: Varian NMR instrument
IAO_0000111: Varian GEMINI spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: An older Varian Broadband NMR spectrometer.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239
IAO_0000232: NMR instrument

column connector
type: Class
subclass of: chromatography device
IAO_0000111: column connector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
IAO_0000232: chromatography device

solid NMR probe
type: Class
subclass of: NMR probe
IAO_0000111: solid NMR probe
IAO_0000114: IAO_0000120
IAO_0000115: An NMR probe that is designed to hold a solid sample.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
IAO_0000232: NMR device

Bruker high resolution probe
type: Class
subclass of: Bruker NMR probe
IAO_0000111: Bruker high resolution probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: HR Probe
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223
IAO_0000232: NMR probe

chromatography detector
type: Class
subclass of: chromatography instrument
IAO_0000111: chromatography detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012

normal phase column
type: Class
subclass of: chromatography column
IAO_0000111: normal phase column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097

APOLLO console
type: Class
subclass of: tecmag NMR console
IAO_0000111: APOLLO console
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.tecmag.com/apollo.htm>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249
IAO_0000232: NMR instrument/NMR console

NMR sample holder
type: Class
subclass of: COB_0001300
IAO_0000111: NMR sample holder
IAO_0000114: IAO_0000120
IAO_0000115: An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212
IAO_0000232: NMR device

chromatography instrument
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
IAO_0000111: chromatography instrument
IAO_0000114: IAO_0000120
IAO_0000115: Any instrument that is used to carry out a chromatography experiment.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262
IAO_0000232: chromatography device, defined class?

continuous wave NMR instrument
type: Class
subclass of: NMR instrument
IAO_0000111: continuous wave NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
IAO_0000232: NMR instrument

fourier transformation NMR instrument
type: Class
subclass of: NMR instrument
IAO_0000111: fourier transformation NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
IAO_0000232: NMR instrument

nitrogen phosphorous detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: nitrogen phosphorous detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089

cation exchange column
type: Class
subclass of: ion exchange column
IAO_0000111: cation exchange column
IAO_0000114: IAO_0000120
IAO_0000115: A cation exchange column is a chromatography column that is used in cation exchange chromatography.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096

direct detection NMR probe
type: Class
subclass of: NMR probe
IAO_0000111: direct detection NMR probe
IAO_0000114: IAO_0000120
IAO_0000115: An NMR probe designed to allow the direct detection of acquisition nuclei.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
IAO_0000232: NMR device

Bruker B-ACS system
type: Class
subclass of: Bruker autosampler
IAO_0000111: Bruker B-ACS system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/automation.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210
IAO_0000232: NMR instrument

rapid resolution column
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
IAO_0000111: rapid resolution column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102

liquid chromatography autosampler
type: Class
subclass of: chromatography instrument
IAO_0000111: liquid chromatography autosampler
IAO_0000114: IAO_0000120
IAO_0000115: Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061

vacuum degasser
type: Class
subclass of: chromatography pump system
IAO_0000111: vacuum degasser
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/topics/vacuum.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053

capillary column
type: Class
subclass of: chromatography column
IAO_0000111: capillary column
IAO_0000114: IAO_0000120
IAO_0000115: A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066

sample inlet
type: Class
subclass of: chromatography device
IAO_0000111: sample inlet
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
IAO_0000232: chromatography device

NMR tube washing system
type: Class
subclass of: COB_0001300
IAO_0000111: NMR tube washing system
IAO_0000114: IAO_0000120
IAO_0000115: An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204
IAO_0000232: NMR instrument

NMR console
type: Class
subclass of: COB_0001300
IAO_0000111: NMR console
IAO_0000114: IAO_0000125
IAO_0000115: A component of an NMR instrument that controls the activities of the other components.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015
IAO_0000232: NMR instrument, TODO: same as or part of acquisition computer?

dual loop autosampler
type: Class
subclass of: liquid chromatography autosampler
IAO_0000111: dual loop autosampler
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063

variable wavelength detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: variable wavelength detector
IAO_0000114: IAO_0000120
IAO_0000115: A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079

Bruker LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: Bruker LC-NMR platform
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276
IAO_0000232: NMR instrument
IAO_0000232: hyphenated NMR instrument platform

sample injection system
type: Class
subclass of: chromatography device
IAO_0000111: sample injection system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057
IAO_0000232: chromatography device

multiple wavelength detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: multiple wavelength detector
IAO_0000114: IAO_0000120
IAO_0000115: A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078

photoionization detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: photoionization detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: PID
IAO_0000119: WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090

gas generator
type: Class
subclass of: gas chromatography equipment
IAO_0000111: gas generator
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033
IAO_0000232: gas chromatography equipment

column jacket
type: Class
subclass of: chromatography device
IAO_0000111: column jacket
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
IAO_0000232: chromatography device

electron capture detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: electron capture detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: ECD
IAO_0000119: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085

reversed phase column
type: Class
subclass of: chromatography column
IAO_0000111: reversed phase column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106

injector lubricant
type: Class
subclass of: chromatography consumable
IAO_0000111: injector lubricant
IAO_0000114: IAO_0000120
IAO_0000115: A lubricant used in liquid chromatography that eases sample injector penetration.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118

isolation of cell population
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
IAO_0000111: isolation of cell population
IAO_0000112: removing CD4+ cells from PBMCs using magnetic beads.
IAO_0000114: IAO_0000123
IAO_0000115: a process in which a population of cells with certain characteristics is isolated from a larger population
IAO_0000117: Person: Bjoern Peters

DISCOVERY console
type: Class
subclass of: tecmag NMR console
IAO_0000111: DISCOVERY console
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247
IAO_0000232: NMR instrument/NMR console

Bruker AMX series NMR instrument
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: Bruker AMX series NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240
IAO_0000232: NMR instrument

chromatofocusing column
type: Class
subclass of: chromatography column
IAO_0000111: chromatofocusing column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209

NMR probe
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: BFO_0000050
  some values from: NMR instrument
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: NMR probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014
IAO_0000232: NMR instrument

NMR magnet
type: Class
subclass of: COB_0001300
IAO_0000111: NMR magnet
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185
IAO_0000232: NMR instrument

trap column
type: Class
subclass of: chromatography column
IAO_0000111: trap column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261

flow probe
type: Class
subclass of: NMR probe
IAO_0000111: flow probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
IAO_0000232: NMR device

clinical chemistry assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: OBI_2000009
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_2000009
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: scattered molecular aggregate
  intersection of: Restriction
    on property: has specified input
    some values from: scattered molecular aggregate
IAO_0000112: Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters.
IAO_0000114: IAO_0000120
IAO_0000115: An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: chemical pathology
IAO_0000118: detection of analyte in blood sample
IAO_0000119: url:https://en.wikipedia.org/wiki/Clinical_chemistry

flame ionization detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: flame ionization detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: FID
IAO_0000119: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197

vial
type: Class
subclass of: container
IAO_0000111: vial
IAO_0000114: IAO_0000120
IAO_0000115: A container made from solid material and primarily used for holding liquid.
IAO_0000117: https://orcid.org/0000-0002-8844-9165
IAO_0000119: https://en.wikipedia.org/wiki/Vial

magic angle spinning rotor
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: BFO_0000050
  some values from: NMR instrument
IAO_0000111: magic angle spinning rotor
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: MAS rotor
IAO_0000119: WEB:<http://www.freepatentsonline.com/4352066.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130
IAO_0000232: NMR instrument

Varian VXR spectrometer
type: Class
subclass of: Varian NMR instrument
IAO_0000111: Varian VXR spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: A Varian NMR spectrometer.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238
IAO_0000232: NMR instrument

splitless GC injector
type: Class
subclass of: sample injection system
IAO_0000111: splitless GC injector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://en.wikipedia.org/wiki/Gas_chromatography>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060

preparative autosampler
type: Class
subclass of: liquid chromatography autosampler
IAO_0000111: preparative autosampler
IAO_0000114: IAO_0000120
IAO_0000115: For preparative LC with injection of sample volumes ranging from L to mL ranges.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062

flow high resolution probe
type: Class
subclass of: Bruker high resolution probe
IAO_0000111: flow high resolution probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: flow HR-probe
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
IAO_0000232: NMR probe

liquid chromatography valve
type: Class
subclass of: chromatography device
IAO_0000111: liquid chromatography valve
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
IAO_0000232: chromatography device

JEOL NMR probe
type: Class
subclass of: NMR probe
IAO_0000111: JEOL NMR probe
IAO_0000114: IAO_0000120
IAO_0000115: An NMR probe that is manufactured by JEOL.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232
IAO_0000232: NMR device

Bruker UltraShield Plus NMR magnet
type: Class
subclass of: Bruker NMR magnet
IAO_0000111: Bruker UltraShield Plus NMR magnet
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190
IAO_0000232: NMR instrument

Bruker CryoProbe
type: Class
subclass of: Bruker NMR probe
IAO_0000111: Bruker CryoProbe
IAO_0000114: IAO_0000120
IAO_0000115: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191
IAO_0000232: NMR probe

column cartridge
type: Class
subclass of: chromatography device
IAO_0000111: column cartridge
IAO_0000114: IAO_0000120
IAO_0000115: A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055

affinity column
type: Class
subclass of: chromatography column
IAO_0000111: affinity column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094

tecmag NMR instrument
type: Class
subclass of: NMR instrument
IAO_0000111: tecmag NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: An NMR instrument that is manufactured by tecmag.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250
IAO_0000232: NMR instrument

gel filtration column
type: Class
subclass of: size exclusion column
IAO_0000111: gel filtration column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104

fraction collector
type: Class
subclass of: chromatography instrument
IAO_0000111: fraction collector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/topics/fraction/collector.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073

copy number variation profiling assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: genetic characteristics information
IAO_0000112: Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796
IAO_0000114: IAO_0000120
IAO_0000115: An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: CNV analysis

in-line filter
type: Class
subclass of: chromatography detector filter
IAO_0000111: in-line filter
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.appliedporous.com/frits-chromatography.htm>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123

imaging NMR probe
type: Class
subclass of: NMR probe
IAO_0000111: imaging NMR probe
IAO_0000114: IAO_0000120
IAO_0000115: An NMR probe that is designed for generating pictures from sample states via NMR imaging.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
IAO_0000232: NMR device

isolation of adherent cells
type: Class
subclass of: isolation of cell population
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
IAO_0000111: isolation of adherent cells
IAO_0000114: IAO_0000123
IAO_0000115: 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.

Bruker AC series NMR instrument
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: Bruker AC series NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: A series of older Bruker NMR magnets, now out of production.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241
IAO_0000232: NMR instrument

gas chromatography equipment
type: Class
subclass of: chromatography device
IAO_0000111: gas chromatography equipment
IAO_0000114: IAO_0000120
IAO_0000115: Any device used in a gas chromatography experiment.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030
IAO_0000232: will become defined class/xps

syringe filter
type: Class
subclass of: chromatography detector filter
IAO_0000111: syringe filter
IAO_0000114: IAO_0000120
IAO_0000115: A small membrane filter of defined pore size, that filters samples from a syringe.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122

Bruker SampleRail system
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: transfer function
IAO_0000111: Bruker SampleRail system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/automation.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207
IAO_0000232: NMR instrument

column compartment
type: Class
subclass of: chromatography device
IAO_0000111: column compartment
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068

capillary pump system
type: Class
subclass of: chromatography pump system
IAO_0000111: capillary pump system
IAO_0000114: IAO_0000120
IAO_0000115: A pump system optimized for capillary chromatography.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051

evaporative light scattering detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: evaporative light scattering detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082

isolation of PBMCs
type: Class
subclass of: isolation of cell population
subclass of: Restriction
  on property: has specified input
  some values from: UBERON_0000178
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
IAO_0000111: isolation of PBMCs
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: a process in which cells with a single nucleus are isolated from a blood sample
IAO_0000117: PERSON: bjoern peters
IAO_0000119: wiki http://en.wikipedia.org/wiki/PBMC

column cartridger
type: Class
subclass of: chromatography instrument
IAO_0000111: column cartridger
IAO_0000114: IAO_0000120
IAO_0000115: A chromatography device where the column cartridge is inserted into and stabilised.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054

nitrogen generator
type: Class
subclass of: gas generator
IAO_0000111: nitrogen generator
IAO_0000114: IAO_0000120
IAO_0000115: A gas generator that generates nitrogen gas.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034

needle assembly
type: Class
subclass of: chromatography device
IAO_0000111: needle assembly
IAO_0000114: IAO_0000120
IAO_0000115: The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065

reverse transcribed polymerase chain reaction
type: Class
subclass of: OBI_0600058
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: polymerase chain reaction
    intersection of: Restriction
      on property: RO_0002087
      some values from: OBI_0600028
subclass of: Restriction
  on property: has specified input
  some values from: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: PCR product
IAO_0000111: reverse transcribed polymerase chain reaction
IAO_0000112: 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
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: RT-PCR
IAO_0000118: reverse transcription polymerase chain reaction

Bruker Capillary LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: Bruker Capillary LC-NMR platform
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279
IAO_0000232: NMR instrument
IAO_0000232: hyphenated NMR instrument platform

gas chromatography oven
type: Class
subclass of: gas chromatography equipment
IAO_0000111: gas chromatography oven
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
IAO_0000232: gas chromatography equipment

autosampler
type: Class
subclass of: COB_0001300
IAO_0000111: autosampler
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002
IAO_0000232: NMR instrument

isocratic pump system
type: Class
subclass of: chromatography pump system
IAO_0000111: isocratic pump system
IAO_0000114: IAO_0000120
IAO_0000115: A pump system optimized for isocratic chromatography.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049

flash pump system
type: Class
subclass of: chromatography pump system
IAO_0000111: flash pump system
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048

Varian UNITY INOVA spectrometer
type: Class
subclass of: Varian NMR instrument
IAO_0000111: Varian UNITY INOVA spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236
IAO_0000232: NMR instrument

liquid NMR probe
type: Class
subclass of: NMR probe
IAO_0000111: liquid NMR probe
IAO_0000114: IAO_0000120
IAO_0000115: An NMR probe that is designed to hold a liquid sample.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
IAO_0000232: NMR device

ion exchange column
type: Class
subclass of: chromatography column
IAO_0000111: ion exchange column
IAO_0000114: IAO_0000120
IAO_0000115: An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105

Bruker NMR probe
type: Class
subclass of: NMR probe
IAO_0000111: Bruker NMR probe
IAO_0000114: IAO_0000120
IAO_0000115: An NMR probe that is manufactured by Bruker.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231
IAO_0000232: NMR device, TODO: May need no definition.

anion trap column
type: Class
subclass of: trap column
IAO_0000111: anion trap column
IAO_0000114: IAO_0000120
IAO_0000115: An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277

fluorescene detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: fluorescene detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080

tecmag EAGLE probe
type: Class
subclass of: solid NMR probe
IAO_0000111: tecmag EAGLE probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
IAO_0000232: NMR probe

electrical conductivity detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: electrical conductivity detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239

NMR instrument
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: An Instrument which is used to carry out a NMR analysis of some sample.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: MRI scanner
IAO_0000118: NMR instrument
IAO_0000118: magnetic resonance imaging scanner
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059
IAO_0000232: NMR instrument

Bruker UltraShield NMR magnet
type: Class
subclass of: Bruker NMR magnet
IAO_0000111: Bruker UltraShield NMR magnet
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187
IAO_0000232: NMR instrument

piston-seal
type: Class
subclass of: chromatography consumable
IAO_0000111: piston-seal
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116

mass selective detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: mass selective detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: mass spectrometry detector
IAO_0000119: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198

spin column
type: Class
subclass of: chromatography column
IAO_0000111: spin column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232

manufacturer role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: Class
    union of: NCBITaxon 9606
    union of: organization
subclass of: Restriction
  on property: BFO_0000054
  all values from: manufacturing
IAO_0000111: manufacturer role
IAO_0000112: 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.
IAO_0000114: IAO_0000123
IAO_0000115: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI

transfer line
type: Class
subclass of: chromatography device
IAO_0000111: transfer line
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.freepatentsonline.com/5702671.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
IAO_0000232: chromatography device

gradient pump system
type: Class
subclass of: chromatography pump system
IAO_0000111: gradient pump system
IAO_0000114: IAO_0000120
IAO_0000115: A pump system optimized for gradient chromatography.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050

high temperature column
type: Class
subclass of: chromatography column
IAO_0000111: high temperature column
IAO_0000114: IAO_0000120
IAO_0000115: A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233

Bruker Ultrastabilized NMR magnet
type: Class
subclass of: Bruker NMR magnet
IAO_0000111: Bruker Ultrastabilized NMR magnet
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188
IAO_0000232: NMR instrument

scattered molecular aggregate
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  on property: has grain
  some values from: COB_0000013
subclass of: Restriction
  on property: has grain
  all values from: COB_0000013
IAO_0000111: scattered molecular aggregate
IAO_0000112: the sodium and chloride ions in a glass of salt water
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000118: Collective
IAO_0000119: 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

obsolete_molecular concentration
type: Class
subclass of: ObsoleteClass
IAO_0000112: the phosphate concentration should be 0.1M
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000119: Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
IAO_0000231: IAO_0000228
deprecated: true

NMR sample tube
type: Class
subclass of: test tube
subclass of: Restriction
  on property: BFO_0000050
  some values from: NMR instrument
IAO_0000111: NMR sample tube
IAO_0000114: IAO_0000120
IAO_0000115: The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132
IAO_0000232: NMR device

Varian UNITY spectrometer
type: Class
subclass of: Varian NMR instrument
IAO_0000111: Varian UNITY spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: The predecessor series of the Varian UNITY INOVA spectrometer.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237
IAO_0000232: NMR instrument

AVANCE II spectrometer
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: AVANCE II spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197
IAO_0000232: NMR instrument

y-column connector
type: Class
subclass of: column connector
IAO_0000111: y-column connector
IAO_0000114: IAO_0000120
IAO_0000115: A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237

Bruker LC-NMR/MS platform
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: Bruker LC-NMR/MS platform
IAO_0000114: IAO_0000120
IAO_0000115: Includes the connection to a high-resolution TOF-LC-MS system.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277
IAO_0000232: NMR instrument
IAO_0000232: hyphenated NMR instrument platform

refractive index detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: refractive index detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081

anion exchange column
type: Class
subclass of: ion exchange column
IAO_0000111: anion exchange column
IAO_0000114: IAO_0000120
IAO_0000115: An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095

plunger column
type: Class
subclass of: chromatography column
IAO_0000111: plunger column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108

flame photometric detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: flame photometric detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: FPD
IAO_0000119: WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091

chromatography pump system
type: Class
subclass of: chromatography instrument
IAO_0000111: chromatography pump system
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://en.wikipedia.org/wiki/Column_chromatography>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046

Bruker 1mm MicroProbe
type: Class
subclass of: Bruker NMR probe
IAO_0000111: Bruker 1mm MicroProbe
IAO_0000114: IAO_0000120
IAO_0000115: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194
IAO_0000232: NMR probe

Bruker BEST NMR system
type: Class
subclass of: Bruker autosampler
IAO_0000111: Bruker BEST NMR system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: Bruker Efficient Sample Transfer NMR
IAO_0000119: WEB:<http://www.bruker-biospin.com/automation.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206
IAO_0000232: NMR instrument

chromatography detector filter
type: Class
subclass of: chromatography consumable
IAO_0000111: chromatography detector filter
IAO_0000114: IAO_0000120
IAO_0000115: An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121

cation trap column
type: Class
subclass of: trap column
IAO_0000111: cation trap column
IAO_0000114: IAO_0000120
IAO_0000115: A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278

column adapter
type: Class
subclass of: chromatography device
IAO_0000111: column adapter
IAO_0000114: IAO_0000120
IAO_0000115: An Adapter that enabled the connection of a column to additional devices.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
IAO_0000232: chromatography device

pulsed amperometric detector
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: pulsed amperometric detector
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: PAD
IAO_0000119: WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240

Bruker NMR instrument
type: Class
subclass of: NMR instrument
IAO_0000111: Bruker NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: An NMR instrument that is manufactured by Bruker.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198
IAO_0000232: NMR instrument

Bruker NMR magnet
type: Class
subclass of: NMR magnet
IAO_0000111: Bruker NMR magnet
IAO_0000114: IAO_0000120
IAO_0000115: An NMR magnet that is manufactured by Bruker.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186
IAO_0000232: NMR instrument

ozone-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: ozone-induced chemiluminescence detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088

tecmag NMR console
type: Class
subclass of: NMR console
IAO_0000111: tecmag NMR console
IAO_0000114: IAO_0000120
IAO_0000115: An NMR console manufactured by tecmac.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246
IAO_0000232: NMR instrument

JEOL NMR instrument
type: Class
subclass of: NMR instrument
IAO_0000111: JEOL NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: An NMR instrument that is manufactured by JEOL.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226
IAO_0000232: NMR instrument

chromatography consumable
type: Class
subclass of: chromatography device
IAO_0000111: chromatography consumable
IAO_0000114: IAO_0000120
IAO_0000115: A chromatography consumable is a consumable that is used in a chromatography experiment.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115
IAO_0000232: chromatography device

column frit
type: Class
subclass of: chromatography device
IAO_0000111: column frit
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/topics/radial/columns.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
IAO_0000232: chromatography device

liquid chromatography column
type: Class
subclass of: chromatography column
IAO_0000111: liquid chromatography column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227

detector lamp
type: Class
subclass of: chromatography consumable
IAO_0000111: detector lamp
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119

chart recorder
type: Class
subclass of: chromatography device
IAO_0000111: chart recorder
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
IAO_0000232: chromatography device

open tubular column
type: Class
subclass of: chromatography column
IAO_0000111: open tubular column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219

high resolution magic angle spin probe
type: Class
subclass of: Bruker high resolution probe
IAO_0000111: high resolution magic angle spin probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: high resolution MAS, hr-MAS
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
IAO_0000232: NMR probe

hydrogen generator
type: Class
subclass of: gas generator
IAO_0000111: hydrogen generator
IAO_0000114: IAO_0000120
IAO_0000115: A gas generator that generates hydrogen gas.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035

glass column
type: Class
subclass of: chromatography column
IAO_0000111: glass column
IAO_0000114: IAO_0000120
IAO_0000115: A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101

auto injector
type: Class
subclass of: sample injection system
IAO_0000111: auto injector
IAO_0000114: IAO_0000120
IAO_0000115: A gas chromatography device that can auto-inject a small number of samples an inlet.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058

Varian NMR instrument
type: Class
subclass of: NMR instrument
IAO_0000111: Varian NMR instrument
IAO_0000114: IAO_0000120
IAO_0000115: An NMR instrument that is manufactured by Varian.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234
IAO_0000232: NMR instrument

Bruker MATCH tube holder system
type: Class
subclass of: NMR sample holder
IAO_0000111: Bruker MATCH tube holder system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: Bruker Multiple Adjustable Tube Clamp Holder
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211
IAO_0000232: NMR instrument

Bruker SPE-NMR platform
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: Bruker SPE-NMR platform
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278
IAO_0000232: NMR instrument
IAO_0000232: hyphenated NMR instrument platform

guard column
type: Class
subclass of: chromatography device
IAO_0000111: guard column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
IAO_0000232: chromatography device

protein expression profiling assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: Class
        intersection of: OBI_0100051
        intersection of: Restriction
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
IAO_0000112: Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203
IAO_0000114: IAO_0000120
IAO_0000115: An assay that determines protein expression and translation activity using protein extracts collected from a material entity.
IAO_0000117: Phlippe Rocca-Serra
IAO_0000118: proteomic analysis
IAO_0000119: OBI branch derived

high resolution probe with automatic tuning and matching
type: Class
subclass of: Bruker high resolution probe
IAO_0000111: high resolution probe with automatic tuning and matching
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
IAO_0000232: NMR probe

fluorine-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: fluorine-induced chemiluminescence detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087

size exclusion column
type: Class
subclass of: chromatography column
IAO_0000111: size exclusion column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100

chromatography splitter
type: Class
subclass of: chromatography device
IAO_0000111: chromatography splitter
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
IAO_0000232: chromatography device

Bruker micro imaging probe
type: Class
subclass of: Bruker NMR probe
IAO_0000111: Bruker micro imaging probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/probes_microimaging.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225
IAO_0000232: NMR probe

custom made column
type: Class
subclass of: chromatography column
IAO_0000111: custom made column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234

gel permeation column
type: Class
subclass of: chromatography column
IAO_0000111: gel permeation column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103

NMR spectroscopy assay
type: Class
subclass of: assay
IAO_0000112: 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
IAO_0000114: IAO_0000123
IAO_0000115: An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: Nuclear magnetic resonance spectroscopy
IAO_0000119: url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy

Bruker SampleJet system
type: Class
subclass of: Bruker autosampler
IAO_0000111: Bruker SampleJet system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/automation.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208
IAO_0000232: NMR instrument

JEOL ECX NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
IAO_0000111: JEOL ECX NMR spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227
IAO_0000232: NMR instrument

DNA sequencing assay
type: Class
equivalent class: Class
  intersection of: OBI_0600047
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: BFO_0000034
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400103
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: DNA extract
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001573
IAO_0000112: Illumina (Solexa) sequencing is an example of DNA sequencing
IAO_0000114: IAO_0000123
IAO_0000115: A sequencing assay which determines information on the sequence of a DNA molecule.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: nucleotide sequencing
IAO_0000119: url:https://en.wikipedia.org/wiki/DNA_sequencing

quaternary pump system
type: Class
subclass of: chromatography pump system
IAO_0000111: quaternary pump system
IAO_0000114: IAO_0000120
IAO_0000115: A pump system that pump and mix up to four different solvents in parallel.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047

carbon nanotube column
type: Class
subclass of: chromatography column
IAO_0000111: carbon nanotube column
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107

Bruker solid magic angle spinning probe
type: Class
subclass of: Bruker NMR probe
IAO_0000111: Bruker solid magic angle spinning probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: solid MAS probe
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193
IAO_0000232: NMR probe

hematology assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: specimen from organism
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: specimen from organism
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: UPHENO_0001001
IAO_0000112: Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943
IAO_0000114: IAO_0000123
IAO_0000115: An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: blood analysis
IAO_0000118: haematology
IAO_0000119: OBI branch derived

Varian MERCURY spectrometer
type: Class
subclass of: Varian NMR instrument
IAO_0000111: Varian MERCURY spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235
IAO_0000232: NMR instrument

Bruker Metabolic Profiler
type: Class
subclass of: Bruker NMR instrument
IAO_0000111: Bruker Metabolic Profiler
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.bruker-biospin.com/metabolicprofiler.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199
IAO_0000232: NMR instrument
IAO_0000232: hyphenated NMR instrument platform

column heater
type: Class
subclass of: chromatography instrument
IAO_0000111: column heater
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040

DNA methylation profiling assay
type: Class
subclass of: OBI_0002020
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CHEBI 4431
      intersection of: Restriction
        on property: BFO_0000051
        some values from: CHEBI_32875
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: BFO_0000051
      some values from: CHEBI_16991
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000027
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
IAO_0000112: Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979
IAO_0000114: IAO_0000122
IAO_0000115: An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: DNA methylation profiling
IAO_0000119: OBI branch derived

JEOL CapNMR probe
type: Class
subclass of: JEOL NMR probe
IAO_0000111: JEOL CapNMR probe
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233
IAO_0000232: NMR probe

acquisition computer
type: Class
subclass of: OBI_0400107
subclass of: Restriction
  on property: RO_0000085
  some values from: information processor function
IAO_0000111: acquisition computer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
IAO_0000232: NMR instrument

gas chromatography detector
type: Class
subclass of: chromatography detector
IAO_0000111: gas chromatography detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: FID
IAO_0000119: WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083
IAO_0000232: chromatography detector, defined class/xps

gas purifier
type: Class
subclass of: gas chromatography equipment
IAO_0000111: gas purifier
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
IAO_0000232: gas chromatography equipment

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
IAO_0000111: material separation objective
IAO_0000112: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
IAO_0000114: IAO_0000122
IAO_0000115: is an objective to transform a material entity into spatially separated components.
IAO_0000117: PPPB branch
IAO_0000119: PPPB branch

indirect detection probe
type: Class
subclass of: NMR probe
IAO_0000111: indirect detection probe
IAO_0000114: IAO_0000120
IAO_0000115: An NMR probe designed to allow the indirect detection of acquisition nuclei.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:<http://msi-ontology.sourceforge.net>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
IAO_0000232: NMR device

JEOL ECA NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
IAO_0000111: JEOL ECA NMR spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228
IAO_0000232: NMR instrument

atomic emission detector
type: Class
subclass of: gas chromatography detector
IAO_0000111: atomic emission detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Daniel Schober
IAO_0000118: AED
IAO_0000119: WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
IAO_0000119: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086

clustered data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200175
subclass of: IAO_0000100
IAO_0000111: clustered data set
IAO_0000112: A clustered data set is the output of a K means clustering data transformation
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee
IAO_0000118: data set with assigned discovered class labels
IAO_0000232: AR thinks could be a data item instead

data set of features
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200184
subclass of: IAO_0000100
IAO_0000111: data set of features
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee

differential expression analysis data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200031
subclass of: OBI_0200000
IAO_0000111: differential expression analysis data transformation
IAO_0000114: IAO_0000122
IAO_0000115: A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals.
IAO_0000117: Dan Berrios
IAO_0000117: James Malone
IAO_0000117: Melanie Courtot
IAO_0000117: Monnie McGee
IAO_0000119: WEB:

urine specimen
type: Class
equivalent class: Class
  intersection of: OBI_2000009
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: RO_0001000
      some values from: UBERON_0001088
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600005
IAO_0000111: urine specimen
IAO_0000114: IAO_0000120
IAO_0000115: a portion of urine collected from an organism
IAO_0000116: 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
IAO_0000116: 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
IAO_0000116: are we happy calling collection of urine a material separation?

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: COB_0000110
subclass of: Restriction
  on property: has specified input
  some values from: BFO_0000040
subclass of: Restriction
  on property: has specified output
  some values from: BFO_0000040
IAO_0000111: material combination
IAO_0000112: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
IAO_0000114: IAO_0000122
IAO_0000115: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
IAO_0000116: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
IAO_0000117: bp
IAO_0000119: bp

fuzzy clustering objective
type: Class
subclass of: OBI_0200166
IAO_0000111: fuzzy clustering objective
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000119: PERSON: James Malone
IAO_0000119: PERSON: Ryan Brinkman

device setting
type: Class
subclass of: COB_0000502
subclass of: Restriction
  on property: RO_0000052
  some values from: COB_0000026
IAO_0000111: device setting
IAO_0000112: 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
IAO_0000114: IAO_0000123
IAO_0000115: a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
IAO_0000116: There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133
IAO_0000117: PERSON: Frank Gibson

blood specimen
type: Class
equivalent class: Class
  intersection of: OBI_2000009
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: RO_0001000
      some values from: UBERON_0000178
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600005
IAO_0000111: blood specimen
IAO_0000112: blood drawn from a human for glucose assay
IAO_0000114: IAO_0000122
IAO_0000115: a material entity derived from a portion of blood collected from an organism
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

data set of predicted values according to fitted curve
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200072
subclass of: IAO_0000100
IAO_0000111: data set of predicted values according to fitted curve
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee

data representational model
type: Class
subclass of: IAO_0000033
IAO_0000111: data representational model
IAO_0000112: The Cytoscape application is commonly used to visualize data representational models about biological entities. It can read and write several serializations of data representational models, including BioPAX.
IAO_0000112: gene regulatory graph model
IAO_0000112: phylogenetic tree
IAO_0000112: protein interaction network
IAO_0000114: IAO_0000120
IAO_0000115: An information content entity representing the relationships between data items.
IAO_0000117: Melanie Courtot
IAO_0000118: data structure
IAO_0000118: data structure specification
IAO_0000119: GROUP: OBI
IAO_0000232: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009

specimen collection process
type: Class
equivalent class: Class
  intersection of: COB_0000035
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: Restriction
  on property: has specified input
  some values from: BFO_0000040
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100051
IAO_0000112: 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, collecting a stone from a site
IAO_0000114: IAO_0000122
IAO_0000115: A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
IAO_0000116: Definition updated following discussion on 2024-10-07 OBI dev call.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
IAO_0000116: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
IAO_0000117: Bjoern Peters
IAO_0000118: specimen collection
IAO_0000232: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
IAO_0000232: 6/9/09: used at workshop

background corrected data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: background correction data transformation
subclass of: IAO_0000100
IAO_0000111: background corrected data set
IAO_0000114: IAO_0000125
IAO_0000115: A data set that is produced as the output of a background correction data transformation.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Melanie Courtot

enzyme-linked immunosorbent assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: GO_0042571
  intersection of: Restriction
    on property: has specified input
    some values from: GO_0042571
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000118: ELISA
IAO_0000119: IEDB

error corrected data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: error correction data transformation
subclass of: IAO_0000100
IAO_0000111: error corrected data set
IAO_0000114: IAO_0000125
IAO_0000115: 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).
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee

class prediction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has specified output
    some values from: classified data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200179
subclass of: OBI_0200000
IAO_0000111: class prediction data transformation
IAO_0000114: IAO_0000122
IAO_0000115: A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
IAO_0000117: James Malone
IAO_0000118: supervised classification data transformation
IAO_0000119: PERSON: James Malone

BrdU incorporation assay
type: Class
subclass of: cell proliferation assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_472552
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_472552
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

obsolete intracellular cytokine staining assay
type: Class
subclass of: ObsoleteClass
IAO_0000112: Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000118: ICCS
IAO_0000118: ICS
IAO_0000119: IEDB
IAO_0000231: IAO_0000227
IAO_0100001: flow cytometry assay
IEDB alternative term: intracellular cytokine staining (ICS)
deprecated: true

background correction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has specified output
    some values from: background corrected data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200173
subclass of: OBI_0200000
IAO_0000111: background correction data transformation
IAO_0000114: IAO_0000122
IAO_0000115: A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
IAO_0000117: James Malone
IAO_0000119: PERSON: James Malone

obsolete MHC multimer staining assay
type: Class
subclass of: ObsoleteClass
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: IEDB
IAO_0000118: MHC tetramer assay
IAO_0000119: IEDB
IAO_0000231: IAO_0000227
IAO_0100001: OBI_1110179
IEDB alternative term: MHC tetramer/multimer staining
deprecated: true

error correction data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200186
subclass of: OBI_0200000
IAO_0000111: error correction data transformation
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000117: Monnie McGee
IAO_0000119: EDITORS

tritiated thymidine incorporation assay
type: Class
subclass of: cell proliferation assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_53526
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_53526
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: radioactivity detection
    intersection of: OBI_0003368
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

sample from organism
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: RO_0000087
    some values from: material sample role
IAO_0000111: sample from organism
IAO_0000114: IAO_0000002
IAO_0000115: a material obtained from an organism in order to be a representative of the whole
IAO_0000116: 5/29: This is a helper class for now
IAO_0000116: 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
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: OBI_0200000
IAO_0000111: statistical hypothesis test
IAO_0000114: IAO_0000120
IAO_0000115: A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
IAO_0000117: James Malone
IAO_0000119: PERSON: James Malone

center value
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200181
subclass of: IAO_0000027
IAO_0000111: center value
IAO_0000114: IAO_0000125
IAO_0000115: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee
IAO_0000118: median

statistical hypothesis test objective
type: Class
subclass of: OBI_0200166
IAO_0000111: statistical hypothesis test objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000117: Person:Helen Parkinson
IAO_0000118: hypothesis test objective
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing

reduced dimension data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200182
subclass of: IAO_0000100
IAO_0000111: reduced dimension data set
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee

portioning objective
type: Class
subclass of: material separation objective
disjoint with: separation into different composition objective
IAO_0000111: portioning objective
IAO_0000112: The objective to obtain multiple aliquots of an enzyme preparation.
IAO_0000114: IAO_0000123
IAO_0000115: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.

average value
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200170
subclass of: IAO_0000027
IAO_0000111: average value
IAO_0000114: IAO_0000125
IAO_0000115: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Monnie McGee
IAO_0000118: arithmetic mean

whole organism preparation
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: RO_0001000
  some values from: COB_0000022
IAO_0000111: whole organism preparation
IAO_0000112: putting a mouse in the blender. Not: putting a mouse on a scale
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000116: does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.

separation into different composition objective
type: Class
subclass of: material separation objective
IAO_0000111: separation into different composition objective
IAO_0000112: The objective to obtain cells contained in a sample of blood.
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000116: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives

obsolete_study result
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000120
IAO_0000115: Study result is an information content entity that is a specified data output of a study.
IAO_0000119: GROUP: OBI
IAO_0000231: IAO_0000230
deprecated: true

specimen collection objective
type: Class
subclass of: IAO_0000005
IAO_0000112: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
IAO_0000114: IAO_0000122
IAO_0000115: A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
IAO_0000116: OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

creating a mixture of molecules in solution
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: BFO_0000040
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0302729
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
IAO_0000111: creating a mixture of molecules in solution
IAO_0000112: The production of PBS
IAO_0000114: IAO_0000120
IAO_0000115: is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
IAO_0000117: Bjoern Peters
IAO_0000119: PERSON: Helen Parkinson

material combination objective
type: Class
subclass of: material transformation objective
IAO_0000111: material combination objective
IAO_0000114: IAO_0000122
IAO_0000115: is an objective to obtain an output material that contains several input materials.
IAO_0000117: PPPB branch
IAO_0000119: bp

nucleotide overhang cloning
type: Class
subclass of: OBI_0600064
IAO_0000111: nucleotide overhang cloning
IAO_0000112: Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
IAO_0000114: IAO_0000120
IAO_0000115: Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
IAO_0000117: Helen Parkinson

rodent care protocol
type: Class
subclass of: animal care protocol
IAO_0000111: rodent care protocol
IAO_0000112: Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
IAO_0000114: IAO_0000123
IAO_0000115: A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

454 Genome Sequence 20
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000758
IAO_0000111: 454 Genome Sequence 20
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: GS 20

immunoprecipitation
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: GO_0042571
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
IAO_0000111: immunoprecipitation
IAO_0000112: PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
IAO_0000114: IAO_0000123
IAO_0000115: is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: OBI plan and planned process branch

ABI 377 automated sequencer
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000776
IAO_0000111: ABI 377 automated sequencer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: Applied Biosystems

recombination enzyme based cloning
type: Class
subclass of: OBI_0600064
IAO_0000111: recombination enzyme based cloning
IAO_0000114: IAO_0000123
IAO_0000115: 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

MeDIP-seq assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: Restriction
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0000785
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CHEBI 4431
      intersection of: Restriction
        on property: BFO_0000051
        some values from: CHEBI_32875
subclass of: Restriction
  on property: BFO_0000051
  some values from: chromatin immunoprecipitation
subclass of: Restriction
  on property: BFO_0000051
  some values from: library preparation
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_0600047
subclass of: Restriction
  on property: has specified input
  some values from: DNA extract
subclass of: Restriction
  on property: has specified output
  some values from: sequence data
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
IAO_0000112: PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
IAO_0000114: IAO_0000120
IAO_0000115: A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: Methylated DNA immunoprecipitation sequencing assay
IAO_0000119: url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation

animal feeding
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: BFO_0000055
  some values from: feed role
subclass of: Restriction
  on property: has specified input
  some values from: COB_0000022
subclass of: Restriction
  on property: has specified output
  some values from: COB_0000022
IAO_0000111: animal feeding
IAO_0000112: giving crickets to a snake.
IAO_0000114: IAO_0000123
IAO_0000115: animal feeding is a process in which animals are provided with food
IAO_0000116: In an investigation, this will typically be part of an animal care process
IAO_0000117: Bjoern Peters
IAO_0000119: branch derived

chain termination sequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      union of: ABI 377 automated sequencer
      union of: Li-Cor 4300 DNA Analysis System
subclass of: Restriction
  on property: has specified input
  some values from: PCR product
IAO_0000112: PMID: 271968. DNA sequencing with chain-terminating inhibitors.
IAO_0000114: IAO_0000120
IAO_0000115: A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: Sanger sequencing
IAO_0000118: dye terminator sequencing
IAO_0000119: url:https://en.wikipedia.org/wiki/Sanger_sequencing

AB SOLiD System
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000776
IAO_0000111: AB SOLiD System
IAO_0000112: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
IAO_0000114: IAO_0000120
IAO_0000115: is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: Applied Biosystems

Helicos sequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: HeliScope Single Molecule Sequencer
  intersection of: Restriction
    on property: has specified input
    some values from: HeliScope Single Molecule Sequencer
IAO_0000112: PMID: 18388294. Single-molecule DNA sequencing of a viral genome.
IAO_0000114: IAO_0000120
IAO_0000115: A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: true single molecule sequencing
IAO_0000119: url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing

obsolete_DNA ligase
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
IAO_0000117: Kevin Clancy, Bjoern Peters
IAO_0000118: ligase
IAO_0000231: IAO_0000228
deprecated: true

survival assessment assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: COB_0000022
subclass of: Restriction
  on property: has specified output
  some values from: survival rate
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: COB_0000022
IAO_0000114: IAO_0000123
IAO_0000115: An assay that measures the occurrence of death events in one or more organisms over time

support vector machine
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200179
IAO_0000111: support vector machine
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000117: Ryan Brinkman
IAO_0000118: SVM
IAO_0000119: PERSON: Ryan Brinkman

self-organizing map
type: Class
subclass of: OBI_0200000
subclass of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      union of: clustered data set
      union of: topologically preserved clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200178
IAO_0000111: self-organizing map
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000117: Ryan Brinkman
IAO_0000118: SOM
IAO_0000119: PERSON: Ryan Brinkman

454 Genome Sequencer FLX
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000758
IAO_0000111: 454 Genome Sequencer FLX
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: 454 GS FLX
IAO_0000118: GS-FLX
IAO_0000119: 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

Illumina Genome Analyzer II
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000759
IAO_0000111: Illumina Genome Analyzer II
IAO_0000112: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: Illumina Corporation

decision tree induction objective
type: Class
subclass of: OBI_0200166
IAO_0000111: decision tree induction objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: James Malone

Edman degradation
type: Class
subclass of: OBI_0600047
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: RO_0000052
        some values from: BFO_0000040
  intersection of: Restriction
    on property: has specified input
    some values from: BFO_0000040
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000030
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: SO_0000104
IAO_0000112: Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

SOLiD sequencing assay
type: Class
subclass of: DNA sequencing by ligation assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: AB SOLiD System
  intersection of: Restriction
    on property: has specified input
    some values from: AB SOLiD System
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: paired-end library
    union of: single fragment library
    union of: PR_000023089
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing

decision tree building data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
subclass of: OBI_0200000
IAO_0000111: decision tree building data transformation
IAO_0000114: IAO_0000120
IAO_0000115: A decision tree building data transformation is a data transformation that has objective decision tree induction.
IAO_0000117: James Malone
IAO_0000119: PERSON: James Malone

laboratory animal care
type: Class
equivalent class: Restriction
  on property: BFO_0000055
  some values from: Restriction
    on property: RO_0000059
    some values from: animal care protocol
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: COB_0000022
    intersection of: Restriction
      on property: RO_0001025
      some values from: BFO_0000029
IAO_0000111: laboratory animal care
IAO_0000114: IAO_0000123
IAO_0000115: a process that realizes an animal care protocol that specifies how animals are kept and maintained

yeast artificial chromosome vector
type: Class
subclass of: CHEBI 4705
subclass of: Restriction
  on property: RO_0000087
  some values from: cloning vector role
IAO_0000111: yeast artificial chromosome vector
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000116: this should be a child of 'chromosome' if we import that from another source
IAO_0000117: Kevin Clancy, Bjoern Peters
IAO_0000118: YAC

Li-Cor 4300 DNA Analysis System
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000769
IAO_0000111: Li-Cor 4300 DNA Analysis System
IAO_0000114: IAO_0000120
IAO_0000115: is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: OBI and Li-Cor

library preparation
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI 4705
subclass of: Restriction
  on property: has specified output
  some values from: Class
    union of: clonal cDNA library
    union of: paired-end library
    union of: single fragment library
    union of: OBI_1000029
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: library preparation
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: library construction

pathogen challenge
type: Class
subclass of: OBI_0003456
subclass of: Restriction
  on property: BFO_0000055
  some values from: host role
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: RO_0000081
      some values from: Class
        intersection of: COB_0000022
        intersection of: Restriction
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: RO_0000081
      some values from: Class
        intersection of: COB_0000022
        intersection of: Restriction
IAO_0000111: pathogen challenge
IAO_0000114: IAO_0000123
IAO_0000115: The administration of a live pathogenic organism to a host.

GenePattern software
type: Class
subclass of: IAO_0000010
IAO_0000111: GenePattern software
IAO_0000114: IAO_0000120
IAO_0000115: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
IAO_0000117: James Malone
IAO_0000117: Person:Helen Parkinson
IAO_0000119: WEB: http://www.broadinstitute.org/cancer/software/genepattern/

graph of vertices
type: Class
subclass of: IAO_0000038
IAO_0000111: graph of vertices
IAO_0000112: For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Bjoern Peters
IAO_0000117: Chris Stoeckert
IAO_0000117: James Malone
IAO_0000119: WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html

animal care protocol
type: Class
subclass of: protocol
IAO_0000111: animal care protocol
IAO_0000112: Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
IAO_0000114: IAO_0000123
IAO_0000115: An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

ChIP-seq assay
type: Class
equivalent class: Class
  intersection of: OBI_0001954
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: BFO_0000034
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400103
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: DNA sequencing assay
      intersection of: OBI_0003368
IAO_0000112: PMID: 19275939
IAO_0000114: IAO_0000122
IAO_0000115: An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin
IAO_0000117: Bjoern Peters
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: chromatin immunoprecipitation sequencing assay
IAO_0000119: url:https://en.wikipedia.org/wiki/ChIP-sequencing

HeliScope Single Molecule Sequencer
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000757
IAO_0000111: HeliScope Single Molecule Sequencer
IAO_0000114: IAO_0000120
IAO_0000115: is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
IAO_0000117: Philippe Rocca-Serra

pathogen role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: COB_0000022
subclass of: Restriction
  on property: BFO_0000054
  all values from: OGMS_0000063
IAO_0000111: pathogen role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: GROUP: Role Branch
IAO_0000119: OBI
IAO_0000232: 6 April 2009: from the Vaccine Community

vaccine production
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: vaccine preparation
IAO_0000112: The production of B. pertussis vaccine.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process with the objective to create a vaccine.
IAO_0000119: OBI

immunologic adjuvant role
type: Class
subclass of: OBI_1110092
subclass of: Restriction
  on property: BFO_0000054
  all values from: GO_0006955
IAO_0000111: immunologic adjuvant role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen.
IAO_0000116: 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'.
IAO_0000117: GROUP: Role branch
IAO_0000119: Vaccine Ontology, Wikipedia, OBI
IAO_0000232: 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

glucose tolerance test
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100017
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0600007
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: measuring glucose concentration in blood serum assay
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: HP_0000855
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: biological feature identification objective
IAO_0000112: PMID: 19527607
IAO_0000114: IAO_0000122
IAO_0000115: An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: NuGO OBI plan branch

paired-end library
type: Class
subclass of: COB_0000026
IAO_0000111: paired-end library
IAO_0000112: 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.
IAO_0000114: IAO_0000123
IAO_0000115: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: mate-paired library
IAO_0000118: paired-end tag (PET) library
IAO_0000119: adapted from information provided by Solid web site

DNA sequencing by ligation assay
type: Class
subclass of: DNA sequencing assay
subclass of: Restriction
  on property: has specified input
  some values from: PR_000023089
IAO_0000112: ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing).
IAO_0000114: IAO_0000123
IAO_0000115: A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: url:https://en.wikipedia.org/wiki/Sequencing_by_ligation

Solexa sequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: Illumina Genome Analyzer II
  intersection of: Restriction
    on property: has specified input
    some values from: Illumina Genome Analyzer II
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: paired-end library
    union of: single fragment library
IAO_0000112: PMID: 18987734
IAO_0000114: IAO_0000120
IAO_0000115: A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: reversible terminator sequencing
IAO_0000119: Solexa web site (SS_DNAsequencing.pdf document available on july 2009)

host role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: COB_0000022
IAO_0000111: host role
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000116: 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
IAO_0000117: GROUP: Role Branch
IAO_0000119: 30 Mar09 submitted by vaccine community
IAO_0000119: OBI
IAO_0000119: http://en.wikipedia.org/wiki/Host_(biology)

peak matching
type: Class
subclass of: OBI_0200000
IAO_0000111: peak matching
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: James Malone
IAO_0000117: Ryan Brinkman
IAO_0000119: PERSON: Ryan Brinkman

k-nearest neighbors
type: Class
subclass of: OBI_0200000
subclass of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200178
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200172
IAO_0000111: k-nearest neighbors
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000118: k-NN
IAO_0000119: PERSON: James Malone

rodent care
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: BFO_0000051
  some values from: animal feeding
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: contain function
    intersection of: Restriction
      on property: RO_0000052
      some values from: OBI_0400171
subclass of: Restriction
  on property: BFO_0000055
  some values from: Restriction
    on property: RO_0000059
    some values from: rodent care protocol
subclass of: Restriction
  on property: has specified input
  some values from: NCBITaxon 9989
subclass of: Restriction
  on property: has specified output
  some values from: NCBITaxon 9989
IAO_0000111: rodent care
IAO_0000112: keeping animal
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: PPPB branch
IAO_0000119: PPPB branch

cloning plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: RO_0000087
    some values from: cloning vector role
IAO_0000111: cloning plasmid
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: Note: 'cloning vector role' is really a function. Should be dealt with globally

pyrosequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      union of: 454 Genome Sequence 20
      union of: 454 Genome Sequencer FLX
IAO_0000112: Pyrosequencing sheds light on DNA sequencing. PMID:1115661
IAO_0000114: IAO_0000120
IAO_0000115: A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: url:http://en.wikipedia.org/wiki/Pyrosequencing

recombinant vector
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600064
subclass of: COB_0000026
IAO_0000111: recombinant vector
IAO_0000114: IAO_0000123
IAO_0000115: 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.

restriction enzyme
type: Class
subclass of: PR_000000001
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0003824
IAO_0000111: restriction enzyme
IAO_0000112: The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
IAO_0000114: IAO_0000123
IAO_0000115: an enzyme that has a specific target cleavage sites within nucleic acids
IAO_0000117: Kevin Clancy, Bjoern Peters
IAO_0000232: 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments

DNA sequencing by synthesis assay
type: Class
subclass of: DNA sequencing assay
subclass of: Restriction
  on property: has specified input
  some values from: GO_0042575
IAO_0000112: Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing
IAO_0000114: IAO_0000123
IAO_0000115: A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html

NTP-2000
type: Class
subclass of: COB_0000026
subclass of: Restriction
  on property: is specified output of
  some values from: manufacturing
subclass of: Restriction
  on property: RO_0000087
  some values from: feed role
IAO_0000111: NTP-2000
IAO_0000114: IAO_0000123
IAO_0000115: a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
IAO_0000117: Jennifer Fostel, Bjoern Peters

single fragment library
type: Class
subclass of: COB_0000026
IAO_0000111: single fragment library
IAO_0000114: IAO_0000123
IAO_0000115: is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: fragment library

cloning vector
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: RO_0000087
    some values from: cloning vector role
subclass of: Restriction
  on property: is specified output of
  some values from: COB_0000110
IAO_0000111: cloning vector
IAO_0000114: IAO_0000123
IAO_0000115: A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.

restriction enzyme based cloning
type: Class
subclass of: OBI_0600064
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0302892
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: cloning vector role
    intersection of: Restriction
      on property: RO_0000081
      some values from: nucleic acid restriction enzyme digest
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: cloning insert role
    intersection of: Restriction
      on property: RO_0000081
      some values from: nucleic acid restriction enzyme digest
IAO_0000111: restriction enzyme based cloning
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Kevin Clancy, Bjoern Peters

Student's t-test
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: has specified output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
IAO_0000111: Student's t-test
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000119: WEB: http://en.wikipedia.org/wiki/T-test

material sample role
type: Class
subclass of: specimen role
IAO_0000111: material sample role
IAO_0000112: 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.
IAO_0000114: IAO_0000125
IAO_0000115: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
IAO_0000116: 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.
IAO_0000233: https://github.com/obi-ontology/obi/issues/1013

topologically preserved clustered data set
type: Class
subclass of: clustered data set
IAO_0000111: topologically preserved clustered data set
IAO_0000112: the output data set generated from a self-organizing map.
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000119: PERSON: James Malone

nucleic acid restriction enzyme digest
type: Class
equivalent class: Class
  intersection of: CHEBI_33696
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600050
      intersection of: Restriction
        on property: has specified input
        some values from: CHEBI_33696
      intersection of: Restriction
        on property: RO_0000057
        some values from: restriction enzyme
IAO_0000111: nucleic acid restriction enzyme digest
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Kevin Clancy, Bjoern Peters

immune response assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0006955
IAO_0000112: Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA.
IAO_0000114: IAO_0000123
IAO_0000115: An assay that determines information about an immune response
IAO_0000117: Bjoern Peters
IAO_0000117: Randi Vita
IAO_0000119: IEDB

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection process
  intersection of: Restriction
    on property: has specified input
    some values from: BFO_0000040
  intersection of: Restriction
    on property: has specified output
    some values from: material sample
IAO_0000111: material sampling process
IAO_0000114: IAO_0000123
IAO_0000115: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
IAO_0000118: sample collection
IAO_0000118: sampling
IAO_0000233: https://github.com/obi-ontology/obi/issues/1002

material sample
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: RO_0000087
    some values from: material sample role
IAO_0000111: material sample
IAO_0000112: 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.
IAO_0000114: IAO_0000123
IAO_0000115: A material entity that has the material sample role
IAO_0000117: OBI: workshop
IAO_0000118: sample
IAO_0000118: sample population
IAO_0000233: https://github.com/obi-ontology/obi/issues/1013

bisulfite sequencing assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CHEBI 4431
      intersection of: Restriction
        on property: BFO_0000051
        some values from: CHEBI_32875
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: DNA sequencing assay
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified input
  some values from: DNA extract
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: IAO_0000109
    intersection of: OBI_0001573
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
IAO_0000117: Philippe Rocca-Serra
IAO_0000117: Sagar Jain
IAO_0000119: url:https://en.wikipedia.org/wiki/Bisulfite_sequencing

CART
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
IAO_0000111: CART
IAO_0000114: IAO_0000122
IAO_0000115: A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
IAO_0000117: James Malone
IAO_0000118: classification and regression trees
IAO_0000119: BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.

study design independent variable
type: Class
subclass of: IAO_0000033
subclass of: Restriction
  on property: BFO_0000050
  some values from: OBI_0500000
IAO_0000111: independent variable specification
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000116: 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.
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000118: experimental factor
IAO_0000118: independent variable
IAO_0000119: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
IAO_0000232: 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.
ISA alternative term: study factor

study design dependent variable
type: Class
subclass of: IAO_0000033
subclass of: Restriction
  on property: BFO_0000050
  some values from: OBI_0500000
IAO_0000111: dependent variable specification
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000118: dependent variable
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
IAO_0000232: 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.

anticoagulant-containing test tube
type: Class
subclass of: test tube
subclass of: Restriction
  on property: RO_0002219
  some values from: Restriction
    on property: BFO_0000051
    some values from: Restriction
      on property: has grain
      some values from: CHEBI_32142
IAO_0000111: anticoagulant-containing test tube
IAO_0000114: IAO_0000120
IAO_0000115: A 'blue top' test tube that contains anticoagulant for storing blood specimens'
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

study design controlled variable
type: Class
subclass of: IAO_0000033
subclass of: Restriction
  on property: BFO_0000050
  some values from: OBI_0500000
IAO_0000111: controlled variable specification
IAO_0000112: 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.
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000116: In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000118: controlled variable
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Control_variable
IAO_0000232: 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.

human antithrombin-III in blood assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: scattered molecular aggregate
      intersection of: Restriction
        on property: has grain
        some values from: PR_000003252
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000032
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0007596
IAO_0000112: PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
IAO_0000114: IAO_0000122
IAO_0000115: An assay that measures the amount of antithrombin III in blood.
IAO_0000117: Alan Ruttenberg
IAO_0000118: AT-III assay
IAO_0000119: url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06

fluorescently labeled MHC multimer
type: Class
subclass of: COB_0000026
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0002744
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600038
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0000018
IAO_0000111: fluorescently labeled MHC multimer
IAO_0000114: IAO_0000123
IAO_0000115: 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

survival rate
type: Class
subclass of: IAO_0000109
IAO_0000111: survival rate
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Oliver He
IAO_0000119: adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate

recombinant BAC cloning
type: Class
subclass of: OBI_0600064
IAO_0000111: recombinant BAC cloning
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000119: http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome

multiple testing correction objective
type: Class
subclass of: OBI_0200186
IAO_0000111: multiple testing correction objective
IAO_0000112: Application of the Bonferroni correction
IAO_0000114: IAO_0000120
IAO_0000115: A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
IAO_0000118: multiple comparison correction objective
IAO_0000119: http://en.wikipedia.org/wiki/Multiple_Testing_Correction

statistical model validation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200188
subclass of: OBI_0200000
IAO_0000111: statistical model validation
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
IAO_0000117: Helen Parkinson
IAO_0000119: http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29

double blind study execution
type: Class
equivalent class: Class
  intersection of: treatment portion of study execution
  intersection of: Restriction
    on property: BFO_0000051
    all values from: Class
      complement of: Class
        union of: informing investigator of subject study arm
        union of: informing subject of study arm
subclass of: treatment portion of study execution
IAO_0000111: double blind study execution
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: http://clinicaltrials.gov/ct2/info/glossary#double
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

obsolete transcription factor binding site
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000002
IAO_0000119: SO:0000235
IAO_0000231: IAO_0000228
IAO_0000232: PLace_holder for sequence ontology term
IAO_0000233: https://github.com/obi-ontology/obi/issues/1553
IAO_0100001: SO_0000235
deprecated: true

glucometer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: glucometer
IAO_0000112: Diabetic patients use glucometers to determine their glucose levels
IAO_0000114: IAO_0000122
IAO_0000115: A measurement device with the function to measure and record the level/amount of glucose in a blood sample
IAO_0000117: PERSON:Frank Gibson
IAO_0000117: PERSON:Helen Parkinson
IAO_0000118: glucose meter
IAO_0000119: http://en.wikipedia.org/wiki/Glucose_meter

purification objective
type: Class
subclass of: separation into different composition objective
IAO_0000111: purification objective
IAO_0000112: the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON:Bjoern Peters
IAO_0000118: isolation objective
IAO_0000119: BP
IAO_0000232: 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality

obsolete_primary structure of protein
type: Class
subclass of: ObsoleteClass
IAO_0000112: SIINFEKL' is the primary structure of a peptide
IAO_0000115: 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
IAO_0000117: Person:Bjoern Peters
IAO_0000231: IAO_0000228
deprecated: true

capsule shell
type: Class
subclass of: BFO_0000040
IAO_0000111: capsule shell
IAO_0000114: IAO_0000120
IAO_0000115: a small rounded gelatinous container
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: http://www.golovchenko.org/cgi-bin/wnsearch#2n
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

recombinant phage cloning
type: Class
subclass of: OBI_0600064
IAO_0000111: recombinant phage cloning
IAO_0000112: Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Helen Parkinson
IAO_0000119: http://www.ncbi.nlm.nih.gov/books/bv.fcgi

cross linking
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified output
  some values from: COB_0000013
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: cross linking
IAO_0000112: cross linking can be used as a probe to link proteins together, to check protein protein interactions
IAO_0000114: IAO_0000120
IAO_0000115: A process in which bonds are created that link one polymer to another
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000119: http://en.wikipedia.org/wiki/Cross-link

spike train datum
type: Class
subclass of: IAO_0000109
IAO_0000111: spike train datum
IAO_0000112: Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
IAO_0000114: IAO_0000120
IAO_0000115: A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
IAO_0000116: needs more work to see exactly what the data set looks like - HP
IAO_0000117: Helen Parkinson, Alan Ruttenberg
IAO_0000118: spike train measurement
IAO_0000119: Jessica Turner, NIF

prothrombin time assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000032
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0007596
IAO_0000112: PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
IAO_0000114: IAO_0000120
IAO_0000115: An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample.
IAO_0000117: Alan Ruttenberg
IAO_0000119: url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06

denaturing
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_33696
    union of: PR_000000001
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: denaturing
IAO_0000112: Denaturing DNA in alcohol
IAO_0000114: IAO_0000123
IAO_0000115: Is a process in which the tertiary or secondary structure of a polymer is disrupted
IAO_0000119: http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29

informing investigator of subject study arm
type: Class
subclass of: COB_0000035
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Restriction
      on property: IAO_0000219
      some values from: Restriction
        on property: RO_0000053
        some values from: participant under investigation role
  intersection of: Restriction
    on property: RO_0000057
    some values from: Restriction
      on property: RO_0000087
      some values from: investigation agent role
IAO_0000111: informing investigator of subject study arm
IAO_0000112: Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process with the objective to make the investigator aware of which study arm a patient is participating in.
IAO_0000116: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

antithrombin-III berichrome assay
type: Class
subclass of: human antithrombin-III in blood assay
subclass of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: IAO_0000032
  intersection of: Restriction
    on property: RO_0000057
    some values from: Berichrom(r) Antithrombin III (A) Kit
  intersection of: Restriction
    on property: has specified output
    cardinality: 1
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000118: AT-III assay
IAO_0000119: url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06

material maintenance objective
type: Class
subclass of: IAO_0000005
IAO_0000111: material maintenance objective
IAO_0000114: IAO_0000122
IAO_0000115: An objective specification maintains some or all of the qualities of a material over time.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: PERSON: Bjoern Peters

presentation of stimulus
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: COB_0000022
    intersection of: Restriction
      on property: RO_0000087
      some values from: participant under investigation role
IAO_0000111: presentation of stimulus
IAO_0000112: The presentation of a flashing light to a monkey during reward training
IAO_0000114: IAO_0000120
IAO_0000115: A planned process with the objective to expose an organism to a stimulus.
IAO_0000117: Helen Parkinson, Jessica Turner, Dirk Derom
IAO_0000118: stimulation of organism
IAO_0000119: Helen Parkinson, Jessica Turner, Dirk Derom

spectrolyse heparin antifactor-Xa assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000032
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0007596
IAO_0000112: PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
IAO_0000114: IAO_0000120
IAO_0000115: An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration.
IAO_0000117: Alan Ruttenberg
IAO_0000119: url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06

amplified DNA
type: Class
equivalent class: Class
  intersection of: CHEBI_16991
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600058
subclass of: BFO_0000040
IAO_0000111: amplified DNA
IAO_0000112: Amplied DNA created by PCR
IAO_0000114: IAO_0000122
IAO_0000115: DNA that has been produced in an enzymatic amplification process
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000119: Alan Ruttenberg

informed consent process
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: has specified input
  some values from: NCBITaxon 9606
subclass of: Restriction
  on property: RO_0000057
  some values from: Restriction
    on property: RO_0000087
    some values from: investigation agent role
IAO_0000111: informed consent process
IAO_0000114: IAO_0000122
IAO_0000115: A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate.
IAO_0000116: 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.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: http://clinicaltrials.gov/ct2/info/glossary#informed
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

obsolete primary structure of DNA macromolecule
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues
IAO_0000116: placeholder for SO
IAO_0000117: BP et al
IAO_0000231: IAO_0000103
deprecated: true

measuring neural activity in the caudate nucleus assay
type: Class
subclass of: extracellular electrophysiology recording assay
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: An assay that measures neural activity in the caudate nucleus
IAO_0000117: Helen Parkinson
IAO_0000119: Dirk Derom, OBI
IAO_0000119: Jessica Turner, NIF

to be treated with active ingredient role
type: Class
subclass of: participant under investigation role
IAO_0000111: to be treated with active ingredient role
IAO_0000112: Role of a patient in a group treated with an active substance in a clinical trial
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: PERSON: Helen Parkinson
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

guar gum
type: Class
subclass of: BFO_0000040
IAO_0000111: guar gum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Helen Parkinson
IAO_0000119: http://en.wikipedia.org/wiki/Guar_gum

Berichrom(r) Antithrombin III (A) Kit
type: Class
subclass of: COB_0000026
IAO_0000111: Berichrom(r) Antithrombin III (A) Kit
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

micro electrode
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: micro electrode
IAO_0000112: A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Helen Parkinson, Jessica Turner, Dirk Derom
IAO_0000118: micro electrode measuring device
IAO_0000119: Jessica Turner, Dirk Derom

fucoidan
type: Class
subclass of: COB_0000013
IAO_0000111: fucoidan
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: Helen Parkinson
IAO_0000119: http://en.wikipedia.org/wiki/Fucoidan

calibration
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: BFO_0000051
  some values from: assay
subclass of: Restriction
  on property: has specified output
  some values from: measurement device
IAO_0000111: calibration
IAO_0000112: the process of using pH buffer adjust a pH meter
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: GROUP: OBI Philly workshop
IAO_0000119: WEB:http://en.wikipedia.org/wiki/calibration

anticoagulant tube storage of blood specimen
type: Class
subclass of: OBI_0302893
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      intersection of: anticoagulant-containing test tube
      intersection of: Restriction
        on property: RO_0002219
        some values from: OBI_0100017
IAO_0000111: anticoagulant tube storage of blood specimen
IAO_0000114: IAO_0000120
IAO_0000115: Storage of a blood specimen in a tube with anticoagulant
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

activated partial thromboplastin time assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: Class
        union of: blood specimen
        union of: OBI_0100016
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000416
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0007596
IAO_0000112: The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660)
IAO_0000114: IAO_0000120
IAO_0000115: An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy.
IAO_0000116: There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant).
IAO_0000117: Alan Ruttenberg
IAO_0000117: OBI call
IAO_0000118: aPTT assay
IAO_0000119: url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310

filled capsule
type: Class
subclass of: pill
subclass of: Restriction
  on property: BFO_0000051
  some values from: capsule shell
IAO_0000111: filled capsule
IAO_0000114: IAO_0000120
IAO_0000115: A pill in the form of a small rounded gelatinous container with medicine inside.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: http://www.golovchenko.org/cgi-bin/wnsearch#2n
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

single blind study execution
type: Class
equivalent class: Class
  intersection of: treatment portion of study execution
  intersection of: Restriction
    on property: BFO_0000051
    all values from: Class
      complement of: informing subject of study arm
subclass of: treatment portion of study execution
IAO_0000111: single blind study execution
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: http://clinicaltrials.gov/ct2/info/glossary#single
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

thrombin time assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000032
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0007596
IAO_0000112: PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
IAO_0000114: IAO_0000120
IAO_0000115: An assay that measures the time between the addition of the thrombin and the clot formation in plasma.
IAO_0000117: Alan Ruttenberg
IAO_0000119: url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06

recombinant YAC cloning
type: Class
subclass of: OBI_0600064
IAO_0000111: recombinant YAC cloning
IAO_0000112: Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Helen Parkinson
IAO_0000119: http://www.ncbi.nlm.nih.gov/books/bv.fcgi

to be treated with placebo role
type: Class
subclass of: participant under investigation role
IAO_0000111: to be treated with placebo role
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

treatment portion of study execution
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: BFO_0000050
  some values from: study design execution
IAO_0000111: treatment portion of study execution
IAO_0000114: IAO_0000120
IAO_0000115: A planned process, part of a study design execution, during which the treatment of subjects is ongoing
IAO_0000116: 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

pill
type: Class
subclass of: COB_0000026
IAO_0000111: pill
IAO_0000114: IAO_0000120
IAO_0000115: A dose of medicine or placebo in the form of a small pellet.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: http://www.golovchenko.org/cgi-bin/wnsearch#2n
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

research organization
type: Class
subclass of: organization
IAO_0000111: research organization
IAO_0000112: The SALK institute is a research organization.
IAO_0000114: IAO_0000123
IAO_0000115: An organization formed with a goal to have its members conduct investigations
IAO_0000117: Person:Bjoern Peters

obsolete_primary structure of sequence macromolecule
type: Class
subclass of: ObsoleteClass
IAO_0000115: 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
IAO_0000117: Person:Bjoern Peters
IAO_0000231: IAO_0000228
deprecated: true

DNA residue methylation
type: Class
subclass of: PATO_0001241
IAO_0000111: DNA residue methylation
IAO_0000114: IAO_0000123
IAO_0000115: a quality of a DNA residue that has a methyl group attached to it

measurement device
type: Class
equivalent class: Class
  intersection of: COB_0001300
  intersection of: Restriction
    on property: RO_0000085
    some values from: measure function
IAO_0000111: measurement device
IAO_0000112: A ruler, a microarray scanner, a Geiger counter.
IAO_0000114: IAO_0000122
IAO_0000115: A device in which a measure function inheres.
IAO_0000117: GROUP:OBI Philly workshop
IAO_0000119: OBI

high molecular weight DNA extract
type: Class
subclass of: DNA extract
IAO_0000111: high molecular weight DNA extract
IAO_0000112: Extraction of chromosomal DNA from mammalian cells by first isolating nucei
IAO_0000114: IAO_0000120
IAO_0000115: The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000119: OBI

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: NCBITaxon 9606
    union of: organization
  intersection of: Restriction
    on property: RO_0000087
    some values from: manufacturer role
subclass of: BFO_0000040
IAO_0000111: manufacturer
IAO_0000114: IAO_0000123
IAO_0000115: A person or organization that has a manufacturer role.

test tube
type: Class
subclass of: vial
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
IAO_0000111: test tube
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Bjoern Peters
IAO_0000118: collection tube
IAO_0000118: sample tube
IAO_0000119: http://en.wikipedia.org/wiki/Test_tube

oral ingestion of pill
type: Class
equivalent class: Class
  intersection of: oral administration
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: RO_0000081
        some values from: pill
  intersection of: Restriction
    on property: has specified input
    some values from: pill
IAO_0000111: oral ingestion of pill
IAO_0000115: An adding a material entity to target with the entity is a pill and the target is the mouth
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: COB_0000035
IAO_0000111: material maintenance
IAO_0000114: IAO_0000123
IAO_0000115: A planned process with the objective to maintain some or all of the characteristics of an input material over time.

labeled oligonucleotide
type: Class
subclass of: COB_0000026
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0002744
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600038
IAO_0000111: labeled oligonucleotide
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000116: 2010-01-31: Philippe Rocca-Serra placeholder
IAO_0000117: Person: Philippe Rocca-Serra

unblinding process
type: Class
subclass of: COB_0000035
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000050
    some values from: study design execution
  intersection of: Restriction
    on property: BFO_0000050
    some values from: informing subject of study arm
IAO_0000111: unblinding process
IAO_0000114: IAO_0000120
IAO_0000115: A planned process that is 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.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

subject agrees they understand informed consent document
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: BFO_0000050
  some values from: informed consent process
IAO_0000111: subject agrees they understand informed consent document
IAO_0000114: IAO_0000120
IAO_0000115: A planned process in which a subject receives an informed consent document and agrees that they have understood it.
IAO_0000116: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

informing subject of study arm
type: Class
subclass of: COB_0000035
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000050
    some values from: informed consent process
  intersection of: Restriction
    on property: RO_0000057
    some values from: Restriction
      on property: RO_0000087
      some values from: participant under investigation role
IAO_0000111: informing subject of study arm
IAO_0000112: Informing participants whether they are receiving a placebo or a treatment with an investigational compound.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process with the objective to make the subject aware of which study arm they are participating in.
IAO_0000116: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

Sysmex CA-6000 Coagulation Analyzer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000829
IAO_0000111: Sysmex CA-6000 Coagulation Analyzer
IAO_0000114: IAO_0000120
IAO_0000115: The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

obsolete hospital
type: Class
subclass of: ObsoleteClass
IAO_0000112: 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]
IAO_0000114: IAO_0000120
IAO_0000115: A medical organization at which sick or injured people are given clinical care
IAO_0000117: Person:Alan Ruttenberg
IAO_0000117: Person:Helen Parkinson
IAO_0000119: modified from the wording of the wordnet definition; http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
IAO_0000231: IAO_0000228
IAO_0000233: https://github.com/obi-ontology/obi/issues/1295
IAO_0100001: OMRSE_00000056
deprecated: true

obsolete primary structure of RNA molecule
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Person:Bjoern Peters
IAO_0000231: IAO_0000103
deprecated: true

test substance role
type: Class
subclass of: BFO_0000023
IAO_0000111: test substance role
IAO_0000112: fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: Group:OBI

polyA RNA extraction
type: Class
subclass of: OBI_0666666
IAO_0000111: polyA RNA extraction
IAO_0000114: IAO_0000120
IAO_0000115: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
IAO_0000117: Person: Chris Stoeckert
IAO_0000117: Person: Jie Zheng
IAO_0000119: UPenn Group

organellar RNA extraction
type: Class
subclass of: OBI_0666666
IAO_0000111: organellar RNA extraction
IAO_0000114: IAO_0000120
IAO_0000115: A RNA extraction process in which the desired output material is RNA in the organelle(s).
IAO_0000117: Person: Chris Stoeckert
IAO_0000117: Person: Jie Zheng
IAO_0000119: UPenn Group

obsolete_diethyl pyrocarbonate
type: Class
subclass of: ObsoleteClass
IAO_0000231: IAO_0000228
deprecated: true

record of missing knowledge
type: Class
subclass of: IAO_0000030
IAO_0000111: record of missing knowledge
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: An information content entity created to indicate that information about something is not available to the person recording it.
IAO_0000116: 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.
IAO_0000117: Bjoern Peters

western blot assay
type: Class
subclass of: OBI_0001978
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_16670
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_16670
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: IEDB
IAO_0000119: Philippe Rocca-Serra

total RNA extraction
type: Class
subclass of: OBI_0666666
IAO_0000111: total RNA extraction
IAO_0000114: IAO_0000120
IAO_0000115: A RNA extraction process in which total cellular and organelle RNA are extracted.
IAO_0000117: Person: Chris Stoeckert
IAO_0000117: Person: Jie Zheng
IAO_0000119: UPenn Group

obsolete intracellular material detection by flow cytometry assay
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000231: IAO_0000227
IAO_0100001: flow cytometry assay
IEDB alternative term: intracellular staining
deprecated: true

complementary nucleotide probe role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: CHEBI_33696
IAO_0000111: complementary nucleotide probe role
IAO_0000112: A primer in a PCR reaction. A probe on an Affymetrix chip.
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON:Bjoern Peters

record of unknown sex
type: Class
subclass of: record of missing knowledge
subclass of: Restriction
  on property: IAO_0000136
  some values from: PATO_0000047
IAO_0000111: record of unknown sex
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: a record indicating that the biological sex of an organism is not known.
IAO_0000116: 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.
IAO_0000117: Bjoern Peters

cytoplasmic RNA extraction
type: Class
subclass of: OBI_0666666
IAO_0000111: cytoplasmic RNA extraction
IAO_0000114: IAO_0000120
IAO_0000115: A RNA extraction process in which the desired output material is RNA in the cytoplasm.
IAO_0000117: Person: Chris Stoeckert
IAO_0000117: Person: Jie Zheng
IAO_0000119: UPenn Group

northern blot assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_33697
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
IAO_0000112: The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay.
IAO_0000114: IAO_0000123
IAO_0000115: An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
IAO_0000117: Philippe Rocca-Serra
IAO_0000117: Richard Scheuermann
IAO_0000118: northern blot

Likelihood-ratio test
type: Class
subclass of: OBI_0200000
IAO_0000111: Likelihood-ratio test
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Tina Boussard

nuclear RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is specified output of
  some values from: nuclear RNA extraction
IAO_0000111: nuclear RNA extract
IAO_0000112: 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)
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: UPenn Group

96-well neutralization assay
type: Class
subclass of: serum neutralization of viral infectivity assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400076
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400076
IAO_0000114: IAO_0000120
IAO_0000115: A serum neutralization of viral infectivity assay which is performed in a 96-well plate.
IAO_0000117: Bjoern Peters
IAO_0000117: Melanie Courtot
IAO_0000118: microneutralization assay

establishing cancer cell line
type: Class
subclass of: OBI_0001867
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0001906
IAO_0000111: establishing cancer cell line
IAO_0000112: Establishment of HeLa immortal cell line
IAO_0000114: IAO_0000123
IAO_0000115: 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
comment: Helen Parkinson

pattern matching objective
type: Class
subclass of: OBI_0200166
IAO_0000111: pattern matching objective
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: Tina Boussard
IAO_0000119: http://en.wikipedia.org/wiki/Pattern_matching

polyA RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is specified output of
  some values from: polyA RNA extraction
IAO_0000111: polyA RNA extract
IAO_0000112: 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.)
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: UPenn Group

single-nucleotide-resolution nucleic acid structure mapping assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: secondary structure of sequence macromolecule
IAO_0000114: IAO_0000120
IAO_0000115: An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: RNAO

viral hemagglutination assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: BFO_0000051
  some values from: induced hemagglutination
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
IAO_0000112: Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells.
IAO_0000114: IAO_0000120
IAO_0000115: An assay that quantifies viruses by their hemagglutination activity.
IAO_0000117: Bjoern Peters
IAO_0000117: Melanie Courtot
IAO_0000117: Randi Vita
IAO_0000118: HA
IAO_0000118: HI
IAO_0000118: viral haemagglutinin assay
IAO_0000119: url:http://en.wikipedia.org/wiki/Hemagglutination_assay

serum neutralization of viral infectivity assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100017
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: NCBITaxon_10239
  intersection of: Restriction
    on property: has specified input
    some values from: NCBITaxon_10239
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0097282
IAO_0000114: IAO_0000120
IAO_0000115: An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
IAO_0000117: Bjoern Peters
IAO_0000117: Melanie Courtot
IAO_0000118: influenza neutralization assay
IAO_0000119: url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/

pre-mortem specimen
type: Class
equivalent class: Class
  intersection of: specimen with pre- or post-mortem status
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
IAO_0000111: pre-mortem specimen
IAO_0000112: material obtained through a liver biopsy from a human patient
IAO_0000114: IAO_0000120
IAO_0000115: a specimen that was taken from a live organism
IAO_0000117: Bjoern Peters
IAO_0000119: MO_705 premortem

detection of specific nucleic acid polymers with complementary probes
type: Class
equivalent class: Class
  intersection of: analyte assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: CHEBI_33696
        intersection of: Restriction
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: analyte role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: CHEBI_33696
IAO_0000112: Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

viral hemagglutination inhibition assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: NCBITaxon_10239
  intersection of: Restriction
    on property: has specified input
    some values from: NCBITaxon_10239
subclass of: Restriction
  on property: BFO_0000051
  some values from: induced hemagglutination
IAO_0000112: 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.
IAO_0000115: An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors.
IAO_0000117: Bjoern Peters
IAO_0000117: Melanie Courtot
IAO_0000117: Randi Vita
IAO_0000118: HAI
IAO_0000118: HIA
IAO_0000118: biological activity
IAO_0000118: hemagglutination inhibition
IAO_0000118: viral haemagglutinin inhibition assay
IAO_0000119: OBI branch derived

cytoplasmic RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: cytoplasmic RNA extraction
IAO_0000111: cytoplasmic RNA extract
IAO_0000112: 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.)
IAO_0000114: IAO_0000120
IAO_0000115: A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000119: UPenn Group

cell line immortalization
type: Class
subclass of: OBI_0001867
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0001907
subclass of: Restriction
  on property: has specified output
  some values from: CLO_0009828
IAO_0000111: cell line immortalization
IAO_0000112: Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000116: 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.
IAO_0000117: Bjoern Peters
IAO_0000118: 'establishing immortal cell line through directed genetic modification'
IAO_0000119: OBI
comment: 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.

random primed DNA labeling
type: Class
subclass of: OBI_0600038
IAO_0000111: random primed DNA labeling
IAO_0000112: PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9.
IAO_0000114: IAO_0000120
IAO_0000115: a labeling in which random primers are used to uniformly label input DNA
IAO_0000116: need to add Klenow subunit of DNA polymerase I under material entity
IAO_0000117: Person: Bjoern Peters Person: Chris Stoeckert
IAO_0000117: Person: Philippe Rocca-Serra
IAO_0000119: 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.

RNA extract
type: Class
equivalent class: Class
  intersection of: nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0666666
  intersection of: Restriction
    on property: has grain
    some values from: CHEBI_33697
IAO_0000111: RNA extract
IAO_0000114: IAO_0000120
IAO_0000115: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: Group: UPenn Group

cell-cell killing assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Restriction
    on property: has specified input
    some values from: CL_0000000
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: GO_0001906
IAO_0000112: 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.
IAO_0000115: A cytometry assay that monitors a cell population to track how many are killed by other cells.
IAO_0000117: IEDB
IAO_0000119: IEDB

in vivo cell killing assay
type: Class
equivalent class: Class
  intersection of: cell-cell killing assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: COB_0000022
        intersection of: Restriction
IAO_0000112: 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.
IAO_0000115: A cell killing assay that measures if and how many target cells are killed within an organism.
IAO_0000117: IEDB
IAO_0000119: IEDB

secondary structure of sequence macromolecule
type: Class
subclass of: PATO_0001241
IAO_0000111: secondary structure of sequence macromolecule
IAO_0000114: IAO_0000002
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000117: Person: Philippe Rocca-Serra
IAO_0000119: Wikipedia

nuclear RNA extraction
type: Class
subclass of: OBI_0666666
IAO_0000111: nuclear RNA extraction
IAO_0000114: IAO_0000120
IAO_0000115: A RNA extraction process in which the desired output material is RNA in the nucleus.
IAO_0000117: Person: Chris Stoeckert
IAO_0000117: Person: Jie Zheng
IAO_0000119: UPenn Group

survival curve
type: Class
subclass of: IAO_0000573
subclass of: Restriction
  on property: IAO_0000136
  some values from: survival rate
IAO_0000111: survival curve
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000117: PERSON:James Malone
IAO_0000117: PERSON:Melanie Courtot
IAO_0000119: WEB: http://www.graphpad.com/www/book/survive.htm

cell proliferation assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: GO_0008283
IAO_0000112: Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
IAO_0000115: A cytometry assay which measures the degreee to which input cells are replicating.
IAO_0000117: IEDB
IAO_0000119: IEDB

Southern blot assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_16991
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_16991
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0302903
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: detection of specific nucleic acid polymers with complementary probes
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: BFO_0000029
IAO_0000112: PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing.
IAO_0000114: IAO_0000120
IAO_0000115: An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity.
IAO_0000117: Marcus Chibucos
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: Southern blot
IAO_0000119: OBI

real time polymerase chain reaction assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: BFO_0000051
  some values from: polymerase chain reaction
IAO_0000114: IAO_0000120
IAO_0000115: An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
IAO_0000117: Bjoern Peters
IAO_0000117: Melanie Courtot
IAO_0000118: Q-PCR
IAO_0000118: kinetic polymerase chain reaction
IAO_0000118: qPCR
IAO_0000118: quantitative real time polymerase chain reaction
IAO_0000119: url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction

protein extract
type: Class
subclass of: extract
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000000001
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302884
IAO_0000111: protein extract
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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,
IAO_0000117: Person: Philippe Rocca-Serra
IAO_0000119: OBI & wikipedia

total RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: total RNA extraction
IAO_0000111: total RNA extract
IAO_0000112: Extraction of total RNA from cells with Qiagen mini RNeasy kit
IAO_0000114: IAO_0000120
IAO_0000115: A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: UPenn Group

secondary structure of RNA molecule
type: Class
subclass of: secondary structure of sequence macromolecule
IAO_0000111: secondary structure of RNA molecule
IAO_0000112: PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
IAO_0000114: IAO_0000123
IAO_0000116: 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
IAO_0000117: Person: Philippe Rocca-Serra

DEPC structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: RNA ontology

organellar RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: organellar RNA extraction
IAO_0000111: organellar RNA extract
IAO_0000112: Extraction of organellar RNA from plant cells using organellar RNA binding protein.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: UPenn Group

post mortem specimen
type: Class
equivalent class: Class
  intersection of: specimen with pre- or post-mortem status
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
IAO_0000111: post mortem specimen
IAO_0000112: the spleen taken from a dead mouse
IAO_0000114: IAO_0000120
IAO_0000115: a specimen that was taken from a dead organism
IAO_0000117: Bjoern Peters
IAO_0000119: MO_416 postmortem

in vitro cell killing assay
type: Class
equivalent class: Class
  intersection of: cell-cell killing assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: OBI_0100060
        intersection of: Restriction
IAO_0000112: 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.
IAO_0000115: A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
IAO_0000117: IEDB
IAO_0000119: IEDB

reporter cell line analyte detection bioassay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CLO_0000031
  intersection of: Restriction
    on property: has specified input
    some values from: CLO_0000031
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0600024
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

sequence feature annotation
type: Class
subclass of: IAO_0000030
IAO_0000111: sequence feature annotation
IAO_0000114: IAO_0000120
IAO_0000115: Information about a sequence region
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters
comment: place holder for sequence ontology term

induced hemagglutination
type: Class
subclass of: COB_0000110
subclass of: Restriction
  on property: has specified input
  some values from: CL_0000232
IAO_0000111: induced hemagglutination
IAO_0000114: IAO_0000120
IAO_0000115: The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
IAO_0000116: 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'.
IAO_0000117: person: Bjoern Peters
IAO_0000117: person: Melanie Courtot
IAO_0000118: hemeagglutination
IAO_0000119: WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination

supplying
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: has specified input
  some values from: BFO_0000040
IAO_0000111: supplying
IAO_0000112: Jackson Labs supplies mouse strains.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process with the objective to provide material entities to be used in an investigation.
IAO_0000117: Jennifer Fostel
IAO_0000119: Jennifer Fostel
IAO_0000232: 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.

labeled DNA extract
type: Class
equivalent class: Class
  intersection of: labeled nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has specified input
        some values from: DNA extract
  intersection of: Restriction
    on property: has grain
    some values from: CHEBI_16991
IAO_0000111: labeled DNA extract
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000117: Group: OBI group
IAO_0000119: Group: OBI group

cloacal specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: RO_0001000
      some values from: UBERON_0000162
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600005
IAO_0000111: cell specimen
IAO_0000112: type of sample used in the PCIRN influenza network
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Melanie Courtot
IAO_0000119: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf

radio immuno assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000053
        some values from: PATO_0001741
IAO_0000112: To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

real time reverse-transcription polymerase chain reaction assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0600028
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: real time polymerase chain reaction assay
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000030
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0010467
IAO_0000114: IAO_0000120
IAO_0000115: An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay.
IAO_0000117: Bjoern Peters
IAO_0000117: Melanie Courtot
IAO_0000118: RRT-PCR
IAO_0000118: RT-rt PCR
IAO_0000118: qRT-PCR

X-ray crystallography 3D molecular structure determination assay
type: Class
subclass of: OBI_0003117
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: X-ray source
  intersection of: Restriction
    on property: has specified input
    some values from: X-ray source
IAO_0000112: Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
IAO_0000115: A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest.
IAO_0000117: IEDB
IAO_0000119: IEDB

promoter activity detection by reporter gene assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: CL_0000000
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0001046
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

nasopharyngeal aspirate specimen
type: Class
subclass of: OBI_2000007
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: RO_0001000
    some values from: UBERON_0001728
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0002785
IAO_0000111: nasopharyngeal aspirate specimen
IAO_0000112: type of sample used in the PCIRN influenza network
IAO_0000114: IAO_0000120
IAO_0000115: A specimen which derives from nasopharyngeal mucosa after aspiration.
IAO_0000117: PERSON: Melanie Courtot
IAO_0000119: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf

freezing storage
type: Class
subclass of: OBI_0302893
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0001985
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0001985
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
IAO_0000111: freezing storage
IAO_0000112: a fozen pellet used for later assay
IAO_0000114: IAO_0000120
IAO_0000115: A storage process in temperature that maintenance the frozen status of the stored entities.
IAO_0000116: 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.
IAO_0000117: Person: Alan Ruttenberg, Mathias Brochhausen
IAO_0000119: MO_481 frozen_storage
IAO_0000119: OBI

flow cytometry assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: BFO_0000034
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400044
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: fluorescence detection assay
      intersection of: OBI_0003368
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000118: FACS
IAO_0000119: IEDB

nasal swab specimen
type: Class
equivalent class: Class
  intersection of: OBI_2000006
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0002600
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: UBERON_0001826
IAO_0000111: nasal swab specimen
IAO_0000112: type of sample used in the PCIRN influenza network
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Melanie Courtot
IAO_0000119: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf

Dulbecco's modified Eagle medium
type: Class
subclass of: culture medium
subclass of: Class
  intersection of: Restriction
    on property: has grain
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has grain
    some values from: CHEBI_33709
IAO_0000111: Dulbecco's modified Eagle medium
IAO_0000114: IAO_0000123
IAO_0000115: A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
IAO_0000116: Logical definition should contain all components listed in textual definition at some point.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000118: D-MEM
IAO_0000118: DMEM

animal euthanization
type: Class
subclass of: OBI_0600006
subclass of: Restriction
  on property: has specified input
  some values from: NCBITaxon 7742
IAO_0000111: animal euthanization
IAO_0000112: Rats were euthanized with CO2
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Helen Parkinson and Melissa Haendel
IAO_0000118: animal sacrifice
IAO_0000119: Melissa Haendel
comment: may later be refined with more specific list of organisms

cytometric bead array assay
type: Class
equivalent class: Class
  intersection of: analyte assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_1000207
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: fluorescence detection assay
      intersection of: OBI_0003368
IAO_0000112: Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture.
IAO_0000115: An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest.
IAO_0000117: IEDB
IAO_0000118: Luminex assay
IAO_0000119: IEDB

labeled RNA extract
type: Class
equivalent class: Class
  intersection of: labeled nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has specified input
        some values from: RNA extract
  intersection of: Restriction
    on property: has grain
    some values from: CHEBI_33697
IAO_0000111: labeled RNA extract
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000117: Group: OBI group
IAO_0000119: Group: OBI group

frozen specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: freezing storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
IAO_0000111: frozen specimen
IAO_0000112: Frozen blood plasma
IAO_0000114: IAO_0000123
IAO_0000115: A specimen that has been frozen in order to store it.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: MO_610 frozen_sample

surface plasmon resonance binding assay
type: Class
subclass of: binding assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: surface plasmon resonance instrument
  intersection of: Restriction
    on property: has specified input
    some values from: surface plasmon resonance instrument
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

labeled specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: BFO_0000051
    some values from: OBI_0002744
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600038
IAO_0000111: labeled specimen
IAO_0000114: IAO_0000123
IAO_0000115: A specimen that has been modified in order to be able to detect it in future experiments
IAO_0000116: added during call 3/1/2010
IAO_0000117: OBI group

infectious agent
type: Class
equivalent class: Restriction
  on property: RO_0000053
  some values from: OBI_1110093
subclass of: COB_0000022
IAO_0000111: infectious agent
IAO_0000114: IAO_0000123
IAO_0000115: is a material entity bearing the disposition to infect an organism
IAO_0000117: IEDB
IAO_0000119: IEDB

obsolete_ambidexterious handedness
type: Class
subclass of: ObsoleteClass
IAO_0000231: IAO_0000103
deprecated: true

lyophilization storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: has specified input
  some values from: BFO_0000040
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
IAO_0000111: lyophilization storage
IAO_0000114: IAO_0000123
IAO_0000115: a storage process with input material entity and output freeze dried material for long time storage
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed

material combination function
type: Class
subclass of: BFO_0000034
IAO_0000111: material combination function
IAO_0000112: A stirrer has a material combination function
IAO_0000114: IAO_0000120
IAO_0000115: A material separation function is a function that decreases the resolution between two or more material entities.
IAO_0000117: Helen Parkinson
IAO_0000119: OBI

obsolete_training service provider role
type: Class
subclass of: ObsoleteClass
IAO_0000112: EBI provides training on databases and tools and has a training service provider role
IAO_0000114: IAO_0000123
IAO_0000115: a service provider role which is realized by a servicer provider organization performing some training
IAO_0000117: PERSON:Helen Parkinson
IAO_0000119: OBI
IAO_0000231: IAO_0000103
deprecated: true

calorimeter
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: calorimeter
IAO_0000114: IAO_0000120
IAO_0000115: A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000118: calorimetry instrument?
IAO_0000119: http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm

study intervention
type: Class
subclass of: COB_0000035
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0100051
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0100051
subclass of: Restriction
  on property: BFO_0000050
  some values from: Class
    intersection of: study design execution
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Restriction
        on property: RO_0000059
        some values from: intervention design
IAO_0000111: study intervention
IAO_0000114: IAO_0000120
IAO_0000115: A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: GROUP: OBI

material separation device
type: Class
equivalent class: Class
  intersection of: COB_0001300
  intersection of: Restriction
    on property: RO_0000085
    some values from: material separation function
IAO_0000111: material separation device
IAO_0000112: flow cytometer
IAO_0000114: IAO_0000123
IAO_0000115: A device with a separation function realized in a planed process

positron emission tomography scanner
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
IAO_0000111: positron emission tomography scanner
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000118: PET scanner?
IAO_0000119: http://en.wikipedia.org/wiki/Positron_emission_tomography

intramuscular injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: syringe
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: RO_0000081
        some values from: UBERON_0001134
IAO_0000111: intramuscular injection
IAO_0000115: 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
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: micromanipulator
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000119: http://en.wikipedia.org/wiki/Micromanipulator

obsolete_material access provider role
type: Class
subclass of: ObsoleteClass
IAO_0000112: A person or organization who provides access to a DNA sequencer.
IAO_0000114: IAO_0000123
IAO_0000115: a service provider role which is realized by a servicer provider organization performing access to some material
IAO_0000117: PERSON:Helen Parkinson
IAO_0000119: OBI
IAO_0000231: IAO_0000103
deprecated: true

obsolete_left handedness
type: Class
subclass of: ObsoleteClass
IAO_0000231: IAO_0000228
deprecated: true

categorical measurement datum
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: has value specification
  some values from: OBI_0001930
IAO_0000111: categorical measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: A measurement datum that is reported on a categorical scale.
IAO_0000117: Bjoern Peters
IAO_0000118: nominal mesurement datum
IAO_0000119: Bjoern Peters

training process
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: training objective
subclass of: BFO_0000015
IAO_0000111: training process
IAO_0000112: e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility
IAO_0000114: IAO_0000123
IAO_0000115: a process that achieves a training objective

optical microscope
type: Class
subclass of: OBI_0400169
IAO_0000111: optical microscope
IAO_0000114: IAO_0000120
IAO_0000115: A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
IAO_0000117: PERSON:Bjoern Peters

service consumer role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: Class
    union of: NCBITaxon 9606
    union of: organization
IAO_0000111: service consumer role
IAO_0000112: A biologist who uses a sequencing services fulfills the role of a service consumer
IAO_0000114: IAO_0000120
IAO_0000115: a role which inheres in a person who uses a service
IAO_0000117: Person:Helen Parkinson
IAO_0000119: OBI

intradermal injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: syringe
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: RO_0000081
        some values from: UBERON_0002067
IAO_0000111: intradermal injection
IAO_0000115: 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
IAO_0000117: PERSON: Melanie Courtot

chemical cleavage
type: Class
subclass of: BFO_0000015
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100051
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: COB_0000013
    intersection of: Restriction
      on property: RO_0000087
      some values from: reagent role
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: chemical cleavage
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON:Philippe Rocca-Serra
IAO_0000119: RNA ontology group

handedness assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: PATO_0002201
IAO_0000112: The Edinburgh handedness assay is a specific method of determing handedness
IAO_0000114: IAO_0000120
IAO_0000115: An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
IAO_0000117: Helen Parkinson
IAO_0000118: handedness test
IAO_0000119: url:http://en.wikipedia.org/wiki/Handedness

vibration isolation table
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: vibration isolation table
IAO_0000114: IAO_0000120
IAO_0000115: A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000119: United States Patent 6877711

sterilization function
type: Class
subclass of: BFO_0000034
IAO_0000111: sterilization function
IAO_0000114: IAO_0000123
IAO_0000115: a function to remove viable organisms from an input material

service provider role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: Class
    union of: NCBITaxon 9606
    union of: organization
subclass of: Restriction
  on property: BFO_0000054
  all values from: COB_0000035
IAO_0000111: service provider role
IAO_0000112: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: PERSON:Helen Parkinson

oscilloscope
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: oscilloscope
IAO_0000114: IAO_0000120
IAO_0000115: 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).
IAO_0000117: PERSON:Bjoern Peters
IAO_0000119: http://en.wikipedia.org/wiki/Oscilloscope

accessed material role
type: Class
subclass of: BFO_0000023
IAO_0000111: accessed material role
IAO_0000112: the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
IAO_0000114: IAO_0000123
IAO_0000115: is realized in a planned process where the bearer participates
IAO_0000116: 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

paraffin specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: paraffin storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
IAO_0000111: paraffin specimen
IAO_0000112: liver tissue embedded in paraffin
IAO_0000114: IAO_0000123
IAO_0000115: a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: MO_990 paraffin_sample

compound treatment design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: study intervention
        intersection of: administration of material to specimen
IAO_0000111: compound treatment design
IAO_0000114: IAO_0000120
IAO_0000115: an intervention design in which the treatment is the administration of a compound
IAO_0000116: This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: MO_555 compound_treatment_design

oral administration
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: RO_0000081
        some values from: UBERON_0000165
IAO_0000111: oral administration
IAO_0000115: An administering substance in vivo into the mouth of an organism
IAO_0000117: PERSON: Melanie Courtot

processed specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Class
    intersection of: COB_0000026
    intersection of: OBI_0100051
IAO_0000111: processed specimen
IAO_0000114: IAO_0000122
IAO_0000115: A specimen that has been intentionally physically modified.
IAO_0000116: A tissue sample that has been sliced and stained for a histology study.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

subcutaneous injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: syringe
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: RO_0000081
        some values from: UBERON_0002072
IAO_0000111: subcutaneous injection
IAO_0000115: 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
IAO_0000117: PERSON: Melanie Courtot

electrode puller
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: electrode puller
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000119: http://faculty.plattsburgh.edu/donald.slish/Puller1.html

obsolete_handedness
type: Class
subclass of: ObsoleteClass
IAO_0000231: IAO_0000228
IAO_0100001: PATO_0002201
deprecated: true

self reported handedness assessment
type: Class
subclass of: handedness assay
subclass of: Restriction
  on property: has specified output
  some values from: categorical measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: PATO_0002201
IAO_0000114: IAO_0000123
IAO_0000115: An assay where a person makes a statement that indicates what handedness he has from a choice of different categories.

vibrotome
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
subclass of: Restriction
  on property: RO_0000085
  some values from: Restriction
    on property: BFO_0000054
    all values from: OBI_0600014
IAO_0000111: vibrotome
IAO_0000114: IAO_0000123
IAO_0000115: A preparation device that uses a vibrating razor blade to cut through tissue.

reagent application function
type: Class
subclass of: BFO_0000034
IAO_0000111: reagent application function
IAO_0000112: An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
IAO_0000114: IAO_0000120
IAO_0000115: A function that is realized when a reagent is automatically added to some research material.
IAO_0000117: PERSON: Nicole Vasilevsky, Matthew Brush
IAO_0000119: PERSON: Nicole Vasilevsky, Matthew Brush
IAO_0000232: 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?

addition of molecular tracer function
type: Class
subclass of: reagent application function
IAO_0000111: addition of molecular tracer function
IAO_0000112: Immunohistochemical labeling of tissue sections by an autostainer staining system.
IAO_0000114: IAO_0000120
IAO_0000115: A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen.
IAO_0000117: PERSON: Nicole Vasilevsky, Matthew Brush
IAO_0000119: PERSON: Nicole Vasilevsky, Matthew Brush

training objective
type: Class
subclass of: IAO_0000005
IAO_0000111: training objective
IAO_0000112: A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package
IAO_0000114: IAO_0000120
IAO_0000115: An objective specification which is fulfilled by the provision of some training.
IAO_0000117: Helen Parkinson
IAO_0000119: OBI

categorical label
type: Class
subclass of: IAO_0000009
IAO_0000111: categorical label
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

in live cell assay
type: Class
subclass of: assay
IAO_0000114: IAO_0000123
IAO_0000115: An assay in which a measurement is made by observing entities located in a live cell.

lyophilized specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: lyophilization storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
IAO_0000111: lyophilized specimen
IAO_0000112: freezing dried DNA
IAO_0000114: IAO_0000123
IAO_0000115: a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: MO_589 freeze_dried_sample

in live organism assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0001025
      some values from: Class
        intersection of: COB_0000022
        intersection of: Restriction
IAO_0000112: Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
IAO_0000114: IAO_0000120
IAO_0000115: An assay in which a measurement is made by observing entities located in an organism.
IAO_0000117: Bjoern Peters
IAO_0000118: in vivo assay

container
type: Class
equivalent class: Class
  intersection of: COB_0001300
  intersection of: Restriction
    on property: RO_0000085
    some values from: contain function
IAO_0000111: container
IAO_0000114: IAO_0000123
IAO_0000115: A device that can be used to restrict the location of material entities over time
IAO_0000116: 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?)
IAO_0000117: PERSON: Bjoern Peters

obsolete device
type: Class
subclass of: ObsoleteClass
IAO_0000112: A voltmeter is a measurement device which is intended to perform some measure function.
IAO_0000112: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
IAO_0000114: IAO_0000122
IAO_0000115: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000117: PERSON: Helen Parkinson
IAO_0000118: instrument
IAO_0000119: OBI development call 2012-12-17.
IAO_0000231: IAO_0000228
IAO_0100001: COB_0001300
deprecated: true

dose specification
type: Class
subclass of: IAO_0000033
IAO_0000111: dose specification
IAO_0000112: a protocol specifying to administer 1 ml of vaccine to a mouse
IAO_0000114: IAO_0000123
IAO_0000115: a directive information entity that describes the dose that will be administered to a target

scalar score from composite inputs
type: Class
subclass of: IAO_0000109
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0200000
subclass of: Restriction
  on property: IAO_0000004
  min cardinality: 1
IAO_0000111: scalar score from composite inputs
IAO_0000114: IAO_0000120
IAO_0000115: A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
IAO_0000116: 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.
IAO_0000117: Person: Jessica Turner
IAO_0000118: questionaire score
IAO_0000119: Person: Jessica Turner
IAO_0000232: JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?

fresh specimen
type: Class
subclass of: specimen with known storage state
IAO_0000111: fresh specimen
IAO_0000112: a liver freshly removed from a rat
IAO_0000114: IAO_0000123
IAO_0000115: a specimen that is output of a specimen creation process used for an investigation without storage.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: MO_730 fresh_sample

obsolete_electrically powered device
type: Class
subclass of: ObsoleteClass
IAO_0000115: a processed material created to have a function and which requires electrical power to execute
IAO_0000231: IAO_0000103
deprecated: true

sequence data
type: Class
subclass of: Class
  intersection of: IAO_0000027
  intersection of: Restriction
    on property: IAO_0000136
    some values from: SO_0000001
IAO_0000111: sequence data
IAO_0000112: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
IAO_0000114: IAO_0000120
IAO_0000115: A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
IAO_0000117: Person:Chris Stoeckert
IAO_0000119: GROUP: OBI

obsolete_right handedness
type: Class
subclass of: ObsoleteClass
IAO_0000231: IAO_0000228
deprecated: true

cell-cell binding detection by flow cytometry assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: flow cytometry assay
      intersection of: OBI_0003368
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: OBI_0001588
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

handedness categorical measurement datum
type: Class
subclass of: categorical measurement datum
subclass of: Restriction
  on property: IAO_0000221
  some values from: PATO_0002201
subclass of: Restriction
  on property: has category label
  some values from: Class
    one of: OBI_0000958
    one of: OBI_0000979
    one of: OBI_0000998
IAO_0000111: handedness categorical measurement datum
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: PERSON:Alan Ruttenberg
IAO_0000117: PERSON:Jessica Turner

paraffin storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: COB_0000022
    union of: UBERON_0000465
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
IAO_0000111: paraffin storage
IAO_0000114: IAO_0000120
IAO_0000115: a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: UPenn Group
comment: need to specify paraffin or wax is one of specified input of the process

in container assay
type: Class
subclass of: assay
IAO_0000114: IAO_0000123
IAO_0000115: An assay in which a measurement is made by observing entities located in a container.

obsolete_protocol service provider role
type: Class
subclass of: ObsoleteClass
IAO_0000112: DNA sequencing of a sample by a core lab which returns data to the consumer
IAO_0000114: IAO_0000120
IAO_0000115: a service provider role which is realized by a servicer provider organization performing a protocol execution
IAO_0000117: PERSON:Helen Parkinson
IAO_0000231: IAO_0000103
deprecated: true

agar stab specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: agar stab storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
IAO_0000111: agar stab specimen
IAO_0000114: IAO_0000123
IAO_0000115: a specimen that is output of a process that cell culture inoculated into agar for long term storage.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: MO_971 agar_stab

computed tomography scanner
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
IAO_0000111: computed tomography scanner
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000118: CT scanner
IAO_0000118: X-ray computed tomography scanner
IAO_0000119: http://en.wikipedia.org/wiki/X-ray_computed_tomography

intranasal mucosal administration
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: RO_0000081
        some values from: UBERON_0005022
IAO_0000111: intranasal mucosal administration
IAO_0000115: The administration of a substance into the intranasal mucosis of an organism
IAO_0000117: PERSON: Melanie Courtot

dose
type: Class
subclass of: IAO_0000109
IAO_0000111: dose
IAO_0000112: An organism has been injected 1ml of vaccine
IAO_0000114: IAO_0000123
IAO_0000115: 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.

growth condition intervention design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: study intervention
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: growth environment
IAO_0000111: growth condition intervention design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which the independent variable is the environmental condition in which the specimen is growing
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: MO_588 growth_condition_design

obsolete_DNA sequencing training service
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
IAO_0000231: IAO_0000103
deprecated: true

obsolete_general scalar measurement datum
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000124
IAO_0000231: IAO_0000103
deprecated: true

obsolete performing a diagnosis
type: Class
subclass of: ObsoleteClass
IAO_0000112: Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache.
IAO_0000114: IAO_0000123
IAO_0000115: The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
IAO_0000231: IAO_0000103
IAO_0000233: https://github.com/obi-ontology/obi/issues/623
deprecated: true

PCR instrument
type: Class
subclass of: OBI_0400116
subclass of: Restriction
  on property: RO_0000085
  some values from: Restriction
    on property: BFO_0000054
    all values from: polymerase chain reaction
IAO_0000111: PCR instrument
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000116: 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.

electron microscope
type: Class
subclass of: OBI_0400169
IAO_0000111: electron microscope
IAO_0000114: IAO_0000123
IAO_0000115: A microscope that produces an image of an object by targeting it with an electron beam

Edinburgh score
type: Class
subclass of: scalar score from composite inputs
subclass of: Restriction
  on property: IAO_0000221
  some values from: PATO_0002201
subclass of: Restriction
  on property: IAO_0000004
  min cardinality: 1
IAO_0000111: Edinburgh score
IAO_0000114: IAO_0000123
IAO_0000115: A score that measures the dominance of a person's right or left hand in everyday activities.
IAO_0000117: Person: Alan Ruttenberg
IAO_0000117: Person:Jessica Turner
IAO_0000119: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
IAO_0000119: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html

DNA sequencing service
type: Class
equivalent class: Class
  intersection of: OBI_0001904
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: DNA sequencing assay
subclass of: Restriction
  on property: BFO_0000055
  some values from: service consumer role
subclass of: Restriction
  on property: BFO_0000055
  some values from: service provider role
IAO_0000111: DNA sequencing service
IAO_0000114: IAO_0000123
IAO_0000115: A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
IAO_0000116: Eagle-i will supply better English definition

service provision objective
type: Class
subclass of: IAO_0000005
IAO_0000111: service provision objective
IAO_0000112: A sequencing centre has a service provision objective
IAO_0000114: IAO_0000120
IAO_0000115: An objective which is fulfilled by the provision of some service e.g. a training service
IAO_0000117: Helen Parkinson
IAO_0000119: OBI

intravenous injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: syringe
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: RO_0000081
        some values from: UBERON_0001638
IAO_0000111: intravenous injection
IAO_0000115: 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
IAO_0000117: PERSON: Melanie Courtot

administration of material to specimen
type: Class
subclass of: material combination
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: RO_0000081
      some values from: OBI_0100051
IAO_0000111: administration of material to specimen
IAO_0000112: Staining cells in a tissue slice with a dye.
IAO_0000114: IAO_0000120
IAO_0000115: The directed combination of a material entity with a specimen.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

device creation objective
type: Class
subclass of: material transformation objective
IAO_0000111: device creation objective
IAO_0000114: IAO_0000120
IAO_0000115: an objective which aims to create a device with a specified function
IAO_0000117: PERSON: Helen Parkinson
IAO_0000119: OBI

growth environment
type: Class
subclass of: BFO_0000040
IAO_0000111: growth environment
IAO_0000114: IAO_0000120
IAO_0000115: The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
IAO_0000116: Right now this may be incomplete. Should also cover e.g. sound, light as well.
IAO_0000117: PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
IAO_0000119: OBI group

questionnaire
type: Class
subclass of: IAO_0000310
IAO_0000111: questionnaire
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000116: Need to clarify if this is a document or a directive information entity (or what their connection is))
IAO_0000117: PERSON: Jessica Turner
IAO_0000119: Merriam-Webster

Edinburgh handedness assay
type: Class
subclass of: handedness assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: NCBITaxon 9606
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: NCBITaxon 9606
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: Edinburgh score
subclass of: Restriction
  on property: has specified input
  has value: OBI_0001004
IAO_0000112: Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)"
IAO_0000114: IAO_0000120
IAO_0000115: An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
IAO_0000117: Alan Ruttenberg
IAO_0000117: Gully Burns (orcid:0000-0003-1493-865X)
IAO_0000117: Jessica Turner
IAO_0000119: PMID:5146491
IAO_0000119: url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory

Faraday cage
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: Faraday cage
IAO_0000114: IAO_0000120
IAO_0000115: A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000118: Faraday shield
IAO_0000119: Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
IAO_0000232: isolation function? HP

agar stab storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
IAO_0000111: agar stab storage
IAO_0000114: IAO_0000120
IAO_0000115: a storage process with input cell culture and agar and output agar stab for long time storage
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: UPenn Group
comment: need to specify that agar is one of input for this process

RNASE CL3 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000025478
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025478
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:16453415
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using RNAse CL3
IAO_0000119: RNA ontology

CMCT structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:2422386 and PMID:2446263
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using CMCT probe
IAO_0000119: RNA ontology

image creation
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: has specified input
  some values from: BFO_0000040
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000101
IAO_0000111: image acquisition
IAO_0000112: Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
IAO_0000114: IAO_0000123
IAO_0000115: A planned process that captures an image of an object.
IAO_0000117: PERSON: Jie Zheng
IAO_0000118: image acquisition

MPE-Fe(II) structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:6209709
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using Fe-MP probe
IAO_0000119: RNA ontology

obsolete_qualitative binding detection assay
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
IAO_0000231: IAO_0000103
deprecated: true

nucleic acid extract
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0666667
IAO_0000111: nucleic acid extract
IAO_0000114: IAO_0000120
IAO_0000115: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
IAO_0000117: Person: Jie Zheng
IAO_0000119: UPenn Group

ENU structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:7002606 and PMID:2446263
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using ENU probe
IAO_0000119: RNA ontology

RNASE V1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000025477
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025477
subclass of: Restriction
  on property: has specified output
  some values from: secondary structure of RNA molecule
IAO_0000112: PMID:7031604
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using RNAse V1
IAO_0000119: RNA ontology

kethoxal structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: single nucleotide resolution mapping assay using Kethoxal probe
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: RNA ontology

single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
type: Class
equivalent class: Class
  intersection of: single-nucleotide-resolution nucleic acid structure mapping assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: enzyme
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: secondary structure of sequence macromolecule
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: RNAO and OBI
IAO_0000233: https://github.com/obi-ontology/obi/issues/808

DMS structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:6159633 and PMID:2446263
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using DMS probe
IAO_0000119: RNA Ontology

DNASE 1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000006592
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000006592
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:3773731
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: DNAse footprinting assay
IAO_0000118: single nucleotide resolution mapping assay using DNAse I
IAO_0000119: RNA ontology

single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
type: Class
equivalent class: Class
  intersection of: single-nucleotide-resolution nucleic acid structure mapping assay
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: COB_0000013
        intersection of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: secondary structure of sequence macromolecule
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes.
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: RNAO and OBI

Rhodium DNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:2843807
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using Rhodium probe
IAO_0000119: RNA ontology

RNA ADA I RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000003745
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000003745
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:7527340
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using RNA adenosine deaminase I
IAO_0000119: RNA ontology

Lead structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:2686708
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using Lead probe
IAO_0000119: RNA ontology

RNASE T2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000014060
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000014060
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:6207483
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using RNAse T2
IAO_0000119: RNA ontology

gene dosage assay
type: Class
subclass of: assay
IAO_0000114: IAO_0000120
IAO_0000115: An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene.
IAO_0000117: Bjoern Peters
IAO_0000119: David Osumi Sutherland

Fe-BABE RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID: 7862644
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using Fe-BABE probe
IAO_0000119: RNA ontology

RNASE U2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000025475
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025475
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:409999
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using RNAse U2
IAO_0000119: RNA ontology

binding constant determination assay
type: Class
subclass of: binding assay
subclass of: Restriction
  on property: has specified output
  some values from: binding constant
IAO_0000112: Determination of KD value for an antibody binding a protein using a BIACORE assay.
IAO_0000114: IAO_0000123
IAO_0000115: A binding assay where the specified output is a binding constant
IAO_0000117: Bjoern Peters
IAO_0000117: Jason Greenbaum
IAO_0000117: Randi Vita
IAO_0000119: IEDB

NMIA RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID: 15796531
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: SHAPE mapping assay
IAO_0000118: single nucleotide resolution mapping assay using NMIA probe
IAO_0000119: RNA ontology

Terbium RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:10772868
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using Terbium probe
IAO_0000119: RNA ontology

feature extraction
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: has specified input
  some values from: IAO_0000101
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000027
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200005
IAO_0000111: feature extraction
IAO_0000114: IAO_0000123
IAO_0000115: A planed process with objective of obtaining quantified values from an image.
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: MO_928: feature_extraction

OH-radical structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:2501870
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: MOHCA assay
IAO_0000118: OH footprinting assay
IAO_0000118: single nucleotide resolution mapping assay using OH-radical probe
IAO_0000119: RNA ontology

RNASE T1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000025467
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025467
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:114514
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using RNAse T1
IAO_0000119: RNA ontology

array image creation
type: Class
subclass of: image creation
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0400147
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000101
IAO_0000111: array image acquisition
IAO_0000114: IAO_0000123
IAO_0000115: An image creation process that generate an image from the array.
IAO_0000117: PERSON: Jie Zheng
IAO_0000118: array image acquisition
IAO_0000119: MO_929: image_acquisition

light emission device
type: Class
equivalent class: Class
  intersection of: COB_0001300
  intersection of: Restriction
    on property: RO_0000085
    some values from: light emission function
IAO_0000111: light emission device
IAO_0000112: A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
IAO_0000114: IAO_0000120
IAO_0000115: A device which has a function to emit light.
IAO_0000117: Person:Helen Parkinson
IAO_0000119: OBI

perturbation device
type: Class
equivalent class: Class
  intersection of: COB_0001300
  intersection of: Restriction
    on property: RO_0000085
    some values from: perturb function
IAO_0000111: perturbation device
IAO_0000112: A homogenizer is a perturbation device.
IAO_0000114: IAO_0000123
IAO_0000115: A perturbation device is a device which is designed to perform a perturb function
IAO_0000117: Helen Parkinson
IAO_0000119: OBI Vancouver workshop 2010
IAO_0000119: PERSON: Helen Parkinson

environmental control device
type: Class
equivalent class: Class
  intersection of: COB_0001300
  intersection of: Restriction
    on property: RO_0000085
    some values from: Class
      union of: heat function
      union of: cool function
      union of: environment control function
IAO_0000111: environmental control device
IAO_0000112: A growth chamber is an environmental control device.
IAO_0000114: IAO_0000120
IAO_0000115: An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
IAO_0000117: Helen Parkinson
IAO_0000119: OBI

Nuclease S1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000025471
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025471
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of sequence macromolecule
IAO_0000112: PMID:363143
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe.
IAO_0000117: Philippe Rocca-Serra
IAO_0000118: single nucleotide resolution mapping assay using Nuclease S1
IAO_0000119: RNA ontology

specimen fixation function
type: Class
subclass of: BFO_0000034
IAO_0000111: specimen fixation function
IAO_0000112: e.g the function of a bar code reader used to read slide bar codes
IAO_0000114: IAO_0000123
IAO_0000115: a function that allows specific identification of individual speciment from one another.
IAO_0000117: EAGLE-I

obsolete_specimen fixation function
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000123
IAO_0000115: A specimen fixation function is a function that holds or fastens an entity in a fixed position.
IAO_0000117: EAGLE-I
IAO_0000231: IAO_0000227
deprecated: true

Ruthenium structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: CHEBI_16991
    union of: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:3016894
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: RNA Ontology

inline probing RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000109
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: secondary structure of RNA molecule
IAO_0000112: PMID:10573122 and PMID: 18369975
IAO_0000114: IAO_0000122
IAO_0000115: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: RNA ontology

current amplification function
type: Class
subclass of: BFO_0000034
IAO_0000111: current amplification function
IAO_0000114: IAO_0000123
IAO_0000115: A current amplification function is an amplification function that increases the amplitude of a current.
IAO_0000117: EAGLE-I

stabilization function
type: Class
subclass of: BFO_0000034
IAO_0000111: stabilization function
IAO_0000114: IAO_0000123
IAO_0000115: 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.
IAO_0000117: EAGLE-I
IAO_0000118: isolation function

pump function
type: Class
subclass of: transfer function
IAO_0000111: pump function
IAO_0000114: IAO_0000123
IAO_0000115: a transfer unction where the transfer requires work to move the entity, often against a gradient.
IAO_0000117: EAGLE-I

cell transfer function
type: Class
subclass of: transfer function
IAO_0000111: cell transfer function
IAO_0000112: A cell harvester has a cell transfer function.
IAO_0000114: IAO_0000123
IAO_0000115: is a transfer function that displaces cells from one place to another
IAO_0000117: EAGLE-I

angiograph
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: record function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: angiograph
IAO_0000114: IAO_0000120
IAO_0000115: A device that records the patterns of pulse waves inside blood vessels.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://medical-dictionary.thefreedictionary.com/angiograph

capillary blotter
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: transfer function
IAO_0000111: capillary blotter
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.biometra.de/

bioreactor
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: bioreactor
IAO_0000114: IAO_0000120
IAO_0000115: A device or system that supports a biologically active environment.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Bioreactor

pH meter
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: pH meter
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to measure the pH (acidity or alkalinity) of a liquid.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/PH_meter

digital camera
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
IAO_0000111: digital camera
IAO_0000114: IAO_0000120
IAO_0000115: An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Digital_camera

chip spotting device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: transfer function
IAO_0000111: chip spotting device
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: United States Patent 7416705

RNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
IAO_0000111: RNA extraction/purification instrument
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to isolate and collect RNA for subsequent molecular analysis.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

DNA extract
type: Class
equivalent class: Class
  intersection of: nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: DNA extraction
  intersection of: Restriction
    on property: has grain
    some values from: CHEBI_16991
IAO_0000111: DNA extract
IAO_0000114: IAO_0000120
IAO_0000115: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
IAO_0000117: Person: Jie Zheng
IAO_0000119: Group: UPenn group

two-photon laser/detector
type: Class
subclass of: OBI_0400065
IAO_0000111: two-photon laser/detector
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy

electrophoresis system
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
IAO_0000111: electrophoresis system
IAO_0000114: IAO_0000120
IAO_0000115: A device that moves charged particles through a medium by using an electric field induced by electrodes.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Category:Electrophoresis

PET synthesizer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: synthesizing function
IAO_0000111: PET synthesizer
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

spinning-disk confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: spinning-disk confocal microscope
IAO_0000114: IAO_0000120
IAO_0000115: A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Nipkow_disk

DNA synthesizer
type: Class
subclass of: OBI_0400113
IAO_0000111: DNA synthesizer
IAO_0000114: IAO_0000120
IAO_0000115: An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers

high performance liquid chromatography instrument
type: Class
subclass of: liquid chromatography instrument
IAO_0000111: high performance liquid chromatography instrument
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/High_performance_liquid_chromatography

microplate reader
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: microplate reader
IAO_0000114: IAO_0000120
IAO_0000115: A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Plate_reader

ELISA microplate reader
type: Class
subclass of: microplate reader
IAO_0000111: ELISA microplate reader
IAO_0000114: IAO_0000120
IAO_0000115: A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

spot cutter
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: spot cutter
IAO_0000114: IAO_0000120
IAO_0000115: A robotic device that is used to excise spots from gels.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

microwave synthesis system
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: excitation function
subclass of: Restriction
  on property: RO_0000085
  some values from: synthesizing function
IAO_0000111: microwave synthesis system
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to apply microwave irradiation to chemical reactions.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Microwave_chemistry

densitometer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: densitometer
IAO_0000114: IAO_0000120
IAO_0000115: A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Densitometer

automatic staining machine
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: addition of molecular tracer function
IAO_0000111: automatic staining machine
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to automatically stain tissue sections on slides or tissue specimens.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

automatic tissue processor
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: reagent application function
IAO_0000111: automatic tissue processor
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: United States Patent 3762362

stereo microscope
type: Class
subclass of: optical microscope
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: stereo microscope
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope

top loading balance
type: Class
subclass of: balance
IAO_0000111: top loading balance
IAO_0000114: IAO_0000120
IAO_0000115: A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

perfusion station
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: specimen fixation function
IAO_0000111: perfusion station
IAO_0000114: IAO_0000120
IAO_0000115: A device or system in which perfusion units are integrated.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

SPECT scanner
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: SPECT scanner
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography

array manufacturer role
type: Class
subclass of: manufacturer role
subclass of: Restriction
  on property: BFO_0000054
  all values from: Class
    intersection of: manufacturing
    intersection of: Restriction
      on property: has specified output
      some values from: OBI_0400147
IAO_0000111: array manufacturer role
IAO_0000114: IAO_0000120
IAO_0000115: a manufacturer role which is played by the person or organization that manufactured the array
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_695 array_manufacturer

scintillation counter
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: scintillation counter
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to measure ionizing radiation.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Scintillation_counter

programmable array microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: programmable array microscope
IAO_0000114: IAO_0000120
IAO_0000115: A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8

cryostat
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: cool function
IAO_0000111: cryostat
IAO_0000114: IAO_0000120
IAO_0000115: A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Cryostat

microtome knife maker
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: microtome knife maker
IAO_0000114: IAO_0000120
IAO_0000115: A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

cryofixation device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: specimen fixation function
IAO_0000111: cryofixation device
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Cryofixation

hybridization oven
type: Class
subclass of: incubator
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: hybridization oven
IAO_0000114: IAO_0000120
IAO_0000115: A device that creates an appropriate environment for nucleic acid hybridization.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

incubator shaker
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: environment control function
IAO_0000111: incubator shaker
IAO_0000114: IAO_0000120
IAO_0000115: An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

small-animal image acquisition device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: small-animal image acquisition device
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to image small laboratory animals (e.g., rats and mice) in vivo.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

infrared image acquisition device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: infrared image acquisition device
IAO_0000114: IAO_0000120
IAO_0000115: An image acquisition device that is responsive to an infrared emissive target within a given field of view.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: United States Patent 4107530

confocal microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: confocal microscope
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Confocal_microscopy

patch clamp device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: patch clamp device
IAO_0000114: IAO_0000120
IAO_0000115: A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Patch_clamp

gel imaging system
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: gel imaging system
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to acquire images of laboratory gels.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

protein separation apparatus
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
IAO_0000111: protein separation apparatus
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used for the separation of proteins.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

multichannel electronic pipette
type: Class
subclass of: multichannel pipette
IAO_0000111: multichannel electronic pipette
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.faqs.org/patents/app/20090196797

vitrification apparatus
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: vitrification apparatus
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to effect the transition of a substance into a glass.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Glass_transition

radiography instrument
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: radiography instrument
IAO_0000114: IAO_0000120
IAO_0000115: An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Medical_radiography

radiation measurement device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: record function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: radiation measurement device
IAO_0000114: IAO_0000120
IAO_0000115: A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

lyophilizer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: freeze function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: lyophilizer
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to freeze dry material.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Freeze_drying

tandem mass spectrometer
type: Class
subclass of: mass spectrometer
IAO_0000111: tandem mass spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://goldbook.iupac.org/T06250.html

microhardness tester
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: microhardness tester
IAO_0000114: IAO_0000120
IAO_0000115: A hardness testing device that is used in light-optical microscopes.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: United States Patent 4611487

multimode microplate reader
type: Class
subclass of: microplate reader
IAO_0000111: multimode microplate reader
IAO_0000114: IAO_0000120
IAO_0000115: A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

mechanical balance
type: Class
subclass of: balance
IAO_0000111: mechanical balance
IAO_0000114: IAO_0000120
IAO_0000115: A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.britannica.com/EBchecked/topic/49765/balance

computer cluster
type: Class
subclass of: OBI_0400107
IAO_0000111: computer cluster
IAO_0000114: IAO_0000120
IAO_0000115: A group of linked computers, working together closely so that in many respects they form a single computer.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Cluster_(computing)

microtome knife sharpener
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: microtome knife sharpener
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to sharpen knives used in microtomy.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

plate shaker
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: plate shaker
IAO_0000114: IAO_0000120
IAO_0000115: A device that provides shaking motion for microplates.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

coagulation analyzer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: coagulation analyzer
IAO_0000114: IAO_0000120
IAO_0000115: A device for automatically analyzing blood coagulation in a clinical laboratory.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: United States Patent 5439646

laser capture microdissection microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: laser capture microdissection microscope
IAO_0000114: IAO_0000120
IAO_0000115: A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine

liquid extraction robot
type: Class
subclass of: OBI_0400112
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: liquid extraction robot
IAO_0000114: IAO_0000120
IAO_0000115: A liquid handling device that provides automatic liquid extraction.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

ultrasound machine
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: ultrasound machine
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Sonography

immunoblot scanner
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: immunoblot scanner
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used for the imaging of immunoblots.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

microcentrifuge
type: Class
subclass of: OBI_0400106
IAO_0000111: microcentrifuge
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Laboratory_centrifuge

electronic repeater pipette
type: Class
subclass of: micropipette
IAO_0000111: electronic repeater pipette
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.faqs.org/patents/app/20090196797

electron paramagnetic resonance spectrometer
type: Class
subclass of: OBI_0400115
IAO_0000111: electron paramagnetic resonance spectrometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance

rocker
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: rocker
IAO_0000114: IAO_0000120
IAO_0000115: A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

analytical balance
type: Class
subclass of: balance
IAO_0000111: analytical balance
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Weighing_scale

scanning force microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: scanning force microscope
IAO_0000114: IAO_0000120
IAO_0000115: A microscope that forms images of surfaces using a physical probe that scans the specimen.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Scanning_probe_microscopy

pulsed-field gel electrophoresis system
type: Class
subclass of: gel electrophoresis system
IAO_0000111: pulsed-field gel electrophoresis system
IAO_0000114: IAO_0000120
IAO_0000115: A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis

tissue embedding station
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: tissue embedding station
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to perform paraffin embedding of tissue specimens.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

nucleic acid sequencer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: nucleic acid sequencer
IAO_0000114: IAO_0000120
IAO_0000115: An device that is used to determine the order of nucleotides in nucleic acid sequences.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

bead array reader
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: image acquisition function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: bead array reader
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to acquire and image bead array data.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

real-time PCR machine
type: Class
subclass of: PCR instrument
IAO_0000111: real-time PCR machine
IAO_0000114: IAO_0000120
IAO_0000115: An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction

paraffin oven
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: heat function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: paraffin oven
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used for the warming of paraffin embedding medium.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

autoclave
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: heat function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: sterilization function
IAO_0000111: autoclave
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave

microplate washer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: microplate washer
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037

nucleic acid extraction/purification instrument
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
IAO_0000111: nucleic acid extraction/purification instrument
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

ELISA microplate washer
type: Class
subclass of: microplate washer
IAO_0000111: ELISA microplate washer
IAO_0000114: IAO_0000120
IAO_0000115: A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

vacuum manifold
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: vacuum manifold
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

DNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
IAO_0000111: DNA extraction/purification instrument
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to isolate and collect DNA for subsequent molecular analysis.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/DNA_extraction

multichannel pipette
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: multichannel pipette
IAO_0000114: IAO_0000120
IAO_0000115: A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

cell harvester
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: cell transfer function
IAO_0000111: cell harvester
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

portable fluorometer
type: Class
subclass of: OBI_0400143
IAO_0000111: portable fluorometer
IAO_0000114: IAO_0000120
IAO_0000115: A compact fluorometer that can be carried or moved with ease.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

gel electrophoresis system
type: Class
subclass of: electrophoresis system
IAO_0000111: gel electrophoresis system
IAO_0000114: IAO_0000120
IAO_0000115: An electrophoresis system in which an electric field is applied to a gel matrix
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: https://en.wikipedia.org/wiki/Gel_electrophoresis

diffractometer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: diffractometer
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Diffractometer

microdissection instrument
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: microdissection instrument
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used for the dissection of tissues under magnification.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://medical-dictionary.thefreedictionary.com/microdissection

micropipette puller
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: micropipette puller
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to fabricate glass micropipettes.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Micropipette

laser scanning confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: laser scanning confocal microscope
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy

digital microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: digital microscope
IAO_0000114: IAO_0000120
IAO_0000115: A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Digital_microscope

freeze substitution system
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: freeze function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: freeze substitution system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: doi:10.1017/S143192760707866X

micropipette
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: micropipette
IAO_0000114: IAO_0000120
IAO_0000115: A microinjection device that is used to measure very small volumes of liquids.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://www.answers.com/topic/micropipette

voltage clamp device
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: voltage clamp device
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Voltage_clamp

vacuum oven
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: contain function
subclass of: Restriction
  on property: RO_0000085
  some values from: heat function
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
IAO_0000111: vacuum oven
IAO_0000114: IAO_0000120
IAO_0000115: A device that heats materials in a vacuum.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

slide warmer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: heat function
IAO_0000111: slide warmer
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to heat microscope slides.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

capillary electrophoresis instrument
type: Class
subclass of: electrophoresis system
IAO_0000111: capillary electrophoresis instrument
IAO_0000114: IAO_0000120
IAO_0000115: An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Capillary_electrophoresis

denaturing high-performance liquid chromatography instrument
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: material separation function
IAO_0000111: denaturing high-performance liquid chromatography instrument
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: doi:10.1385/1-59259-850-1:173

agarose gel electrophoresis system
type: Class
subclass of: gel electrophoresis system
IAO_0000111: agarose gel electrophoresis system
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis

balance
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: mechanical function
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: balance
IAO_0000114: IAO_0000120
IAO_0000115: A measuring instrument that is used to determine the weight or mass of an object.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Weighing_scale

surface plasmon resonance instrument
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: surface plasmon resonance instrument
IAO_0000114: IAO_0000120
IAO_0000115: A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: http://en.wikipedia.org/wiki/Surface_plasmon_resonance

protein sequencer
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: measure function
IAO_0000111: protein sequencer
IAO_0000114: IAO_0000120
IAO_0000115: An device that is used to determine the order of amino acids in protein sequences.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000119: PERSON: Erik Segerdell

X-ray source
type: Class
subclass of: COB_0001300
subclass of: Restriction
  on property: RO_0000085
  some values from: excitation function
IAO_0000111: X-ray source
IAO_0000114: IAO_0000120
IAO_0000115: A device that is used to generate X-rays.
IAO_0000117: PERSON: Erik Segerdell
IAO_0000118: x-ray generator
IAO_0000119: http://en.wikipedia.org/wiki/X-ray_generator

liquid chromatography instrument
type: Class
subclass of: chromatography device
IAO_0000111: liquid chromatography instrument
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush

spike-in quality control role
type: Class
subclass of: reference substance role
IAO_0000111: spike-in quality control role
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
IAO_0000119: MO_937 spike_quality_control

individual organism identifier
type: Class
subclass of: IAO_0000577
subclass of: Restriction
  on property: IAO_0000219
  all values from: COB_0000022
IAO_0000111: individual organism identifier
IAO_0000114: IAO_0000120
IAO_0000115: a CRID symbol used to distinguish one individual organism from another.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_169 Individual

dye swap quality control role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: RO_0000052
  some values from: labeled nucleic acid extract
IAO_0000111: dye swap quality control role
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_524 dye_swap_quality_control

labeled nucleic acid extract
type: Class
equivalent class: Class
  intersection of: labeled specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has specified input
        some values from: nucleic acid extract
  intersection of: Restriction
    on property: has grain
    some values from: CHEBI_33696
IAO_0000111: labeled nucleic acid extract
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Jie Zheng
IAO_0000118: labeled extract
IAO_0000119: MO_221 labeledExtract

binding constant
type: Class
subclass of: OBI_0003142
IAO_0000111: binding constant
IAO_0000112: 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".
IAO_0000114: IAO_0000123
IAO_0000115: A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed.
IAO_0000116: 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.
IAO_0000117: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum

3D structure determination of bound molecular complex assay
type: Class
equivalent class: Class
  intersection of: OBI_0003117
  intersection of: Restriction
    on property: has specified output
    some values from: 3D structural organization datum
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: COB_0000080
IAO_0000112: Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody.
IAO_0000115: A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration.
IAO_0000117: IEDB
IAO_0000119: IEDB

binding assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: binding datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: OBI_0001588
IAO_0000112: Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
IAO_0000115: An assay with the objective to characterize the disposition of two or more material entities to form a complex.
IAO_0000117: Bjoern Peters
IAO_0000117: Jason Greenbaum
IAO_0000117: Randi Vita

cell culture expansion
type: Class
subclass of: BFO_0000015
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0100060
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: cell culture expansion
IAO_0000114: IAO_0000120
IAO_0000115: a process that results in the increase of cell numbers
IAO_0000116: including grow of yeast and bacteria
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_758 grow
IAO_0000232: BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process.

gene knock out
type: Class
subclass of: OBI_0600043
IAO_0000111: gene knock out
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_771 gene_knock_out

gene knock in
type: Class
subclass of: OBI_0600043
IAO_0000111: gene knock in
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_437 gene_knock_in
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Gene_Knock-in

chromosomal substitution
type: Class
subclass of: OBI_0600043
IAO_0000111: chromosomal substitution
IAO_0000114: IAO_0000120
IAO_0000115: 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'.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_995 chromosomal_substitution

genetically modified material
type: Class
equivalent class: Class
  union of: OBI_0302859
  union of: Class
    intersection of: CL_0000000
    intersection of: Restriction
      on property: is specified output of
      some values from: OBI_0600043
subclass of: BFO_0000040
IAO_0000111: genetically modified material
IAO_0000114: IAO_0000120
IAO_0000115: a material entity, organism or cell, that is the output of a genetic transformation process.
IAO_0000117: PERSON: Jie Zheng
IAO_0000119: GROUP: OBI
IAO_0000232: term is proposed by BP on Oct 25, 2010 dev call

transfection
type: Class
subclass of: OBI_0600043
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0600033
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: Class
      union of: CHEBI_16991
      union of: CHEBI_33697
    intersection of: Restriction
      on property: RO_0000053
      some values from: target of material addition role
IAO_0000111: transfection
IAO_0000114: IAO_0000120
IAO_0000115: a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_366 transfection

genetic transformation objective
type: Class
subclass of: material transformation objective
IAO_0000111: genetic transformation objective
IAO_0000114: IAO_0000120
IAO_0000115: a material transformation objective aims to create genetically modified organism or cell
IAO_0000117: Person: Jie Zheng
IAO_0000119: Person: Jie Zheng
IAO_0000232: suggested to be added by BP and AR during Oct 25, 2010 dev call

induced mutagenesis
type: Class
subclass of: OBI_0600043
IAO_0000111: induced mutagenesis
IAO_0000114: IAO_0000120
IAO_0000115: A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation.
IAO_0000116: Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_564 induced_mutation

3D structural organization datum
type: Class
subclass of: IAO_0000109
IAO_0000111: 3D structural organization datum
IAO_0000112: The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
IAO_0000114: IAO_0000123
IAO_0000115: A measurement datum that describes the structural orientation of a material entity in 3D space.
IAO_0000117: PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters

age since planting measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since planting measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_495 planting
IAO_0000232: Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call

age since hatching measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since hatching measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_745 hatching

age determination assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: COB_0000022
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: COB_0000022
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: age measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted).
IAO_0000116: 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.
IAO_0000117: Alan Ruttenberg
IAO_0000118: age measurement assay
IAO_0000119: OBI group

age since egg laying measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since egg laying measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_767 egg laying

assay validation objective
type: Class
subclass of: IAO_0000005
IAO_0000111: assay validation objective
IAO_0000114: IAO_0000120
IAO_0000115: an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: GROUP: Penn Group

age since germination measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since germination measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_590 germination

validation by reverse transcription PCR design
type: Class
subclass of: OBI_0500000
IAO_0000111: validation by reverse transcription PCR design
IAO_0000114: IAO_0000120
IAO_0000115: a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_986 reverse_transcription_PCR_quality_control

age since eclosion measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since eclosion measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_876 eclosion

age since sowing measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since sowing measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_748 sowing

age since coitus measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since coitus measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_783 coitus

validation by real time PCR design
type: Class
subclass of: OBI_0500000
IAO_0000111: validation by real time PCR design
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_434 real_time_PCR_quality_control

age measurement datum
type: Class
subclass of: IAO_0000416
subclass of: Restriction
  on property: IAO_0000221
  some values from: PATO_0000011
IAO_0000111: age measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: A time measurement datum that is the result of measurement of age of an organism
IAO_0000116: 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.
IAO_0000117: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
IAO_0000119: MO_178 Age
IAO_0000232: 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
IAO_0000232: discussed on Nov 15, dev call All subtype will be defined by textual definition now.

age since fertilization measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since fertilization measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: Definition of fertilization comes from GO.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_701 fertilization

age since birth measurement datum
type: Class
subclass of: age measurement datum
IAO_0000111: age since birth measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON:Chris Stoeckert, Jie Zheng
IAO_0000119: MO_710 birth

reverse transcription polymerase chain reaction assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: RO_0000081
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: RO_0000087
        some values from: evaluant role
subclass of: Restriction
  on property: BFO_0000051
  some values from: reverse transcribed polymerase chain reaction
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000030
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0010467
IAO_0000114: IAO_0000120
IAO_0000115: An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
IAO_0000117: Chris Stoeckert
IAO_0000117: Jie Zheng
IAO_0000119: Penn Group

half life datum (t 1/2)
type: Class
subclass of: IAO_0000416
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000003
IAO_0000111: half life datum (t 1/2)
IAO_0000114: IAO_0000120
IAO_0000115: The time it takes for 50% of a class of stochastic processes to occur.
IAO_0000117: Bjoern Peters
IAO_0000118: t 1/2
IAO_0000119: Bjoern Peters

dose response curve
type: Class
subclass of: IAO_0000573
IAO_0000111: dose response curve
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Bjoern Peters; Randi Vita

service
type: Class
equivalent class: Class
  intersection of: COB_0000035
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: service consumer role
    intersection of: Restriction
      on property: BFO_0000055
      some values from: service provider role
subclass of: Restriction
  on property: BFO_0000051
  some values from: COB_0000035
IAO_0000111: service
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
IAO_0000117: Carlo; Matt
IAO_0000119: OBI workshop San Diego 2011

passive immunization
type: Class
subclass of: OBI_0600007
subclass of: Restriction
  on property: BFO_0000055
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: RO_0000081
      some values from: OBI_1110022
IAO_0000111: passive immunization
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
IAO_0000118: adoptive transfer

selective organism creation objective
type: Class
subclass of: IAO_0000005
IAO_0000111: selective organism creation objective
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29

Individual epitope immunization in vivo
type: Class
subclass of: OBI_1110015
IAO_0000111: Individual epitope immunization in vivo
IAO_0000112: Injection of a peptide T cell epitope into a mouse
IAO_0000114: IAO_0000120
IAO_0000115: An immunization in which an individual epitope is administered into a host organism.
IAO_0000116: 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.
IAO_0000117: PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita

RNA sequencing assay
type: Class
equivalent class: Class
  intersection of: OBI_0600047
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: BFO_0000034
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400103
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: RNA extract
        intersection of: Restriction
  intersection of: Restriction
    on property: BFO_0000051
    some values from: OBI_0600028
  intersection of: Restriction
    on property: has specified input
    some values from: RNA extract
  intersection of: Restriction
    on property: has specified output
    some values from: sequence data
IAO_0000114: IAO_0000120
IAO_0000115: An assay that determines the sequence of an RNA molecule.
IAO_0000117: Bjoern Peters
IAO_0000119: Bjoern Peters

efficacy of epitope intervention experiment
type: Class
subclass of: assay
IAO_0000114: IAO_0000120
IAO_0000115: An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism.
IAO_0000117: Bjoern Peters
IAO_0000118: efficacy of in vivo intervention

epitope protection from infectious challenge experiment
type: Class
subclass of: epitope protection experiment
IAO_0000114: IAO_0000120
IAO_0000115: An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed.
IAO_0000117: Bjoern Peters
IAO_0000118: protection from infectious challenge

half maximal effective concentration (EC50)
type: Class
subclass of: IAO_0000032
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000051
subclass of: Restriction
  on property: IAO_0000136
  some values from: dose response curve
IAO_0000111: half maximal effective concentration (EC50)
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Bjoern Peters; Randi Vita
IAO_0000119: wikipedia

binding datum
type: Class
equivalent class: Class
  intersection of: IAO_0000027
  intersection of: Restriction
    on property: IAO_0000136
    some values from: OBI_0001588
IAO_0000111: binding datum
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Bjoern Peters; Randi Vita

negative binding datum
type: Class
subclass of: OBI_0003141
IAO_0000111: negative binding datum
IAO_0000114: IAO_0000123
IAO_0000115: A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex.

epitope protection from tumor challenge experiment
type: Class
subclass of: epitope protection experiment
IAO_0000114: IAO_0000120
IAO_0000115: An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed.
IAO_0000117: Bjoern Peters
IAO_0000118: protection from tumor challenge

epitope protection experiment
type: Class
subclass of: efficacy of epitope intervention experiment
IAO_0000114: IAO_0000120
IAO_0000115: An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
IAO_0000117: Bjoern Peters
IAO_0000118: protection from challenge

selectively maintained organism
type: Class
equivalent class: Class
  intersection of: COB_0000022
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: COB_0000035
      intersection of: Restriction
        on property: achieves_planned_objective
        some values from: selective organism creation objective
IAO_0000111: selectively maintained organism
IAO_0000114: IAO_0000120
IAO_0000115: An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
IAO_0000117: Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
IAO_0000118: cultivar
IAO_0000118: ecotype
IAO_0000118: strain
IAO_0000119: MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar

epitope protection from infectious challenge experiment based on pathogen burden
type: Class
subclass of: epitope protection from infectious challenge experiment
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Bjoern Peters
IAO_0000118: burden after infectious challenge

infectious agent detection assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: IDO_0000586
IAO_0000112: Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus.
IAO_0000114: IAO_0000120
IAO_0000115: An assay that measures the presence or amount of an infectious agent in an evaluant
IAO_0000117: Bjoern Peters
IAO_0000117: Jason Greenbaum
IAO_0000117: Randi Vita
IAO_0000117: Richard Scheuermann

epitope disease exacerbation experiment
type: Class
subclass of: efficacy of epitope intervention experiment
IAO_0000114: IAO_0000120
IAO_0000115: An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host.
IAO_0000117: Bjoern Peters
IAO_0000118: exacerbation assay

epitope protection experiment based on survival
type: Class
subclass of: epitope protection experiment
IAO_0000114: IAO_0000120
IAO_0000115: An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
IAO_0000117: Bjoern Peters
IAO_0000118: host survival after challenge

epitope treatment experiment
type: Class
subclass of: efficacy of epitope intervention experiment
IAO_0000114: IAO_0000120
IAO_0000115: An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
IAO_0000117: Bjoern Peters
IAO_0000118: decreased disease symptoms after treatment

half maximal inhibitory concentration (IC50)
type: Class
subclass of: IAO_0000032
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000051
subclass of: Restriction
  on property: IAO_0000136
  some values from: dose response curve
IAO_0000111: half maximal inhibitory concentration (IC50)
IAO_0000112: Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Bjoern Peters; Randi Vita
IAO_0000119: wikipedia

epitope specific immune intervention
type: Class
subclass of: OBI_0600007
subclass of: Class
  union of: passive immunization
  union of: Individual epitope immunization in vivo
IAO_0000111: epitope specific immune intervention
IAO_0000114: IAO_0000120
IAO_0000115: An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope
IAO_0000117: Person: Bjoern Peters, Randi Vita, Jason Greenbaum

epitope specific cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0001816
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific cytokine production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071604
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TGFb release|ELISPOT

operator variation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: NCBITaxon 9606
        intersection of: Restriction
IAO_0000111: operator variation design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that assesses the operator performance and relation to data consistency and quality.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_519 operator_variation_design

cytometric bead array assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071612
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects IP-10 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CXCL10/IP-10 release|cytometric bead array

comparative genome hybridization by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: molecular feature identification objective
IAO_0000111: comparative genome hybridization by array design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that detects genomic copy number variations using microarray technology.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_856 comparative_genome_hybridization_design

assay measuring epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032631
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-27 release|biological activity

in vivo design
type: Class
subclass of: OBI_0500000
IAO_0000114: IAO_0000120
IAO_0000115: A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_454 in_vivo_design

genotyping by high throughput sequencing design
type: Class
subclass of: genotyping design
IAO_0000111: genotyping by high throughput sequencing design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_560 genotyping_design

epitope specific tolerance induction by T cells
type: Class
equivalent class: Class
  intersection of: GO_0002507
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific tolerance induction by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

innate behavior design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
IAO_0000111: innate behavior design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_355 innate_behavior_design

detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071604
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TGFb release|RNA/DNA detection

SNP microarray
type: Class
subclass of: OBI_0400148
IAO_0000111: SNP microarray
IAO_0000114: IAO_0000120
IAO_0000115: A DNA microarray used to detect polymorphisms in DNA samples
IAO_0000117: Person: Helen Parkinson
IAO_0000119: EFO_0002703 SNP array

cell component comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: cellular feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: GO_0005575
IAO_0000111: cell component comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that compares samples from different cell components.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_1019 cell_component_comparison_design

ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032604
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: GM-CSF release|ELISPOT

epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071608
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific macrophage inflammatory protein-1 alpha production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific T cell activation
type: Class
equivalent class: Class
  intersection of: GO_0042110
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific T cell activation
IAO_0000114: IAO_0000122
IAO_0000115: A process of T cell activation resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032613
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-10 release|biological activity

cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071604
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects transforming growth factor-beta production by T cells
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TGFb release|cytometric bead array

ex vivo design
type: Class
subclass of: OBI_0500000
IAO_0000111: ex vivo design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_808 ex_vivo_design

epitope specific type IV hypersensitivity by T cells
type: Class
equivalent class: Class
  intersection of: GO_0001806
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific type IV hypersensitivity by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

normalization testing design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: software testing objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: OBI_0200169
IAO_0000111: normalization testing design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that tests different normalization procedures.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_729 normalization_testing_design

intracellular material detection assay measuring epitope specific perforin release
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: OBI_0003317
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects epitope specific perforin release by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: perforin release|intracellular staining

cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032623
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-2 release|bioassay

assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032626
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-22 release|biological activity

assay measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032637
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-8 release|biological activity

epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071610
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific chemokine (C-C motif) ligand 1 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032613
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-10 release|bioassay

ChIP-chip by SNP array assay
type: Class
subclass of: ChIP-chip assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: SNP microarray
  intersection of: Restriction
    on property: has specified input
    some values from: SNP microarray
IAO_0000114: IAO_0000120
IAO_0000115: A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin
IAO_0000117: ArrayExpress production team
IAO_0000119: EFO:0002764

ELISA measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071609
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects RANTES production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL5/RANTES release|ELISA

cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032611
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-1 beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-1b release|cytometric bead array

genetic population background information
type: Class
subclass of: genetic characteristics information
subclass of: Restriction
  on property: BFO_0000050
  some values from: genotype information
IAO_0000111: genetic population background information
IAO_0000112: genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
IAO_0000114: IAO_0000120
IAO_0000115: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
IAO_0000116: proposed and discussed on San Diego OBI workshop, March 2011
IAO_0000117: Group: OBI group
IAO_0000119: Group: OBI group

environmental history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
IAO_0000111: environmental history design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_698 environmental_history_design

ELISPOT assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032635
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunospot assay that detects interleukin-6 production by T cells
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-6 release|ELISPOT

in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0035399
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
IAO_0000115: A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: antibody help|in vivo assay

plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
type: Class
equivalent class: Class
  intersection of: surface plasmon resonance binding assay
  intersection of: Restriction
    on property: has specified output
    some values from: equilibrium dissociation constant (KD)
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: OBI_1110057
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: dissociation constant KD|surface plasmon resonance (SPR)|nM

assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032634
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-5 release|biological activity

ELISA measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071604
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TGFb release|ELISA

assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071609
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects RANTES production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL5/RANTES release|biological activity

assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032604
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: GM-CSF release|biological activity

epigenetic modification identification objective
type: Class
subclass of: molecular feature identification objective
IAO_0000111: epigenetic modification identification objective
IAO_0000114: IAO_0000120
IAO_0000115: A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
IAO_0000117: Chris Stoeckert, Jie Zheng
IAO_0000119: Person: Chris Stoeckert

transcription profiling by tiling array assay
type: Class
subclass of: transcription profiling by array assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: tiling microarray
  intersection of: Restriction
    on property: has specified input
    some values from: tiling microarray
IAO_0000114: IAO_0000120
IAO_0000115: A transcription profiling by array assay that uses a tiling path array.
IAO_0000117: James Malone
IAO_0000119: EFO:0002769

ELISA measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032626
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-22 release|ELISA

assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032625
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-21 release|biological activity

ELISA measuring epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032638
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-9 release|ELISA

transcription profiling by high throughput sequencing design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: transcription profiling identification objective
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: Group: ArrayExpress production team

intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032635
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-6 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-6 release|ICS

cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032633
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-4 release|bioassay

detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032640
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNFa release|RNA/DNA detection

cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071605
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL2/MCP-1 release|cytometric bead array

ELISA measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032627
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-23 release|ELISA

detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: OBI_0003317
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: perforin release|RNA/DNA detection

ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071706
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNF release|ELISA

genotyping by high throughput sequencing assay
type: Class
subclass of: genotyping assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
IAO_0000114: IAO_0000120
IAO_0000115: A genotyping assay that uses a high througput sequencer
IAO_0000117: James Malone
IAO_0000119: EFO:0002771

ChIP-chip assay
type: Class
equivalent class: Class
  intersection of: OBI_0001954
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000055
      some values from: Class
        intersection of: BFO_0000034
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400148
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: OBI_0001985
      intersection of: OBI_0003368
IAO_0000114: IAO_0000120
IAO_0000115: An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin
IAO_0000117: Bjoern Petesr
IAO_0000117: James Malone
IAO_0000118: ChIP-on-chip assay
IAO_0000119: url:http://en.wikipedia.org/wiki/ChIP-on-chip

epitope specific T cell tolerance induction
type: Class
equivalent class: Class
  intersection of: GO_0002517
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific T cell tolerance induction
IAO_0000114: IAO_0000122
IAO_0000115: A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000122
IAO_0000115: An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000231: IAO_0000227
IAO_0100001: flow cytometry assay
IEDB alternative term: T cell degranulation by intracellular staining
deprecated: true

assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032616
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-13 release|biological activity

array platform variation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: methodology testing objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: microarray platform
IAO_0000111: array platform variation design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_899 array_platform_variation_design

assay measuring interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032638
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-9 release|biological activity

epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032632
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-3 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032634
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-5 release|RNA/DNA detection

epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032641
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific lymphotoxin A production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032610
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-1 alpha production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

ChIP-seq design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: protein and DNA interaction identification objective
IAO_0000111: ChIP-seq design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: http://en.wikipedia.org/wiki/Chip-Sequencing

translational bias design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
IAO_0000111: translational bias design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that characterizes the association of transcripts and translation machinery.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_939 translational_bias_design

ELISA measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032632
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-3 release|ELISA

ELISA measuring epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032610
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-1a release|ELISA

epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032631
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-27 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0035398
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
IAO_0000115: A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: T cell help|in vivo assay

assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071604
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TGFb release|biological activity

FWER adjusted p-value
type: Class
subclass of: quantitative confidence value
IAO_0000111: FWER adjusted p-value
IAO_0000112: http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
IAO_0000114: IAO_0000122
IAO_0000115: 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
IAO_0000117: PERS:Philippe Rocca-Serra
IAO_0000119: adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)

DNA methylation profiling by high throughput sequencing assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
IAO_0000114: IAO_0000120
IAO_0000115: A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology
IAO_0000117: ArrayExpress production team
IAO_0000117: Helen Parkinson
IAO_0000117: James Malone
IAO_0000119: EFO:0002761

epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071604
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific transforming growth factor-beta production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032615
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-12 release|RNA/DNA detection

assay measuring epitope specific cytotoxic T cell degranulation
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: Restriction
IAO_0000115: A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: degranulation|biological activity

cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071604
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TGFb release|bioassay

RNA-seq assay
type: Class
subclass of: RNA sequencing assay
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: GO_0010467
IAO_0000114: IAO_0000120
IAO_0000115: An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
IAO_0000117: James Malone
IAO_0000118: transcription profiling by high throughput sequencing
IAO_0000119: EFO:0002770

ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071706
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNF release|ELISPOT

cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032634
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-5 release|bioassay

genotyping by array assay
type: Class
subclass of: genotyping assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
IAO_0000114: IAO_0000120
IAO_0000115: A genotyping assay that uses an array
IAO_0000117: ArrayExpress production team
IAO_0000119: EFO:0002767

epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032619
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-16 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071610
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL1/TCA-3 release|biological activity

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032623
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-2 release|RNA/DNA detection

DNA methylation profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: epigenetic modification identification objective
IAO_0000111: DNA methylation profiling by array design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: GROUP: ArrayExpress production team

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032626
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-22 release|RNA/DNA detection

assay measuring epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032619
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-16 release|biological activity

ELISA measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071612
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects IP-10 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CXCL10/IP-10 release|ELISA

translation profiling assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000119: EFO:0001033

ELISA measuring epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032618
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-15 release|ELISA

cytometric bead array assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032615
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-12 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-12 release|cytometric bead array

in vitro design
type: Class
subclass of: OBI_0500000
IAO_0000111: in vitro design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_347 in_vitro_design

RNAi profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: molecular feature identification objective
IAO_0000111: RNAi profiling by array design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: Group: ArrayExpress production team

ELISA measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032641
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: lymphotoxin A/TNFb release|ELISA

cytometric bead array assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032634
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-5 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-5 release|cytometric bead array

transcription profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: transcription profiling identification objective
IAO_0000111: transcription profiling by array design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_533 transcript_identification_design

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032620
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-17 release|RNA/DNA detection

assay measuring epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032618
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-15 release|biological activity

disease state design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: OGMS_0000031
IAO_0000111: disease state design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_902 disease_state_design

wild type organism genotype information
type: Class
subclass of: genotype information
IAO_0000111: wild type organism genotype information
IAO_0000112: C57BL/6J wild type
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: proposed and discussed on San Diego OBI workshop, March 2011
IAO_0000117: Group: OBI group
IAO_0000119: Group: OBI group

assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032620
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-17 release|biological activity

cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032620
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-17 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-17 release|cytometric bead array

cytometric bead array assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032613
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-10 production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-10 release|cytometric bead array

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032625
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-21 release|RNA/DNA detection

intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032634
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-5 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-5 release|ICS

cytometric bead array assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032623
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-2 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-2 release|cytometric bead array

cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032619
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-16 release|bioassay

ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071608
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL3/MIP-1a release|ELISA

intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032604
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: GM-CSF release|ICS

RNAi profiling by array assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_33697
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_33697
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: James Malone
IAO_0000119: EFO:0001030

genotype information
type: Class
subclass of: genetic characteristics information
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000051
    some values from: genetic population background information
  intersection of: Restriction
    on property: BFO_0000051
    some values from: genetic alteration information
IAO_0000111: genotype information
IAO_0000112: 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
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: discussed on San Diego OBI workshop, March 2011
IAO_0000117: Group: OBI group
IAO_0000119: Group: OBI group

RNA stability design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: molecular feature identification objective
    intersection of: Restriction
      on property: IAO_0000136
      some values from: CHEBI_33697
IAO_0000111: RNA stability design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that examines the stability and/or decay of RNA transcripts.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_553 RNA_stability_design

tiling microarray
type: Class
subclass of: OBI_0400148
IAO_0000111: tiling microarray
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Helen Parkinson
IAO_0000118: genome tiling array
IAO_0000119: EFO_0002704: tiling array

assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071612
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects IP-10 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CXCL10/IP-10 release|biological activity

intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032616
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-13 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-13 release|ICS

species comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: COB_0000022
IAO_0000111: species comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that assays differences between distinct species.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_675 species_design

X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
type: Class
equivalent class: Class
  intersection of: X-ray crystallography 3D molecular structure determination assay
  intersection of: Restriction
    on property: has specified output
    some values from: 3D structural organization datum
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: OBI_0003120
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000019
IAO_0000115: A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: 3D structure|x-ray crystallography|angstroms

transcription profiling by RT-PCR design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: transcription profiling identification objective
IAO_0000111: transcription profiling by RT-PCR design
IAO_0000114: IAO_0000120
IAO_0000115: A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: Group: ArrayExpress production team

epitope specific T cell enhancement of B cell mediated immune response
type: Class
equivalent class: Class
  intersection of: GO_0035399
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific T cell enhancement of B cell mediated immune response
IAO_0000114: IAO_0000122
IAO_0000115: A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071610
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL1/TCA-3 release|ELISA

epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032625
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-21 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
type: Class
subclass of: flow cytometry assay
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0003141
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: OBI_1110057
IAO_0000115: A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: T cell- APC binding|binding assay

proteomic profiling by array assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400149
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400149
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: PR_000000001
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000000001
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: BFO_0000051
      some values from: PR_000000001
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
IAO_0000114: IAO_0000120
IAO_0000115: An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology.
IAO_0000117: James Malone
IAO_0000119: EFO:0002765

cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032609
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IFNg release|bioassay

ELISPOT assay measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: granzyme B release|ELISPOT

microRNA profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: transcription profiling identification objective
IAO_0000111: microRNA profiling by array design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: Group: ArrayExpress production team

in vivo assay measuring T cell epitope specific tolerance induction
type: Class
equivalent class: Class
  intersection of: epitope tolerance induction experiment
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0002517
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
IAO_0000115: An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: tolerance|in vivo assay

detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071609
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: CCL5/RANTES release|RNA/DNA detection

cytometric bead array assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032633
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-4 production by T cells
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-4 release|cytometric bead array

assay measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032641
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: lymphotoxin A/TNFb release|biological activity

organism development design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: UBERON_0000105
        intersection of: Restriction
IAO_0000111: organism development design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_892 development_or_differentiation_design

family history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
IAO_0000111: family history design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_544 family_history_design

ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0035393
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: CXCL9/MIG release|ELISA

transcription profiling identification objective
type: Class
subclass of: molecular feature identification objective
IAO_0000111: transcription profiling identification objective
IAO_0000114: IAO_0000120
IAO_0000115: A molecular feature identification objective that aims to characterize the abundance of transcripts
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: Group: Penn Group

DNA methylation profiling by array assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
IAO_0000114: IAO_0000120
IAO_0000115: A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology
IAO_0000117: James Malone
IAO_0000119: EFO:0002759

assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071608
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL3/MIP-1a release|biological activity

epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071611
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific granulocyte colony stimulating factor production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

microRNA profiling by array assay
type: Class
subclass of: OBI_0001926
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_33697
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_33697
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: BFO_0000051
      some values from: CHEBI_33697
subclass of: Restriction
  on property: has specified output
  some values from: measured expression level
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: SO_0000276
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
IAO_0000114: IAO_0000120
IAO_0000115: An assay that analyses the microRNA component of the transcriptome using a microRNA array.
IAO_0000117: James Malone
IAO_0000119: EFO:0000753

quality control testing design
type: Class
subclass of: OBI_0500000
IAO_0000111: quality control testing design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_981 quality_control_testing_design

clinical history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: IAO_0000136
      some values from: OGMS_0000015
IAO_0000111: clinical history design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_832 clinical_history_design

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032633
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-4 release|RNA/DNA detection

cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032604
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: GM-CSF release|bioassay

intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032625
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-21 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-21 release|ICS

detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071605
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL2/MCP-1 release|RNA/DNA detection

ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071605
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL2/MCP-1 release|ELISA

assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071606
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL4/MIP-1b release|biological activity

ELISA measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032625
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-21 release|ELISA

in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity
type: Class
equivalent class: Class
  intersection of: efficacy of epitope intervention experiment
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0001806
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
IAO_0000115: An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: type IV hypersensitivity (DTH)|in vivo skin test

cytometric bead array assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032616
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-13 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-13 release|cytometric bead array

detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032609
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IFNg release|RNA/DNA detection

epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071706
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific tumor necrosis factor superfamily cytokine production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

allele information
type: Class
subclass of: genetic alteration information
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000050
    some values from: genotype information
  intersection of: Restriction
    on property: IAO_0000136
    some values from: SO_0000001
IAO_0000111: allele information
IAO_0000112: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: discussed on San Diego OBI workshop, March 2011
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_58 Allele

cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032640
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNFa release|cytometric bead array

ELISPOT assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032620
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunospot assay that detects interleukin-17 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-17 release|ELISPOT

detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032608
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IFNb release|RNA/DNA detection

detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032604
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: GM-CSF release|RNA/DNA detection

post-transcriptional modification design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: study intervention
IAO_0000111: post-transcriptional modification design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
IAO_0000116: post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_392 cellular_modification_design

ELISA measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032637
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-8 release|ELISA

cytometric bead array assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032635
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-6 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-6 release|cytometric bead array

transcription profiling by RT-PCR assay
type: Class
subclass of: transcription profiling assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: PCR instrument
  intersection of: Restriction
    on property: has specified input
    some values from: PCR instrument
subclass of: Restriction
  on property: BFO_0000051
  some values from: reverse transcribed polymerase chain reaction
IAO_0000114: IAO_0000120
IAO_0000115: A transcription profiling assay that uses reverse transcription PCR (RT-PCR).
IAO_0000117: Anna Farne
IAO_0000119: EFO:0002943

epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071606
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific chemokine (C-C motif) ligand 4 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032627
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-23 release|biological activity

genetic alteration information
type: Class
subclass of: genetic characteristics information
IAO_0000111: genetic alteration information
IAO_0000114: IAO_0000120
IAO_0000115: a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
IAO_0000116: proposed and discussed on San Diego OBI workshop, March 2011
IAO_0000117: Group: OBI group
IAO_0000119: Group: OBI group

cellular process design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: cellular feature identification objective
    intersection of: Restriction
      on property: IAO_0000136
      some values from: GO_0009987
IAO_0000111: cellular process design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_810 cellular_process_design

epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071609
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific RANTES production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of RANTES production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032613
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-10 release|RNA/DNA detection

cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071706
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNF release|cytometric bead array

wild type allele information
type: Class
subclass of: allele information
IAO_0000111: wild type allele information
IAO_0000114: IAO_0000120
IAO_0000115: an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
IAO_0000116: discussed on San Diego OBI workshop, March 2011
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_605 genotype

intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071606
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL4/MIP-1b release|ICS

epitope specific granzyme B production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071613
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific granzyme B production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of granzyme B production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032637
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-8 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

injury design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
IAO_0000111: injury design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which the response of an organism(s) to injury or damage is studied.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_726 injury_design

intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032632
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-3 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-3 release|ICS

organism status comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
subclass of: Restriction
  on property: RO_0000058
  some values from: Restriction
    on property: BFO_0000054
    some values from: Class
      intersection of: assay
      intersection of: Restriction
        on property: has specified input
        some values from: Class
IAO_0000111: organism status comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that compares samples from live and dead organisms.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_841 organism_status_design

ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071606
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL4/MIP-1b release|ELISA

cytometric bead array assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032609
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interferon-gamma production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IFNg release|cytometric bead array

assay measuring epitope specific interleukin-18 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032621
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-18 release|biological activity

epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032627
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-23 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032631
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-27 release|RNA/DNA detection

detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071612
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CXCL10/IP-10 release|RNA/DNA detection

cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032632
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-3 release|bioassay

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071706
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNF release|ICS

epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071605
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific monocyte chemotactic protein-1 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

genotyping by array design
type: Class
subclass of: genotyping design
IAO_0000111: genotyping by array design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_560 genotyping_design

assay measuring epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032610
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-1a release|biological activity

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032635
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-6 release|RNA/DNA detection

assay measuring epitope specific interferon-beta production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032608
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IFNb release|biological activity

assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032615
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-12 release|biological activity

in vivo assay measuring epitope specific T cell killing
type: Class
equivalent class: Class
  intersection of: in vivo cell killing assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0001913
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
IAO_0000115: An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: cytotoxicity|in vivo assay

comparative genomic hybridization by array assay
type: Class
subclass of: genotyping assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: RO_0000052
        some values from: CHEBI_16991
  intersection of: Restriction
    on property: has specified input
    some values from: CHEBI_16991
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: BFO_0000051
      some values from: CHEBI_16991
subclass of: Restriction
  on property: has specified output
  some values from: genotype information
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
IAO_0000114: IAO_0000120
IAO_0000115: An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
IAO_0000117: James Malone
IAO_0000118: array CGH
IAO_0000119: EFO:0000749

epitope specific cytotoxic T cell degranulation
type: Class
equivalent class: Class
  intersection of: GO_0043316
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific cytotoxic T cell degranulation
IAO_0000114: IAO_0000122
IAO_0000115: A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032627
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-23 release|RNA/DNA detection

stimulus or stress design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: IAO_0000136
      some values from: GO_0050896
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: study intervention
IAO_0000111: stimulus or stress design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_568 stimulus_or_stress_design

cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071611
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: G-CSF release|cytometric bead array

protein and DNA interaction identification objective
type: Class
subclass of: sequence feature identification objective
IAO_0000111: protein and DNA interaction identification objective
IAO_0000114: IAO_0000120
IAO_0000115: A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_933 binding_site_identification_design

epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032626
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-22 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071706
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNF release|biological activity

protocol optimization design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: protocol optimization objective
IAO_0000111: protocol optimization design
IAO_0000114: IAO_0000120
IAO_0000115: A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_934 optimization_design

promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: promoter activity detection by reporter gene assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032623
        intersection of: Restriction
IAO_0000115: A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-2 release|reporter gene assay

ChIP-chip design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: protein and DNA interaction identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: GO_0042571
IAO_0000111: ChIP-chip design
IAO_0000114: IAO_0000120
IAO_0000115: A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000118: ChIP-on-chip design
IAO_0000119: MO_933 binding_site_identification_design

genetic characteristics information
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  on property: IAO_0000136
  some values from: SO_0000001
IAO_0000111: genetic characteristics information
IAO_0000114: IAO_0000120
IAO_0000115: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_66 IndividualGeneticCharacteristics
IAO_0000232: MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)

cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071608
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL3/MIP-1a release|cytometric bead array

assay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032632
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-3 release|biological activity

assay measuring epitope specific T cell activation
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0042110
        intersection of: Restriction
IAO_0000115: A T cell epitope dependent biological activity assay that detects T cell activation.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: activation|biological activity

imprinting design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: molecular feature identification objective
IAO_0000111: imprinting design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_914 imprinting_design

cell cycle design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: cellular feature identification objective
    intersection of: Restriction
      on property: IAO_0000136
      some values from: GO_0007049
IAO_0000111: cell cycle design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_822 cell_cycle_design

translation profiling design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: molecular feature identification objective
IAO_0000111: translation profiling design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: Group: ArrayExpress production team

cell type comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: cellular feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: CL_0000000
IAO_0000111: cell type comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that compares cells of different type, for example different cell lines.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_764 cell_type_comparison_design

cytometric bead array assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071609
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects RANTES production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL5/RANTES release|cytometric bead array

cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032635
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-6 release|bioassay

assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032609
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IFNg release|biological activity

epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032638
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-9 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032640
        intersection of: Restriction
IAO_0000115: An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNFa release|biological activity

ChIP-chip by tiling array design
type: Class
subclass of: ChIP-chip design
IAO_0000111: ChIP-chip by tiling array design
IAO_0000114: IAO_0000120
IAO_0000115: A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: Group: ArrayExpress production team

dose response design
type: Class
subclass of: compound treatment design
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: study intervention
        intersection of: administration of material to specimen
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: dose specification
        intersection of: Restriction
IAO_0000111: dose response design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that examines the relationship between the size of the administered dose and the extent of the response.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_485 dose_response_design

ChIP-chip by tiling array assay
type: Class
subclass of: ChIP-chip assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: tiling microarray
  intersection of: Restriction
    on property: has specified input
    some values from: tiling microarray
IAO_0000114: IAO_0000120
IAO_0000115: A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin
IAO_0000117: ArrayExpress production team
IAO_0000119: EFO:0002762

epitope specific helper T cell enhancement of T cell mediated immune response
type: Class
equivalent class: Class
  intersection of: GO_0035398
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific helper T cell enhancement of T cell mediated immune response
IAO_0000114: IAO_0000122
IAO_0000115: A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific interferon-beta production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032608
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interferon-beta production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

organism part comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: UBERON_0000465
IAO_0000111: organism part comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that compares tissues, regions, organs within or between organisms
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_953 organism_part_comparison_design

intracellular material detection measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects epitope specific granzyme B release by T cells
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: granzyme B release|intracellular staining

protein binding site identification design
type: Class
equivalent class: Restriction
  on property: BFO_0000051
  some values from: protein and DNA interaction identification objective
subclass of: OBI_0500000
IAO_0000111: protein binding site identification design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that investigates protein binding sites on nucleic acids.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_933 binding_site_identification_design

sex comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: PATO_0000047
IAO_0000111: sex comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that assays differences associated with an organism's sex, gender or mating type.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_575 sex_design

transcription profiling by tiling array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: transcription profiling identification objective
IAO_0000111: transcription profiling by tiling array design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_507 tiling_path_design

cell differentiation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: cellular feature identification objective
    intersection of: Restriction
      on property: IAO_0000136
      some values from: GO_0048869
IAO_0000111: cell differentiation design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that assays events associated with cell development or differentiation.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_892 development_or_differentiation_design

transcription profiling design
type: Class
subclass of: OBI_0500000
IAO_0000111: transcription profiling design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that identifies forms and abundance of transcripts in the genome.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_533 transcript_identification_design

operon identification design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: sequence feature identification objective
IAO_0000111: operon identification design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that identifies locations and members of operons in a genome.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_772 operon_identification_design

radio immuno assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: radio immuno assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032609
        intersection of: Restriction
IAO_0000115: A radio immuno assay that detects interferon-gamma production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IFNg release|radio immuno assay (RIA)

DNA methylation profiling by high throughput sequencing design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: epigenetic modification identification objective
IAO_0000111: DNA methylation profiling by high throughput sequencing design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: GROUP: ArrayExpress production team

assay measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: granzyme B release|biological activity

intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0035393
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CXCL9/MIG release|ICS

ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071607
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL9/MIP-1g release|ELISA

epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0035393
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

all pairs design
type: Class
subclass of: OBI_0500000
IAO_0000111: all pairs design
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which all specimens are compared to every other specimen.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_565 all_pairs

proteomic profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: molecular feature identification objective
IAO_0000114: IAO_0000120
IAO_0000115: A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng, Dan Berrios
IAO_0000119: Group: ArrayExpress production team
IAO_0000233: https://github.com/obi-ontology/obi/issues/854

q-value
type: Class
subclass of: quantitative confidence value
IAO_0000111: q-value
IAO_0000112: 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)"
IAO_0000114: IAO_0000122
IAO_0000115: 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.
IAO_0000117: PERS:Philippe Rocca-Serra
IAO_0000118: FDR adjusted p-value
IAO_0000119: Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html

genotyping design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: sequence feature identification objective
IAO_0000111: genotyping design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_560 genotyping_design

assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032623
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-2 release|biological activity

epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032618
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-15 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071607
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific macrophage inflammatory protein-1 gamma production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

individual genetic characteristics comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: genetic characteristics information
IAO_0000111: individual genetic characteristics comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design where genotype, haplotype, or other individual genetic characteristics are compared.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_527 individual_genetic_characteristics_design

assay measuring epitope specific interleukin-1 beta production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032611
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-1b release|biological activity

assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032633
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-4 release|biological activity

assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032635
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-6 release|biological activity

cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032640
        intersection of: Restriction
IAO_0000115: A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNFa release|bioassay

intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032641
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects lymphotoxin A production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: lymphotoxin A/TNFb release|ICS

pathogenicity design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
IAO_0000111: pathogenicity design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_807 pathogenicity_design

ELISPOT assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032634
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunospot assay that detects interleukin-5 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-5 release|ELISPOT

assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071607
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL9/MIP-1g release|biological activity

cytometric bead array assay measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032637
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-8 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-8 release|cytometric bead array

assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0035393
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CXCL9/MIG release|biological activity

genetic modification design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: BFO_0000051
  some values from: biological feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: study intervention
        intersection of: OBI_0600043
IAO_0000111: genetic modification design
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_447 genetic_modification_design

ELISA measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: granzyme B release|ELISA

epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0071612
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific IP-10 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of IP-10 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

transcription profiling by array assay
type: Class
subclass of: transcription profiling assay
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000034
      intersection of: Restriction
        on property: RO_0000052
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
IAO_0000114: IAO_0000120
IAO_0000115: A transcription profiling assay that uses array technology.
IAO_0000117: James Malone
IAO_0000118: RNA profiling by array assay
IAO_0000119: EFO:0002768
IAO_0000233: https://sourceforge.net/p/obi/obi-terms/757/

strain comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: BFO_0000051
  some values from: organism feature identification objective
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: IAO_0000136
      some values from: selectively maintained organism
IAO_0000111: strain comparison design
IAO_0000114: IAO_0000120
IAO_0000115: A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_462 strain_or_line_design

assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071605
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: CCL2/MCP-1 release|biological activity

intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032615
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-12 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: IL-12 release|ICS

in vivo assay measuring T cell epitope specific disease exacerbation
type: Class
equivalent class: Class
  intersection of: epitope disease exacerbation experiment
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
IAO_0000115: An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: disease exacerbation|in vivo assay

cell specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0000000
IAO_0000111: cell specimen
IAO_0000114: IAO_0000123
IAO_0000115: A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
IAO_0000116: 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
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
IAO_0000119: MO_612 cell

monospecific T cell recognition assay measuring MHC ligand processing and presentation
type: Class
subclass of: OBI_1110125
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_1110037
IAO_0000115: 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.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: ligand presentation|T cell recognition

epitope specific interleukin-17F production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0097088
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-17F production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

T cell epitope specific immune intervention
type: Class
subclass of: epitope specific immune intervention
IAO_0000111: T cell epitope specific immune intervention
IAO_0000112: Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
IAO_0000114: IAO_0000120
IAO_0000115: An epitope specific immune intervention in which the induced response targets a T cell epitope
IAO_0000117: PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB

specimen with known storage state
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Class
    union of: fresh specimen
    union of: Class
      intersection of: OBI_0100051
      intersection of: Restriction
        on property: is specified output of
        some values from: OBI_0302893
IAO_0000111: specimen with known storage state
IAO_0000114: IAO_0000123
IAO_0000115: A specimen for which it is known whether it has been subjected to storage of a specified type.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_95 BiosourceType

in vivo assay measuring T cell epitope specific protection after tumor burden challenge
type: Class
equivalent class: Class
  intersection of: OBI_0003458
  intersection of: Restriction
    on property: BFO_0000051
    some values from: OBI_0003414
  intersection of: Restriction
    on property: BFO_0000051
    some values from: OBI_0003455
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
IAO_0000115: An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: tumor burden after challenge|in vivo assay

lowess group transformation
type: Class
subclass of: lowess transformation
IAO_0000111: lowess group transformation
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Elisabetta Manduchi
IAO_0000119: MO_861 lowess_group_normalization

in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden
type: Class
equivalent class: Class
  intersection of: epitope protection from infectious challenge experiment based on pathogen burden
  intersection of: Restriction
    on property: BFO_0000051
    some values from: pathogen challenge
  intersection of: Restriction
    on property: BFO_0000051
    some values from: OBI_0003414
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
IAO_0000115: An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: pathogen burden after challenge|in vivo assay

phage display binding assay
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: BFO_0000051
    some values from: phage display library panning
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: OBI_0003368
      intersection of: OBI_0600047
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_1000029
IAO_0000112: 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.
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

lowess transformation
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200167
IAO_0000111: lowess transformation
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Elisabetta Manduchi
IAO_0000119: MO_720 lowess_normalization

mass spectrometry assay measuring MHC ligand processing and presentation
type: Class
equivalent class: Class
  intersection of: OBI_1110125
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: mass spectrometry assay
      intersection of: OBI_0003368
IAO_0000115: A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: ligand presentation|mass spectrometry

specimen from organism
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
IAO_0000114: IAO_0000122
IAO_0000115: 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).
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000118: tissue specimen
IAO_0000119: MO_954 organism_part

phage display library panning
type: Class
subclass of: COB_0000110
subclass of: Restriction
  on property: has specified input
  some values from: OBI_1000029
IAO_0000111: phage display library panning
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Jason Greenbaum, Randi Vita, Bjoern Peters
IAO_0000119: IEDB, http://en.wikipedia.org/wiki/Phage_display

lowess global transformation
type: Class
subclass of: lowess transformation
IAO_0000111: lowess global transformation
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Elisabetta Manduchi
IAO_0000119: MO_692 lowess_global_normalization

intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071604
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects transforming growth factor-beta production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: TGFb release|ICS

cell collecting
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: has grain
      some values from: CL_0000000
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
IAO_0000111: cell collecting
IAO_0000114: IAO_0000120
IAO_0000115: A planned process that collects cells from culture.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_982 harvest

assay measuring T cell epitope specific in vivo activity
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
IAO_0000115: A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: in vivo activity|biological activity

purified MHC molecule preparation
type: Class
subclass of: BFO_0000040
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042611
  intersection of: Restriction
    on property: is specified output of
    some values from: purification
IAO_0000111: purified MHC molecule preparation
IAO_0000112: HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody.
IAO_0000114: IAO_0000120
IAO_0000115: A mixture containing MHC molecules that was purified to remove non-MHC molecular entities.
IAO_0000116: BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general.
IAO_0000117: Bjoern Peters

disposition to be bound by an MHC protein complex
type: Class
subclass of: BFO_0000016
subclass of: Restriction
  on property: BFO_0000054
  all values from: MHC protein complex binding to ligand
IAO_0000111: disposition to be bound by an MHC protein complex
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
IAO_0000118: MHC ligand disposition
IAO_0000119: IEDB

B cell epitope specific immune intervention
type: Class
subclass of: epitope specific immune intervention
IAO_0000111: B cell epitope specific immune intervention
IAO_0000112: Injecting a mouse with recombinant antibody targeting an anthrax epitope
IAO_0000114: IAO_0000120
IAO_0000115: An epitope specific immune intervention in which the induced response targets a B cell epitope
IAO_0000117: PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB

epitope tolerance induction experiment
type: Class
subclass of: efficacy of epitope intervention experiment
IAO_0000114: IAO_0000120
IAO_0000115: An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response
IAO_0000117: IEDB
IAO_0000118: tolerance induction
IAO_0000119: IEDB

mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC
type: Class
subclass of: mass spectrometry assay measuring MHC ligand processing and presentation
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: mass spectrometry assay
    intersection of: OBI_0003368
IAO_0000115: A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: ligand presentation|cellular MHC/mass spectrometry

cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032604
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: GM-CSF release|cytometric bead array

binding assay using radioactivity detection
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: radioactivity detection
      intersection of: OBI_0003368
IAO_0000114: IAO_0000120
IAO_0000115: A binding assay that uses radioactivity detection as an indicator of binding.
IAO_0000117: Bjoern Peters
IAO_0000117: Randi Vita
IAO_0000119: IEDB

in vivo assay measuring T cell epitope specific protection based on survival
type: Class
equivalent class: Class
  intersection of: epitope protection experiment based on survival
  intersection of: Restriction
    on property: BFO_0000051
    some values from: OBI_0003414
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      complement of: Class
        union of: pathogen challenge
        union of: OBI_0003455
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
IAO_0000115: An in vivo assay measuring T cell epitope specific protection from other challenge using survival.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: survival from challenge|in vivo assay

cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition
type: Class
subclass of: assay measuring binding of a cell-bound-MHC:ligand complex
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_1110037
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0000087
      some values from: OBI_0001955
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: CL_0000000
    intersection of: Restriction
      on property: BFO_0000051
      some values from: GO_0042611
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0003141
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: MHC protein complex binding to ligand
IAO_0000115: A cell bound MHC binding assay that uses a T cell epitope recognition assay.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: qualitative binding|cellular MHC/T cell inhibition

linear amplification
type: Class
subclass of: OBI_0600058
IAO_0000111: linear amplification
IAO_0000112: An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
IAO_0000114: IAO_0000120
IAO_0000115: An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_997 linear_amplification

in vivo assay measuring epitope specific T cell helper activity
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0035397
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: helper response|in vivo assay

intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032626
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-22 production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-22 release|ICS

assay measuring epitope specific perforin release by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: OBI_0003317
        intersection of: Restriction
IAO_0000115: A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: perforin release|biological activity

atmosphere
type: Class
subclass of: growth environment
IAO_0000111: atmosphere
IAO_0000114: IAO_0000120
IAO_0000115: A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_219 atmosphere

binding assay using fluorescence detection
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: fluorescence detection assay
      intersection of: OBI_0003368
IAO_0000114: IAO_0000120
IAO_0000115: A binding assay that uses fluorescence detection as an indicator of binding.
IAO_0000117: Bjoern Peters
IAO_0000117: Randi Vita
IAO_0000119: IEDB

coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand
type: Class
subclass of: OBI_1110125
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_1110037
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0000087
      some values from: positive reference substance role
IAO_0000115: 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.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: ligand presentation|coelution

fluorescence detection assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000053
        some values from: PATO_0000018
IAO_0000112: 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.
IAO_0000115: An assay in which a material's fluorescence is determined.
IAO_0000117: IEDB
IAO_0000119: IEDB

epitope specific perforin production by T cells
type: Class
subclass of: Class
  intersection of: GO_0035944
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific perforin production by T cells
IAO_0000114: IAO_0000120
IAO_0000115: The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope.
IAO_0000116: 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
IAO_0000117: PERSON: Bjoern Peters, Randi Vita

MHC protein complex binding to ligand
type: Class
subclass of: OBI_0001588
subclass of: Class
  intersection of: OBI_0001588
  intersection of: Restriction
    on property: BFO_0000055
    some values from: Class
      intersection of: BFO_0000016
      intersection of: Restriction
        on property: RO_0000052
        some values from: Class
IAO_0000111: MHC protein complex binding to ligand
IAO_0000112: The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex.
IAO_0000114: IAO_0000120
IAO_0000115: The process in which a ligand binds to an MHC molecule to form a stable complex.
IAO_0000116: 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.
IAO_0000117: PERSON: Bjoern Peters; Randi Vita
IAO_0000119: IEDB

dissection
type: Class
subclass of: COB_0000035
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
IAO_0000111: dissection
IAO_0000114: IAO_0000120
IAO_0000115: A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: EFO_0003856 dissection
IAO_0000119: MO_374 dissect

purification
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: purification objective
subclass of: COB_0000035
IAO_0000111: purification
IAO_0000114: IAO_0000120
IAO_0000115: 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
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_406 purify

specimen with pre- or post-mortem status
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
IAO_0000111: specimen with pre- or post-mortem status
IAO_0000114: IAO_0000120
IAO_0000115: A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
IAO_0000116: organizational term, used in description of specimen that is created from known pre- or post-mortem status
IAO_0000117: PERSON: Chris Stoeckert, Jie Zheng
IAO_0000119: MO_84 OrganismStatus

in vivo assay measuring T cell epitope specific treatment of disease
type: Class
equivalent class: Class
  intersection of: epitope treatment experiment
  intersection of: Restriction
    on property: BFO_0000051
    some values from: OBI_0003414
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
IAO_0000115: An efficacy of T cell epitope intervention experiment that detects a decrease in disease.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: decreased disease|in vivo assay

sampling time measurement datum
type: Class
subclass of: IAO_0000416
IAO_0000111: sampling time measurement datum
IAO_0000114: IAO_0000120
IAO_0000115: A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
IAO_0000117: Person: Chris Stoeckert
IAO_0000118: time point
IAO_0000119: MO_738 timepoint

Edman degradation assay measuring MHC ligand processing and presentation
type: Class
equivalent class: Class
  intersection of: OBI_1110125
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: Edman degradation
      intersection of: OBI_0003368
IAO_0000115: A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: ligand presentation|Edman degradation

mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC
type: Class
subclass of: mass spectrometry assay measuring MHC ligand processing and presentation
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: mass spectrometry assay
    intersection of: OBI_0003368
IAO_0000115: A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: ligand presentation|secreted MHC/mass spectrometry

disposition to be a product of antigen processing and presentation
type: Class
subclass of: BFO_0000016
subclass of: Restriction
  on property: BFO_0000054
  all values from: GO_0019882
IAO_0000111: disposition to be a product of antigen processing and presentation
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: IEDB
IAO_0000119: IEDB

cytometric bead array assay measuring epitope specific interleukin-17A production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0097087
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-17A production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-17A release|cytometric bead array

radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex
type: Class
subclass of: binding assay using radioactivity detection
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0000087
      some values from: OBI_0001955
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: purified MHC molecule preparation
    intersection of: Restriction
      on property: BFO_0000051
      some values from: GO_0042611
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0003141
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: MHC protein complex binding to ligand
IAO_0000115: A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: qualitative binding|purified MHC/competitive/radioactivity

minimal inhibitory concentration
type: Class
subclass of: IAO_0000032
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000051
subclass of: Restriction
  on property: IAO_0000136
  some values from: dose response curve
IAO_0000111: minimal inhibitory concentration
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000116: Created following request by Albert Goldfain
IAO_0000117: PERSON:Bjoern Peters
IAO_0000119: Bjoern Peters, coordinated with Albert Goldfain

material maintenance service
type: Class
equivalent class: Class
  intersection of: material service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: material maintenance
IAO_0000111: material maintenance service
IAO_0000112: model organism colony maintanance
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush
comment: Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.

radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_1000036
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003143
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM

radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003144
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM

epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0072535
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl

fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_1000036
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003141
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
IAO_0000115: A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: qualitative binding|lysate MHC/direct/fluorescence

fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003144
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM

ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071611
        intersection of: Restriction
IAO_0000115: An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: G-CSF release|ELISA

sequence assembly algorithm
type: Class
subclass of: IAO_0000064
IAO_0000111: sequence assembly algorithm
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: Person: Chris Stoeckert, Jie Zheng
IAO_0000119: NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC alternative term: Assembly Algorithm
Source: NIAID GSCID-BRC

cytometric bead array assay measuring epitope specific interleukin-17F production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0097088
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-17F production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-17F release|cytometric bead array

fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: equilibrium association constant (KA)
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000285
IAO_0000115: A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: association constant KA|cellular MHC/direct/fluorescence|1/M

PDB file
type: Class
subclass of: 3D structural organization datum
IAO_0000111: PDB file
IAO_0000112: The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum

epitope specific interleukin-17A production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0097087
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-17A production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl

support service
type: Class
subclass of: service
IAO_0000111: support service
IAO_0000112: An help desk for an instrument or a software.
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON; Carlo Torniai

material service
type: Class
equivalent class: Class
  intersection of: service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: Class
      union of: Restriction
        on property: has specified input
        some values from: BFO_0000040
      union of: Restriction
        on property: has specified output
        some values from: BFO_0000040
IAO_0000111: material service
IAO_0000112: A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
IAO_0000114: IAO_0000125
IAO_0000115: A service which has a material entity as specified input and/or specified output.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Carlo Torniai

data analysis service
type: Class
subclass of: data service
subclass of: Restriction
  on property: BFO_0000051
  some values from: OBI_0200000
IAO_0000111: data analysis service
IAO_0000112: Statistaical analysis service, data visualization service
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush

data service
type: Class
subclass of: service
subclass of: Restriction
  on property: has specified input
  some values from: IAO_0000030
subclass of: Restriction
  on property: has specified output
  some values from: IAO_0000030
IAO_0000111: data service
IAO_0000112: Data analysis service such statistical abalysis or storage service such data backup.
IAO_0000114: IAO_0000125
IAO_0000115: A service that has some information content entity as input and output.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Carlo Torniai
comment: Information content entity was used as specified input and output since it was more appropriate then data item or dataset.

fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: purified MHC molecule preparation
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001583
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000031
IAO_0000115: A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: half life|purified MHC/direct/fluorescence|min

cytometric bead array assay measuring epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032638
        intersection of: Restriction
IAO_0000115: A cytometric bead array assay that detects interleukin-9 production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-9 release|cytometric bead array

data storage service
type: Class
subclass of: data service
IAO_0000111: data storage service
IAO_0000112: A service offering data backup
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush

fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex
type: Class
subclass of: binding assay using fluorescence detection
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: BFO_0000040
    intersection of: Restriction
      on property: RO_0000087
      some values from: OBI_0001955
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: purified MHC molecule preparation
    intersection of: Restriction
      on property: BFO_0000051
      some values from: GO_0042611
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0003141
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: IAO_0000136
    some values from: MHC protein complex binding to ligand
IAO_0000115: A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: qualitative binding|purified MHC/competitive/fluorescence

epitope specific interleukin-7 production by T cells
type: Class
equivalent class: Class
  intersection of: GO_0032636
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
IAO_0000111: epitope specific interleukin-7 production by T cells
IAO_0000114: IAO_0000122
IAO_0000115: A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB (QTT)
IAO_0000232: Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl

equilibrium dissociation constant (KD)
type: Class
subclass of: binding constant
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000051
IAO_0000111: equilibrium dissociation constant (KD)
IAO_0000112: KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
IAO_0000114: IAO_0000120
IAO_0000115: A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
IAO_0000117: PERSON: Bjoern Peters, Randi Vita
IAO_0000119: IEDB

fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: purified MHC molecule preparation
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: equilibrium dissociation constant (KD)
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: dissociation constant KD|purified MHC/competitive/fluorescence|nM

training service
type: Class
subclass of: service
subclass of: Restriction
  on property: BFO_0000051
  some values from: training process
IAO_0000111: training service
IAO_0000112: A service that offers training for a specific instrument or technique. A course to learn how to use a microscope
IAO_0000114: IAO_0000125
IAO_0000115: A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush

fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: equilibrium dissociation constant (KD)
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: dissociation constant KD|cellular MHC/competitive/fluorescence|nM

obsolete T cell recognition of eluted MHC ligand assay
type: Class
subclass of: ObsoleteClass
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: An assay that identifies an MHC ligand using a T cell response assay as a readout
IAO_0000117: PERSON: Randi Vita, Bjoern Peters
IAO_0000119: IEDB
IAO_0000231: IAO_0000227
IAO_0100001: monospecific T cell recognition assay measuring MHC ligand processing and presentation
IEDB alternative term: T cell recognition
deprecated: true

fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: purified MHC molecule preparation
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001605
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000281
IAO_0000115: A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: on rate|purified MHC/direct/fluorescence|nM^-1s^-1

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0032616
        intersection of: Restriction
IAO_0000115: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-13 release|RNA/DNA detection

fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: purified MHC molecule preparation
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001581
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM

radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_1000036
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: equilibrium dissociation constant (KD)
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: dissociation constant KD|lysate MHC/competitive/radioactivity|nM

intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0071608
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: CCL3/MIP-1a release|ICS

comparative phenotypic assessment
type: Class
subclass of: drawing a conclusion based on data
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: IAO_0000109
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Class
        union of: COB_0000022
        union of: Restriction
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: IAO_0000144
    intersection of: Restriction
      on property: IAO_0000136
      some values from: Restriction
        on property: RO_0000052
        some values from: Class
IAO_0000111: comparative phenotypic assessment
IAO_0000114: IAO_0000123
IAO_0000115: 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
IAO_0000117: Philly workshop 2011
IAO_0000119: Philly workshop 2011
IAO_0000232: 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2

material analysis service
type: Class
equivalent class: Class
  intersection of: material service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: assay
IAO_0000111: material analysis service
IAO_0000112: Services performing DNA sequencing or Cell Analysis
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush

equilibrium association constant (KA)
type: Class
subclass of: binding constant
IAO_0000111: equilibrium association constant (KA)
IAO_0000112: KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
IAO_0000114: IAO_0000120
IAO_0000115: A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
IAO_0000117: PERSON: Bjoern Peters, Randi Vita
IAO_0000119: IEDB

radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: equilibrium dissociation constant (KD)
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: dissociation constant KD|cellular MHC/competitive/radioactivity|nM

assay measuring binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003141
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
IAO_0000115: A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: qualitative binding|cellular MHC

access service
type: Class
subclass of: service
IAO_0000111: access service
IAO_0000112: A service that provides acess to a mass spectrometer.
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000116: 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.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0072535
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: TNFSF11/RANKL release|ICS

assay measuring a binding constant of a MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: binding constant
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
IAO_0000115: A MHC:ligand binding assay that measures a binding constant.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: binding constant|binding assay

rate measurement datum
type: Class
subclass of: IAO_0000032
IAO_0000111: rate measurement datum
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A scalar measurement datum that represents the number of events occuring over a time interval
IAO_0000117: PERSON: Bjoern Peters, Randi Vita
IAO_0000119: IEDB

assay measuring binding of a purified-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: purified MHC molecule preparation
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003141
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
IAO_0000115: A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: qualitative binding|purified MHC

radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_1000036
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003141
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
IAO_0000115: A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: qualitative binding|lysate MHC/direct/radioactivity

material storage service
type: Class
equivalent class: Class
  intersection of: material service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: OBI_0302893
IAO_0000111: material storage service
IAO_0000112: A service that offers liquid nitrogen stroage.
IAO_0000114: IAO_0000125
IAO_0000115: A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Matthew Brush

radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001583
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000031
IAO_0000115: A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: half life|cellular MHC/direct/radioactivity|min

fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001583
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000031
IAO_0000115: A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: half life|cellular MHC/direct/fluorescence|min

obsolete cell lysate MHC binding constant determination assay
type: Class
subclass of: ObsoleteClass
IAO_0000114: IAO_0000120
IAO_0000115: 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.
IAO_0000117: PERSON: Bjoern Peters
IAO_0000119: IEDB
IAO_0000231: IAO_0000103
deprecated: true

fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using fluorescence detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: CL_0000000
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003143
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM

intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: Class
        intersection of: GO_0097088
        intersection of: Restriction
IAO_0000115: A flow cytometry assay that detects interleukin-17F production by T cells.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: IL-17F release|ICS

material processing service
type: Class
subclass of: material service
subclass of: Restriction
  on property: provides_service_consumer_with
  some values from: COB_0000110
IAO_0000111: material processing service
IAO_0000112: A service for cell line creation. A service providing cel line immortalization.
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000117: PERSON: Carlo Torniai
IAO_0000117: PERSON: Matthew Brush
IAO_0000119: PERSON: Carlo Torniai

radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: RO_0000087
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: purified MHC molecule preparation
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001571
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000065
IAO_0000115: A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value.
IAO_0000117: IEDB
IAO_0000119: IEDB
IEDB alternative term: dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM

radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_1000036
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001583
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000031
IAO_0000115: A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: half life|lysate MHC/direct/radioactivity|min

50% dissociation of binding temperature (Tm)
type: Class
subclass of: OBI_0003142
subclass of: Restriction
  on property: IAO_0000039
  some values from: UO_0000005
IAO_0000111: 50% dissociation of binding temperature (Tm)
IAO_0000112: 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.
IAO_0000114: IAO_0000120
IAO_0000115: A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound.
IAO_0000117: PERSON: Bjoern Peters, Randi Vita
IAO_0000118: melting temperature (Tm)
IAO_0000119: IEDB

radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_1000036
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0042611
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001603
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000136
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: IAO_0000039
      has value: UO_0000106
IAO_0000115: A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: off rate|lysate MHC/direct/radioactivity|1/s

radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
IAO_0000115: A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
IAO_0000117: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IAO_0000119: IEDB
IEDB alternative term: half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM