term editor
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
textual definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
term editor: PERSON:Daniel Schober
editor preferred label: term editor
has curation status: IAO_0000122

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
textual definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: definition source
has curation status: IAO_0000122

has curation status
type: AnnotationProperty
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot
editor preferred label: has curation status

imported from
type: AnnotationProperty

textual definition
type: AnnotationProperty
label: definition
term editor: PERSON:Daniel Schober
editor preferred label: definition
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
textual definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor preferred label: textual definition
textual definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
has curation status: IAO_0000122

label
type: AnnotationProperty
editor preferred label: label

editor preferred label
type: AnnotationProperty
label: editor preferred term~editor preferred label
label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred label
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
textual definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
has curation status: IAO_0000122

has part
type: ObjectProperty
type: TransitiveProperty
textual definition: a core relation that holds between a whole and its part
editor preferred label: has part
imported from: obi.owl

occurs in
type: ObjectProperty
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
textual definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
editor preferred label: occurs in
imported from: obi.owl

contains process
type: ObjectProperty
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
textual definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
editor preferred label: site of
imported from: obi.owl

has measurement unit label
type: ObjectProperty
type: FunctionalProperty
sub property of: has part
imported from: obi.owl

is about
type: ObjectProperty
textual definition: A (currently) primitive relation that relates an information artifact to an entity.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
term editor: person:Alan Ruttenberg
has curation status: IAO_0000125
imported from: obi.owl

denotes
type: ObjectProperty
textual definition: A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
term editor: person:Alan Ruttenberg
sub property of: is about
imported from: obi.owl

has measurement datum
type: ObjectProperty
term editor: Alan Ruttenberg
textual definition: relates a time stamped measurement datum to the measurement datum that was measured
sub property of: has part
has curation status: IAO_0000123
imported from: obi.owl

has_specified_input
type: ObjectProperty
term editor: PERSON: Melanie Coutot
term editor: PERSON: Bjoern Peters
editor preferred label: has_specified_input
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Larry Hunter
textual definition: The inverse property of is_specified_input_of
has curation status: IAO_0000122
sub property of: has participant
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
editor preferred label: is_specified_input_of
term editor: PERSON:Bjoern Peters
textual definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
has curation status: IAO_0000122
sub property of: participates in
imported from: obi.owl

has_specified_output
type: ObjectProperty
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
term editor: PERSON: Larry Hunter
term editor: PERSON: Bjoern Peters
editor preferred label: has_specified_output
textual definition: The inverse property of is_specified_output_of
has curation status: IAO_0000122
sub property of: has participant
imported from: obi.owl

is_manufactured_by
type: ObjectProperty
term editor: Alan Ruttenberg
term editor: Liju Fan
textual definition: 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.
editor preferred label: is_manufactured_by
has curation status: IAO_0000123
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
term editor: Alan Ruttenberg
editor preferred label: is_specified_output_of
term editor: PERSON:Bjoern Peters
textual definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
has curation status: IAO_0000122
sub property of: participates in
imported from: obi.owl

has category label
type: ObjectProperty
editor preferred label: has category label
textual definition: A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
sub property of: has part
has curation status: IAO_0000123
imported from: obi.owl

specifies value of
type: ObjectProperty
editor preferred label: specifies value of
textual definition: A relation between a value specification and an entity which the specification is about.
has curation status: IAO_0000123
sub property of: is about
imported from: obi.owl

has value specification
type: ObjectProperty
term editor: PERSON: James A. Overton
textual definition: A relation between an information content entity and a value specification that specifies its value.
definition source: OBI
editor preferred label: has value specification
sub property of: has part
has curation status: IAO_0000120
imported from: obi.owl

inheres in
type: ObjectProperty
textual definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor preferred label: inheres in
imported from: obi.owl

participates in
type: ObjectProperty
textual definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
editor preferred label: participates in
imported from: obi.owl

has participant
type: ObjectProperty
textual definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor preferred label: has participant
imported from: obi.owl

has member
type: ObjectProperty
type: IrreflexiveProperty
definition source: SIO
textual definition: has member is a mereological relation between a collection and an item.
sub property of: has part
imported from: obi.owl

has specified value
type: DatatypeProperty
definition source: OBI
textual definition: A relation between a value specification and a literal.
editor preferred label: has specified value
has curation status: IAO_0000123
imported from: obi.owl

occurrent
type: Class
textual definition: An entity that has temporal parts and that happens, unfolds or develops through time.
imported from: obi.owl

temporal region
type: Class
imported from: obi.owl

process
type: Class
textual definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
textual definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
imported from: obi.owl

disposition
type: Class
imported from: obi.owl

quality
type: Class
editor preferred label: quality
imported from: obi.owl

role
type: Class
textual definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
imported from: obi.owl

site
type: Class
subclass of: immaterial entity
imported from: obi.owl

material entity
type: Class
textual definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor preferred label: material entity
imported from: obi.owl

immaterial entity
type: Class
imported from: obi.owl

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
textual definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: obi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: deoxyribonucleic acid
textual definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: obi.owl

molecular entity
type: Class
subclass of: material entity
textual definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor preferred label: molecular entity
imported from: obi.owl

nucleic acid
type: Class
subclass of: macromolecule
textual definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
editor preferred label: nucleic acid
imported from: obi.owl

macromolecule
type: Class
subclass of: molecular entity
textual definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
editor preferred label: macromolecule
imported from: obi.owl

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acid
editor preferred label: double-stranded DNA
imported from: obi.owl

measurement unit label
type: Class
subclass of: datum label
textual definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor preferred label: measurement unit label
has curation status: IAO_0000125
imported from: obi.owl

objective specification
type: Class
subclass of: directive information entity
textual definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
editor preferred label: objective specification
has curation status: IAO_0000122
imported from: obi.owl

action specification
type: Class
subclass of: directive information entity
textual definition: A directive information entity that describes an action the bearer will take.
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
has curation status: IAO_0000122
imported from: obi.owl

datum label
type: Class
subclass of: information content entity
textual definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
term editor: GROUP: IAO
editor preferred label: datum label
has curation status: IAO_0000123
imported from: obi.owl

data item
type: Class
subclass of: information content entity
textual definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
editor preferred label: data item
has curation status: IAO_0000125
imported from: obi.owl

symbol
type: Class
subclass of: information content entity
textual definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
term editor: PERSON: James A. Overton
term editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary
editor preferred label: symbol
has curation status: IAO_0000125
imported from: obi.owl

numeral
type: Class
subclass of: symbol
textual definition: A symbol that denotes a number.
term editor: PERSON: Jonathan Rees
editor preferred label: numeral
has curation status: IAO_0000123
imported from: obi.owl

information content entity
type: Class
textual definition: A generically dependent continuant that is about some thing.
definition source: OBI_0000142
term editor: PERSON: Chris Stoeckert
editor preferred label: information content entity
has curation status: IAO_0000122
imported from: obi.owl

integer numeral
type: Class
subclass of: numeral
textual definition: A numeral that denotes an integer
term editor: PERSON: Jonathan Rees
editor preferred label: integer numeral
has curation status: IAO_0000123
imported from: obi.owl

scalar measurement datum
type: Class
subclass of: measurement datum
textual definition: A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
has curation status: IAO_0000120
imported from: obi.owl

directive information entity
type: Class
subclass of: information content entity
textual definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
has curation status: IAO_0000122
imported from: obi.owl

data set
type: Class
subclass of: data item
textual definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
definition source: OBI_0000042
editor preferred label: data set
definition source: group:OBI
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000125
imported from: obi.owl

plan specification
type: Class
subclass of: directive information entity
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
textual definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
editor preferred label: plan specification
has curation status: IAO_0000122
imported from: obi.owl

measurement datum
type: Class
subclass of: data item
textual definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
definition source: OBI_0000305
definition source: group:OBI
editor preferred label: measurement datum
term editor: person:Chris Stoeckert
has curation status: IAO_0000125
imported from: obi.owl

setting datum
type: Class
subclass of: data item
textual definition: A settings datum is a datum that denotes some configuration of an instrument.
has curation status: IAO_0000123
imported from: obi.owl

textual entity
type: Class
subclass of: information content entity
textual definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
term editor: PERSON: Lawrence Hunter
editor preferred label: textual entity
has curation status: IAO_0000123
imported from: obi.owl

document part
type: Class
subclass of: information content entity
textual definition: An information content entity that is part of a document.
term editor: PERSON: Lawrence Hunter
editor preferred label: document part
has curation status: IAO_0000120
imported from: obi.owl

length measurement datum
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that is the result of measurement of length quality
term editor: Alan Ruttenberg
has curation status: IAO_0000123
imported from: obi.owl

mass measurement datum
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that is the result of measurement of mass quality
term editor: Person:Alan Ruttenberg
has curation status: IAO_0000123
imported from: obi.owl

time measurement datum
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that is the result of measuring a temporal interval
term editor: Person:Alan Ruttenberg
has curation status: IAO_0000123
imported from: obi.owl

email address
type: Class
subclass of: information content entity
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart
editor preferred label: email address
has curation status: IAO_0000123
imported from: obi.owl

centrally registered identifier symbol
type: Class
subclass of: symbol
textual definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
has curation status: IAO_0000120
imported from: obi.owl

time stamped measurement datum
type: Class
subclass of: measurement datum
has curation status: IAO_0000123
imported from: obi.owl

notes section
type: Class
subclass of: document part
textual definition: A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
term editor: PERSON: Bill Baumgartner
editor preferred label: notes section
imported from: obi.owl

planned process
type: Class
subclass of: process
textual definition: A process that realizes a plan which is the concretization of a plan specification.
editor preferred label: planned process
definition source: branch derived
term editor: Bjoern Peters
has curation status: IAO_0000122
imported from: obi.owl

material supplier role
type: Class
subclass of: service provider role
editor preferred label: material supplier role
term editor: PERSON:Jennifer Fostel
textual definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
has curation status: IAO_0000120
imported from: obi.owl

processed material
type: Class
subclass of: material entity
textual definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
editor preferred label: processed material
has curation status: IAO_0000122
imported from: obi.owl

investigation
type: Class
subclass of: planned process
term editor: Bjoern Peters
definition source: OBI branch derived
textual definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
editor preferred label: investigation
has curation status: IAO_0000122
imported from: obi.owl

assay
type: Class
subclass of: planned process
textual definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred label: assay
has curation status: IAO_0000122
imported from: obi.owl

culture medium
type: Class
subclass of: processed material
textual definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
definition source: OBI
term editor: Person: Jennifer Fostel, Jie Zheng
editor preferred label: culture medium
has curation status: IAO_0000122
imported from: obi.owl

patient role
type: Class
subclass of: role
editor preferred label: patient role
term editor: GROUP:Role Branch
definition source: OBI, CDISC
textual definition: 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
has curation status: IAO_0000120
imported from: obi.owl

material processing
type: Class
subclass of: planned process
textual definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Frank Gibson
definition source: OBI branch derived
term editor: PERSON: Philippe Rocca Serra
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
editor preferred label: material processing
term editor: PERSON: Bjoern Peters
has curation status: IAO_0000122
imported from: obi.owl

specimen role
type: Class
subclass of: role
term editor: GROUP: Role Branch
definition source: OBI
textual definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor preferred label: specimen role
has curation status: IAO_0000122
imported from: obi.owl

incubator
type: Class
subclass of: environmental control device
textual definition: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
definition source: http://www.medterms.com/script/main/art.asp
editor preferred label: incubator
term editor: Frank Gibson
has curation status: IAO_0000120
imported from: obi.owl

population
type: Class
subclass of: material entity
term editor: PERSON: Philippe Rocca-Serra
textual definition: 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
definition source: adapted from Oxford English Dictionnary
editor preferred label: population
has curation status: IAO_0000125
imported from: obi.owl

organization
type: Class
subclass of: material entity
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Philippe Rocca-Serra
textual definition: 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.
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
term editor: PERSON: Bjoern Peters
editor preferred label: organization
has curation status: IAO_0000122
imported from: obi.owl

DNA extraction
type: Class
subclass of: nucleic acid extraction
textual definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
editor preferred label: DNA extraction
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
has curation status: IAO_0000123
imported from: obi.owl

extract
type: Class
subclass of: processed material
definition source: GROUP: OBI Biomatrial Branch
term editor: PERSON: Philippe Rocca-Serra
textual definition: an extract is a material entity which results from an extraction process
editor preferred label: extract
has curation status: IAO_0000120
imported from: obi.owl

enzyme
type: Class
subclass of: material entity
definition source: GROUP:OBI
editor preferred label: enzyme
term editor: person: Melanie Courtot
textual definition: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
has curation status: IAO_0000125
imported from: obi.owl

plasmid
type: Class
subclass of: double-stranded DNA
definition source: group:OBI
term editor: person:Melanie Courtot
editor preferred label: plasmid
textual definition: plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
has curation status: IAO_0000125
imported from: obi.owl

needle
type: Class
subclass of: device
textual definition: 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.
definition source: OBI Instrument
term editor: Philippe Rocca-Serra
editor preferred label: needle
has curation status: IAO_0000120
imported from: obi.owl

manufacturer role
type: Class
subclass of: role
definition source: OBI
editor preferred label: manufacturer role
term editor: GROUP: Role Branch
textual definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
has curation status: IAO_0000123
imported from: obi.owl

DNA sequencing assay
type: Class
textual definition: A sequencing assay which determines information on the sequence of a DNA molecule.
definition source: url:https://en.wikipedia.org/wiki/DNA_sequencing
editor preferred label: DNA sequencing assay
term editor: Philippe Rocca-Serra
has curation status: IAO_0000123
imported from: obi.owl

material combination
type: Class
subclass of: material processing
editor preferred label: material combination
textual definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
definition source: bp
term editor: bp
has curation status: IAO_0000122
imported from: obi.owl

data representational model
type: Class
subclass of: directive information entity
editor preferred label: data representational model
term editor: Melanie Courtot
textual definition: Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
definition source: GROUP: OBI
has curation status: IAO_0000120
imported from: obi.owl

specimen collection process
type: Class
subclass of: planned process
textual definition: A planned process with the objective of collecting a specimen.
editor preferred label: specimen collection process
term editor: Bjoern Peters
has curation status: IAO_0000122
imported from: obi.owl

average value
type: Class
subclass of: data item
term editor: PERSON: James Malone
editor preferred label: average value
textual definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
term editor: PERSON: Monnie McGee
has curation status: IAO_0000125
imported from: obi.owl

454 Genome Sequence 20
type: Class
subclass of: DNA sequencer
editor preferred label: 454 Genome Sequence 20
term editor: Philippe Rocca-Serra
textual definition: 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.
has curation status: IAO_0000120
imported from: obi.owl

ABI 377 automated sequencer
type: Class
subclass of: DNA sequencer
definition source: Applied Biosystems
textual definition: 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.
editor preferred label: ABI 377 automated sequencer
term editor: Philippe Rocca-Serra
has curation status: IAO_0000120
imported from: obi.owl

AB SOLiD System
type: Class
subclass of: DNA sequencer
term editor: Philippe Rocca-Serra
definition source: Applied Biosystems
textual definition: is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
editor preferred label: AB SOLiD System
has curation status: IAO_0000120
imported from: obi.owl

454 Genome Sequencer FLX
type: Class
subclass of: DNA sequencer
editor preferred label: 454 Genome Sequencer FLX
textual definition: 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.
definition source: 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
term editor: Philippe Rocca-Serra
has curation status: IAO_0000120
imported from: obi.owl

Illumina Genome Analyzer II
type: Class
subclass of: DNA sequencer
term editor: Philippe Rocca-Serra
definition source: Illumina Corporation
editor preferred label: Illumina Genome Analyzer II
textual definition: 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
has curation status: IAO_0000120
imported from: obi.owl

Li-Cor 4300 DNA Analysis System
type: Class
subclass of: DNA sequencer
term editor: Philippe Rocca-Serra
definition source: OBI and Li-Cor
textual definition: is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
editor preferred label: Li-Cor 4300 DNA Analysis System
has curation status: IAO_0000120
imported from: obi.owl

HeliScope Single Molecule Sequencer
type: Class
subclass of: DNA sequencer
editor preferred label: HeliScope Single Molecule Sequencer
term editor: Philippe Rocca-Serra
textual definition: is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
has curation status: IAO_0000120
imported from: obi.owl

pathogen role
type: Class
subclass of: role
definition source: OBI
textual definition: 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
editor preferred label: pathogen role
term editor: GROUP: Role Branch
has curation status: IAO_0000120
imported from: obi.owl

restriction enzyme
type: Class
subclass of: protein
textual definition: an enzyme that has a specific target cleavage sites within nucleic acids
editor preferred label: restriction enzyme
term editor: Kevin Clancy, Bjoern Peters
has curation status: IAO_0000123
imported from: obi.owl

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
textual definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
has curation status: IAO_0000125
imported from: obi.owl

measurement device
type: Class
subclass of: device
editor preferred label: measurement device
textual definition: A device in which a measure function inheres.
definition source: OBI
term editor: GROUP:OBI Philly workshop
has curation status: IAO_0000122
imported from: obi.owl

polyA RNA extract
type: Class
subclass of: RNA extract
term editor: PERSON: Chris Stoeckert
textual definition: 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.
editor preferred label: polyA RNA extract
term editor: PERSON: Jie Zheng
definition source: UPenn Group
has curation status: IAO_0000120
imported from: obi.owl

RNA extract
type: Class
subclass of: nucleic acid extract
term editor: PERSON: Chris Stoeckert
definition source: Group: UPenn Group
term editor: PERSON: Jie Zheng
textual definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
editor preferred label: RNA extract
has curation status: IAO_0000120
imported from: obi.owl

real time polymerase chain reaction assay
type: Class
subclass of: polymerase chain reaction assay
editor preferred label: real time polymerase chain reaction assay
textual definition: 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.
term editor: Melanie Courtot
term editor: Bjoern Peters
definition source: url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
has curation status: IAO_0000120
imported from: obi.owl

total RNA extract
type: Class
subclass of: RNA extract
textual definition: A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
editor preferred label: total RNA extract
definition source: UPenn Group
has curation status: IAO_0000120
imported from: obi.owl

infectious agent
type: Class
subclass of: organism
editor preferred label: infectious agent
term editor: IEDB
definition source: IEDB
textual definition: is a material entity bearing the disposition to infect an organism
has curation status: IAO_0000123
imported from: obi.owl

categorical measurement datum
type: Class
subclass of: measurement datum
definition source: Bjoern Peters
editor preferred label: categorical measurement datum
term editor: Bjoern Peters
textual definition: A measurement datum that is reported on a categorical scale
has curation status: IAO_0000120
imported from: obi.owl

service provider role
type: Class
subclass of: role
term editor: PERSON:Helen Parkinson
textual definition: 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
editor preferred label: service provider role
has curation status: IAO_0000123
imported from: obi.owl

processed specimen
type: Class
subclass of: processed material
subclass of: specimen
textual definition: A specimen that has been intentionally physically modified.
term editor: Bjoern Peters
editor preferred label: processed specimen
comment: A tissue sample that has been sliced and stained for a histology study.
definition source: Bjoern Peters
has curation status: IAO_0000122
imported from: obi.owl

categorical label
type: Class
subclass of: datum label
definition source: Bjoern Peters
textual definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
editor preferred label: categorical label
term editor: Bjoern Peters
has curation status: IAO_0000120
imported from: obi.owl

container
type: Class
subclass of: device
textual definition: A device that can be used to restrict the location of material entities over time
editor preferred label: container
term editor: PERSON: Bjoern Peters
has curation status: IAO_0000123
imported from: obi.owl

device
type: Class
subclass of: processed material
definition source: OBI development call 2012-12-17.
textual definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor preferred label: device
term editor: PERSON: Helen Parkinson
has curation status: IAO_0000122
imported from: obi.owl

sequence data
type: Class
subclass of: measurement datum
editor preferred label: sequence data
term editor: Person:Chris Stoeckert
definition source: GROUP: OBI
textual definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
has curation status: IAO_0000120
imported from: obi.owl

DNA sequencing service
type: Class
subclass of: sequencing service
textual definition: A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
editor preferred label: DNA sequencing service
has curation status: IAO_0000123
imported from: obi.owl

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
textual definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
editor preferred label: nucleic acid extract
term editor: PERSON: Jie Zheng
definition source: UPenn Group
has curation status: IAO_0000120
imported from: obi.owl

environmental control device
type: Class
subclass of: device
textual definition: An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
term editor: Helen Parkinson
definition source: OBI
editor preferred label: environmental control device
has curation status: IAO_0000120
imported from: obi.owl

micropipette
type: Class
subclass of: measurement device
definition source: http://www.answers.com/topic/micropipette
term editor: PERSON: Erik Segerdell
textual definition: A microinjection device that is used to measure very small volumes of liquids.
editor preferred label: micropipette
has curation status: IAO_0000120
imported from: obi.owl

individual organism identifier
type: Class
subclass of: centrally registered identifier symbol
definition source: MO_169 Individual
term editor: PERSON: Chris Stoeckert, Jie Zheng
textual definition: a CRID symbol used to distinguish one individual organism from another.
editor preferred label: individual organism identifier
has curation status: IAO_0000120
imported from: obi.owl

age measurement datum
type: Class
subclass of: time measurement datum
textual definition: A time measurement datum that is the result of measurement of age of an organism
definition source: MO_178 Age
term editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
editor preferred label: age measurement datum
has curation status: IAO_0000120
imported from: obi.owl

age since birth measurement datum
type: Class
subclass of: age measurement datum
definition source: MO_710 birth
term editor: PERSON:Chris Stoeckert, Jie Zheng
textual definition: 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.
editor preferred label: age since birth measurement datum
has curation status: IAO_0000120
imported from: obi.owl

service
type: Class
subclass of: planned process
editor preferred label: service
definition source: OBI workshop San Diego 2011
textual definition: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
term editor: Carlo; Matt
has curation status: IAO_0000120
imported from: obi.owl

RNA sequencing assay
type: Class
subclass of: sequencing assay
editor preferred label: RNA sequencing assay
definition source: Bjoern Peters
term editor: Bjoern Peters
textual definition: An assay that determines the sequence of an RNA molecule.
has curation status: IAO_0000120
imported from: obi.owl

specimen from organism
type: Class
subclass of: specimen
definition source: MO_954 organism_part
term editor: PERSON: Chris Stoeckert, Jie Zheng
textual definition: 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).
editor preferred label: specimen from organism
has curation status: IAO_0000122
imported from: obi.owl

sampling time measurement datum
type: Class
subclass of: time measurement datum
textual definition: A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
definition source: MO_738 timepoint
term editor: Person: Chris Stoeckert
editor preferred label: sampling time measurement datum
has curation status: IAO_0000120
imported from: obi.owl

material maintenance service
type: Class
subclass of: material service
editor preferred label: material maintenance service
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.
definition source: PERSON: Matthew Brush
term editor: PERSON: Matthew Brush
textual definition: 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.
term editor: PERSON: Carlo Torniai
has curation status: IAO_0000125
imported from: obi.owl

material service
type: Class
subclass of: service
textual definition: A service which has a material entity as specified input and/or specified output.
editor preferred label: material service
definition source: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
term editor: PERSON: Carlo Torniai
has curation status: IAO_0000125
imported from: obi.owl

material analysis service
type: Class
subclass of: material service
term editor: PERSON: Matthew Brush
textual definition: 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.
term editor: PERSON: Carlo Torniai
definition source: PERSON: Matthew Brush
editor preferred label: material analysis service
has curation status: IAO_0000125
imported from: obi.owl

material storage service
type: Class
subclass of: material maintenance service
textual definition: A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
definition source: PERSON: Matthew Brush
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
editor preferred label: material storage service
has curation status: IAO_0000125
imported from: obi.owl

GenBank ID
type: Class
subclass of: centrally registered identifier symbol
textual definition: A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
editor preferred label: GenBank ID
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
has curation status: IAO_0000120
imported from: obi.owl

investigation description
type: Class
subclass of: comment on investigation
textual definition: A textual entity that describes an investigation.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred label: investigation description
has curation status: IAO_0000120
imported from: obi.owl

specimen identifier
type: Class
subclass of: centrally registered identifier symbol
textual definition: A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred label: specimen identifier
has curation status: IAO_0000120
imported from: obi.owl

PubMed ID
type: Class
subclass of: centrally registered identifier symbol
textual definition: A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred label: PubMed ID
definition source: Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
has curation status: IAO_0000120
imported from: obi.owl

specimen collection time measurement datum
type: Class
subclass of: time measurement datum
textual definition: A time measurement datum that is the measure of the time when the specimens are collected.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred label: specimen collection time measurement datum
has curation status: IAO_0000120
imported from: obi.owl

latitude coordinate measurement datum
type: Class
subclass of: measurement datum
textual definition: A measurement datum that is the measure of the latitude coordinate of a site.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred label: latitude coordinate measurement datum
has curation status: IAO_0000120
imported from: obi.owl

longitude coordinate measurement datum
type: Class
subclass of: measurement datum
textual definition: A measurement datum that is the measure of the longitude coordinate of a site.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred label: longitude coordinate measurement datum
has curation status: IAO_0000120
imported from: obi.owl

investigation title
type: Class
subclass of: comment on investigation
textual definition: A textual entity that denotes an investigation.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person:Chris Stoeckert, Jie Zheng
editor preferred label: investigation title
has curation status: IAO_0000120
imported from: obi.owl

country name
type: Class
subclass of: textual entity
textual definition: A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Website: http://en.wikipedia.org/wiki/Country
editor preferred label: country name
has curation status: IAO_0000120
imported from: obi.owl

investigation identifier
type: Class
subclass of: centrally registered identifier symbol
textual definition: A CRID symbol used to identify an investigation.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zhneg
editor preferred label: investigation identifier
has curation status: IAO_0000120
imported from: obi.owl

grant identifier
type: Class
subclass of: centrally registered identifier symbol
textual definition: A CRID symbol used to identify a grant.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred label: grant identifier
has curation status: IAO_0000120
imported from: obi.owl

contact representative role
type: Class
subclass of: role
term editor: Person: Chris Stoeckert
textual definition: A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
editor preferred label: contact representative role
has curation status: IAO_0000123
imported from: obi.owl

reagent
type: Class
subclass of: processed material
definition source: PERSON:Matthew Brush
term editor: PERSON:Matthew Brush
comment: (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some…
textual definition: A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
editor preferred label: reagent
has curation status: IAO_0000120
imported from: obi.owl

organization of specimen provider principal investigator
type: Class
subclass of: organization
definition source: NIAID GSCID-BRC metadata working group
textual definition: An organization that is the affiliation of the principal investigator providing the specimens for the investigation
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: organization of specimen provider principal investigator
has curation status: IAO_0000120
imported from: obi.owl

target material in specimen specification
type: Class
subclass of: plan specification
definition source: NIAID GSCID-BRC metadata working group
term editor: PERSON: Chris Stoeckert, Jie Zheng
textual definition: A plan specification which specifies the type of material that will be assayed in an investigation.
editor preferred label: target material in specimen specification
has curation status: IAO_0000120
imported from: obi.owl

specimen-based scope of investigation specification
type: Class
subclass of: plan specification
term editor: PERSON: Chris Stoeckert, Jie Zheng
textual definition: A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
definition source: NIAID GSCID-BRC metadata working group
editor preferred label: specimen-based scope of investigation specification
has curation status: IAO_0000120
imported from: obi.owl

specimen repository organization
type: Class
subclass of: organization
definition source: NIAID GSCID-BRC metadata working group
textual definition: An organization that provides a service to store and distribute specimens
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: specimen repository organization
has curation status: IAO_0000120
imported from: obi.owl

sequencing facility organization
type: Class
subclass of: molecular analysis facility organization
textual definition: An organization that provides sequence determination service
definition source: NIAID GSCID-BRC metadata working group
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: sequencing facility organization
has curation status: IAO_0000120
imported from: obi.owl

specification of data to be generated in an investigation
type: Class
subclass of: objective specification
textual definition: An objective specification which indicates the type of data that will be generated and submitted to a database.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
editor preferred label: specification of data to be generated in an investigation
has curation status: IAO_0000120
imported from: obi.owl

organization of specimen collector
type: Class
subclass of: organization
textual definition: An organization that is the affiliation of the person collecting the specimen
definition source: NIAID GSCID-BRC metadata working group
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: organization of specimen collector
has curation status: IAO_0000120
imported from: obi.owl

email address of sequencing facility contact person
type: Class
subclass of: email address
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
textual definition: An email address of the contact representative at the sequencing facility
editor preferred label: email address of sequencing facility contact person
has curation status: IAO_0000120
imported from: obi.owl

investigation assay specification
type: Class
subclass of: plan specification
textual definition: A plan specification which indicates the assay type used to obtain data.
definition source: NIAID GSCID-BRC metadata working group
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: investigation assay specification
has curation status: IAO_0000120
imported from: obi.owl

organization of sequencing facility contact person
type: Class
subclass of: organization
textual definition: An organization that is the affiliation of the contact representative at the sequencing facility
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
editor preferred label: organization of sequencing facility contact person
has curation status: IAO_0000120
imported from: obi.owl

comment on investigation
type: Class
subclass of: textual entity
definition source: NIAID GSCID-BRC metadata working group
textual definition: A textual entity that is about any of the aspects of an investigation worth noting
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: comment on investigation
has curation status: IAO_0000120
imported from: obi.owl

target capture specification
type: Class
subclass of: plan specification
textual definition: A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
editor preferred label: target capture specification
has curation status: IAO_0000120
imported from: obi.owl

specimen identifier assigned by specimen repository
type: Class
subclass of: specimen identifier
textual definition: A specimen identifier which is assigned by a specimen repository
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
editor preferred label: specimen identifier assigned by specimen repository
has curation status: IAO_0000120
imported from: obi.owl

specimen identifier assigned by sequencing facility
type: Class
subclass of: specimen identifier
textual definition: A specimen identifier which is assigned by a sequencing facility
definition source: NIAID GSCID-BRC metadata working group
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: specimen identifier assigned by sequencing facility
has curation status: IAO_0000120
imported from: obi.owl

email address of specimen provider principal investigator
type: Class
subclass of: email address
definition source: NIAID GSCID-BRC metadata working group
textual definition: An email address of the principal investigator providing the specimens for the investigation
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred label: email address of specimen provider principal investigator
has curation status: IAO_0000120
imported from: obi.owl

sequencing service
type: Class
subclass of: material analysis service
term editor: Person: Jie Zheng
definition source: Adpated from 'DNA sequencing service'
textual definition: A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
editor preferred label: sequencing service
has curation status: IAO_0000120
imported from: obi.owl

categorical value specification
type: Class
subclass of: value specification
textual definition: A value specification that is specifies one category out of a fixed number of nominal categories
editor preferred label: categorical value specification
term editor: PERSON:Bjoern Peters
has curation status: IAO_0000123
imported from: obi.owl

scalar value specification
type: Class
subclass of: value specification
textual definition: A value specification that consists of two parts: a numeral and a unit label
term editor: PERSON:Bjoern Peters
editor preferred label: scalar value specification
has curation status: IAO_0000123
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
textual definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
term editor: PERSON:Bjoern Peters
has curation status: IAO_0000122
imported from: obi.owl

N50
type: Class
subclass of: scalar measurement datum
term editor: Alejandra Gonzalez-Beltran
editor preferred label: N50
term editor: Philippe Rocca-Serra
definition source: adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html"
textual definition: the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
has curation status: IAO_0000125
imported from: obi.owl

contig N50
type: Class
subclass of: N50
textual definition: N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
editor preferred label: contig N50
has curation status: IAO_0000125
imported from: obi.owl

grant agency
type: Class
subclass of: organization
definition source: NIAID GSCID-BRC metadata working group
term editor: PERSON: Jie Zheng, Chris Stoeckert
textual definition: An organization that provides funding support for projects such as investigations.
editor preferred label: grant agency
has curation status: IAO_0000120
imported from: obi.owl

Genome Analyzer IIx
type: Class
subclass of: Illumina Genome Analyzer II
definition source: ENCODE group
editor preferred label: Genome Analyzer IIx
textual definition: An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.
term editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
has curation status: IAO_0000120
imported from: obi.owl

Illumina HiSeq 2000
type: Class
subclass of: DNA sequencer
textual definition: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.
editor preferred label: Illumina HiSeq 2000
term editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
has curation status: IAO_0000120
imported from: obi.owl

Illumina HiSeq 2500
type: Class
subclass of: DNA sequencer
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf
textual definition: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.
term editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
editor preferred label: Illumina HiSeq 2500
has curation status: IAO_0000120
imported from: obi.owl

MiSeq
type: Class
subclass of: DNA sequencer
textual definition: A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.
term editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf
editor preferred label: MiSeq
has curation status: IAO_0000120
imported from: obi.owl

SOLiD 3 Plus System
type: Class
subclass of: AB SOLiD System
definition source: http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf
textual definition: A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
term editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
editor preferred label: SOLiD 3 Plus System
has curation status: IAO_0000120
imported from: obi.owl

PacBio RS II
type: Class
subclass of: DNA sequencer
textual definition: A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.
term editor: PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
definition source: http://www.pacificbiosciences.com/products/
editor preferred label: PacBio RS II
has curation status: IAO_0000120
imported from: obi.owl

NextSeq 500
type: Class
subclass of: DNA sequencer
textual definition: A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
editor preferred label: NextSeq 500
definition source: http://systems.illumina.com/systems/nextseq-sequencer.html
term editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
has curation status: IAO_0000120
imported from: obi.owl

Illumina HiSeq 1000
type: Class
subclass of: DNA sequencer
term editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
textual definition: A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
editor preferred label: Illumina HiSeq 1000
has curation status: IAO_0000120
imported from: obi.owl

SOLiD 4 System
type: Class
subclass of: AB SOLiD System
definition source: http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html
editor preferred label: SOLiD 4 System
textual definition: An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
term editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
has curation status: IAO_0000120
imported from: obi.owl

Genome Analyzer IIe
type: Class
subclass of: Illumina Genome Analyzer II
editor preferred label: Genome Analyzer IIe
term editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
definition source: http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf
textual definition: An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories.
has curation status: IAO_0000120
imported from: obi.owl

Illumina HiSeq 3000
type: Class
subclass of: DNA sequencer
term editor: PERSON: Sagar Jain, Richard Scheuermann
editor preferred label: Illumina HiSeq 3000
definition source: http://www.illumina.com/systems/hiseq-3000-4000.html
textual definition: A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
has curation status: IAO_0000120
imported from: obi.owl

Illumina HiSeq 4000
type: Class
subclass of: DNA sequencer
term editor: PERSON: Sagar Jain, Richard Scheuermann
definition source: http://www.illumina.com/systems/hiseq-3000-4000.html
textual definition: A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
editor preferred label: Illumina HiSeq 4000
has curation status: IAO_0000120
imported from: obi.owl

specimen container
type: Class
subclass of: container
textual definition: A container with the function of containing a specimen.
term editor: Chris Stoeckert
definition source: Duke Biobank, OBIB
editor preferred label: specimen container
has curation status: IAO_0000122
imported from: obi.owl

Illumina Genome Analyzer
type: Class
subclass of: DNA sequencer
editor preferred label: Illumina Genome Analyzer
definition source: http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html
term editor: Person: Chris Stoeckert, Jason Hilton
textual definition: A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.
has curation status: IAO_0000125
imported from: obi.owl

Illumina HiSeq X Ten
type: Class
subclass of: DNA sequencer
textual definition: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
definition source: http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html
term editor: Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann
editor preferred label: Illumina HiSeq X Ten
has curation status: IAO_0000125
imported from: obi.owl

molecular analysis facility organization
type: Class
subclass of: organization
textual definition: An organization that provides molecular analysis service.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
editor preferred label: molecular analysis facility organization
has curation status: IAO_0000122
imported from: obi.owl

adapter-sequence trimming
type: Class
subclass of: sequence trimming
definition source: Dan Berrios
editor preferred label: adapter-sequence trimming
term editor: Dan Berrios
textual definition: A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed).
has curation status: IAO_0000120
imported from: obi.owl

sequence trimming
type: Class
subclass of: data transformation
editor preferred label: sequence trimming
textual definition: A data transformation in which subsequences of a molecular sequence are cut (removed).
has curation status: IAO_0000123
imported from: obi.owl

swab specimen
type: Class
subclass of: specimen
definition source: OBIB/OBI
term editor: Chris Stoeckert
editor preferred label: swab specimen
textual definition: A specimen that is stored on a swab as the output of a collecting specimen with swab process.
has curation status: IAO_0000122
imported from: obi.owl

collecting specimen with swab
type: Class
subclass of: specimen collection process
term editor: Chris Stoeckert
textual definition: A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
editor preferred label: collecting specimen with swab
definition source: OBIB
has curation status: IAO_0000122
imported from: obi.owl

ribosomal RNA-depleted RNA extract
type: Class
subclass of: RNA extract
definition source: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1
textual definition: An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
term editor: Dan Berrios
editor preferred label: ribosomal RNA-depleted RNA extract
has curation status: IAO_0000125
imported from: obi.owl

Illumina NovaSeq 6000
type: Class
subclass of: DNA sequencer
term editor: Dan Berrios
editor preferred label: Illumina NovaSeq 6000
definition source: http://www.illumina.com/systems/sequencing-platforms/novaseq.html
textual definition: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.
has curation status: IAO_0000120
imported from: obi.owl

PacBio Sequel
type: Class
subclass of: DNA sequencer
editor preferred label: PacBio Sequel
term editor: Bonita Lam
term editor: Dan Berrios
definition source: http://www.pacb.com/products-and-services/pacbio-systems/sequel/
textual definition: A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation
has curation status: IAO_0000120
imported from: obi.owl

PacBio Sequel II
type: Class
subclass of: DNA sequencer
definition source: http://www.pacb.com/products-and-services/pacbio-systems/sequel/
editor preferred label: PacBio Sequel II
textual definition: A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation.
term editor: Dan Berrios
term editor: Bonita Lam
has curation status: IAO_0000120
imported from: obi.owl

biopsy
type: Class
subclass of: collecting specimen from organism
editor preferred label: biopsy
term editor: Nicole Vasilevsky
textual definition: A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.
term editor: Damion Dooley
definition source: https://en.wikipedia.org/wiki/Biopsy
has curation status: IAO_0000122
imported from: obi.owl

image guided biopsy
type: Class
subclass of: needle biopsy
editor preferred label: image guided biopsy
definition source: https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922
term editor: Damion Dooley
textual definition: A biopsy which uses an imaging procedure to guide a needle biopsy.
has curation status: IAO_0000122
imported from: obi.owl

needle biopsy
type: Class
subclass of: biopsy
definition source: https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749
textual definition: A biopsy that uses a hollow needle to extract cells.
term editor: Damion Dooley
editor preferred label: needle biopsy
has curation status: IAO_0000122
imported from: obi.owl

polymerase chain reaction assay
type: Class
subclass of: assay
editor preferred label: polymerase chain reaction assay
term editor: VEuPathDB
textual definition: An assay that uses polymerase chain reaction technique to amplify DNA.
definition source: VEuPathDB
has curation status: IAO_0000120
imported from: obi.owl

Oxford Nanopore MinION
type: Class
subclass of: DNA sequencer
definition source: https://nanoporetech.com/products/minion
term editor: PERSON: Bonita Lam
textual definition: A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.
editor preferred label: Oxford Nanopore MinION
has curation status: IAO_0000120
imported from: obi.owl

Oxford Nanopore GridION Mk1
type: Class
subclass of: DNA sequencer
textual definition: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually.
editor preferred label: Oxford Nanopore GridION Mk1
term editor: PERSON: Bonita Lam
definition source: https://nanoporetech.com/products/gridion
has curation status: IAO_0000120
imported from: obi.owl

Oxford Nanopore PromethION
type: Class
subclass of: DNA sequencer
textual definition: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.
term editor: PERSON: Bonita Lam
definition source: https://nanoporetech.com/products/promethion
editor preferred label: Oxford Nanopore PromethION
has curation status: IAO_0000120
imported from: obi.owl

cDNA library
type: Class
subclass of: processed material
textual definition: A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription.
term editor: Dan Berrios
editor preferred label: cDNA library
definition source: modified from Wikipedia
has curation status: IAO_0000120
imported from: obi.owl

tracheal aspirate specimen
type: Class
subclass of: swab specimen
term editor: Asiyah Yu Lin ORCID:0000-0003-2620-0345
definition source: PMID:25338241
editor preferred label: tracheal aspirate specimen
textual definition: A specimen that is collected with a suctioning tube from the trachea.
has curation status: IAO_0000120
imported from: obi.owl

personal protective device
type: Class
subclass of: device
editor preferred label: personal protective device
definition source: https://en.wikipedia.org/wiki/Personal_protective_equipment
textual definition: A device which is a wearable garment designed to protect the wearer's body from injury or infection.
term editor: https://orcid.org/0000-0002-8844-9165
has curation status: IAO_0000122
imported from: obi.owl

face mask
type: Class
subclass of: personal protective device
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles.
definition source: Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask
editor preferred label: face mask
has curation status: IAO_0000122
imported from: obi.owl

non-medical mask
type: Class
subclass of: face mask
definition source: https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: non-medical mask
textual definition: A face mask not manufactured according to medical equipment standards.
has curation status: IAO_0000122
imported from: obi.owl

medical mask
type: Class
subclass of: face mask
textual definition: A face mask manufactured according to a recognized medical equipment standard.
definition source: https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html
editor preferred label: medical mask
term editor: https://orcid.org/0000-0002-9578-0788
has curation status: IAO_0000122
imported from: obi.owl

N95 respirator
type: Class
subclass of: face mask
textual definition: A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles.
editor preferred label: N95 respirator
definition source: https://en.wikipedia.org/wiki/N95_mask
term editor: https://orcid.org/0000-0002-8844-9165
has curation status: IAO_0000122
imported from: obi.owl

face shield
type: Class
subclass of: personal protective device
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials.
definition source: https://en.wikipedia.org/wiki/Face_shield
editor preferred label: face shield
has curation status: IAO_0000122
imported from: obi.owl

patient gown
type: Class
subclass of: personal protective clothing item
editor preferred label: patient gown
term editor: https://orcid.org/0000-0002-8844-9165
definition source: https://en.wikipedia.org/wiki/Patient_gown
textual definition: A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff.
has curation status: IAO_0000122
imported from: obi.owl

scrubs
type: Class
subclass of: personal protective clothing item
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap.
definition source: https://en.wikipedia.org/wiki/Scrubs_(clothing)
editor preferred label: scrubs
has curation status: IAO_0000122
imported from: obi.owl

reusable patient gown
type: Class
subclass of: patient gown
definition source: https://en.wikipedia.org/wiki/Patient_gown
textual definition: A patient gown intended to be reused after being laundered.
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: reusable patient gown
has curation status: IAO_0000122
imported from: obi.owl

disposable patient gown
type: Class
subclass of: patient gown
definition source: https://en.wikipedia.org/wiki/Patient_gown
textual definition: A patient gown intended for a single period of continuous use and then disposed of.
editor preferred label: disposable patient gown
term editor: https://orcid.org/0000-0002-8844-9165
has curation status: IAO_0000122
imported from: obi.owl

medical gown
type: Class
subclass of: personal protective clothing item
textual definition: A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional.
definition source: https://en.wikipedia.org/wiki/Medical_gown
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: medical gown
has curation status: IAO_0000122
imported from: obi.owl

surgical gown
type: Class
subclass of: medical gown
term editor: https://orcid.org/0000-0002-8844-9165
definition source: OBI
editor preferred label: surgical gown
textual definition: A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures.
has curation status: IAO_0000122
imported from: obi.owl

personal protective glove
type: Class
subclass of: personal protective clothing item
definition source: OBI
editor preferred label: personal protective glove
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A personal protective device which is a glove.
has curation status: IAO_0000122
imported from: obi.owl

personal protective clothing item
type: Class
subclass of: personal protective device
editor preferred label: personal protective clothing item
textual definition: A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing.
definition source: OBI
term editor: https://orcid.org/0000-0002-8844-9165
has curation status: IAO_0000122
imported from: obi.owl

laboratory coat
type: Class
subclass of: personal protective clothing item
definition source: https://en.wikipedia.org/wiki/White_coat
textual definition: A personal protective clothing item which is an overcoat worn by medical or laboratory professionals.
editor preferred label: laboratory coat
term editor: https://orcid.org/0000-0002-8844-9165
has curation status: IAO_0000122
imported from: obi.owl

medical glove
type: Class
subclass of: personal protective glove
textual definition: A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients.
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: medical glove
definition source: https://en.wikipedia.org/wiki/Medical_glove
has curation status: IAO_0000122
imported from: obi.owl

nitrile glove
type: Class
subclass of: personal protective glove
term editor: https://orcid.org/0000-0002-8844-9165
definition source: https://en.wikipedia.org/wiki/Medical_glove
editor preferred label: nitrile glove
textual definition: A personal protective glove which is made out of nitrile rubber.
has curation status: IAO_0000122
imported from: obi.owl

footwear cover
type: Class
subclass of: personal protective clothing item
definition source: https://en.wiktionary.org/wiki/shoecover
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants.
editor preferred label: footwear cover
has curation status: IAO_0000122
imported from: obi.owl

disposable footwear cover
type: Class
subclass of: footwear cover
textual definition: A footwear cover which is designed for a single period of continuous use and then disposed of.
editor preferred label: disposable footwear cover
term editor: https://orcid.org/0000-0002-8844-9165
definition source: OBI
has curation status: IAO_0000122
imported from: obi.owl

reusable footwear cover
type: Class
subclass of: footwear cover
definition source: OBI
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: reusable footwear cover
textual definition: A footwear cover which is designed for repeated use.
has curation status: IAO_0000122
imported from: obi.owl

surgical N95 respirator
type: Class
subclass of: N95 respirator
definition source: https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf
editor preferred label: surgical N95 respirator
textual definition: A N95 respirator which has been approved by the FDA as a surgical mask.
term editor: https://orcid.org/0000-0002-8844-9165
has curation status: IAO_0000122
imported from: obi.owl

protective coverall
type: Class
subclass of: personal protective clothing item
definition source: https://www.safeopedia.com/definition/863/disposable-coveralls
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: protective coverall
textual definition: A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination.
has curation status: IAO_0000122
imported from: obi.owl

protective sleeve
type: Class
subclass of: personal protective clothing item
term editor: https://orcid.org/0000-0002-8844-9165
definition source: https://www.safeopedia.com/definition/974/protective-sleeves
textual definition: A personal protective clothing item which is a protective cover worn over the arm.
editor preferred label: protective sleeve
has curation status: IAO_0000122
imported from: obi.owl

protective apron
type: Class
subclass of: personal protective clothing item
definition source: https://en.wikipedia.org/wiki/Apron
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A personal protective clothing item which is an apron.
editor preferred label: protective apron
has curation status: IAO_0000122
imported from: obi.owl

medical cap
type: Class
subclass of: personal protective clothing item
term editor: https://orcid.org/0000-0002-8844-9165
definition source: https://en.wikipedia.org/wiki/Scrubs_(clothing)
editor preferred label: medical cap
textual definition: A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp.
has curation status: IAO_0000122
imported from: obi.owl

specimen collection device
type: Class
subclass of: device
editor preferred label: specimen collection device
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A container used to collect a specimen.
has curation status: IAO_0000122
imported from: obi.owl

specimen pad
type: Class
subclass of: specimen collection device
definition source: Derived from NCIT sponge definition.
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter.
editor preferred label: specimen pad
has curation status: IAO_0000122
imported from: obi.owl

specimen collection swab stick
type: Class
subclass of: specimen collection device
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material.
editor preferred label: specimen collection swab stick
definition source: https://medical-dictionary.thefreedictionary.com/swab
has curation status: IAO_0000122
imported from: obi.owl

drag swab
type: Class
subclass of: specimen collection device
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: drag swab
textual definition: A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string
definition source: https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses
has curation status: IAO_0000122
imported from: obi.owl

pre-moistened swab stick
type: Class
subclass of: specimen collection swab stick
editor preferred label: pre-moistened swab stick
term editor: https://orcid.org/0000-0002-8844-9165
textual definition: A specimen collection swab stick that is pre-moistened with liquid prior to sampling.
has curation status: IAO_0000122
imported from: obi.owl

surface wipe
type: Class
subclass of: specimen collection device
term editor: https://orcid.org/0000-0002-8844-9165
editor preferred label: surface wipe
textual definition: A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces.
definition source: https://www.science.gov/topicpages/s/surface+wipe+sampling.html
has curation status: IAO_0000122
imported from: obi.owl

Illumina MiniSeq
type: Class
subclass of: DNA sequencer
definition source: url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html
term editor: PERSON: Bonita Lam
textual definition: A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run.
editor preferred label: Illumina MiniSeq
has curation status: IAO_0000120
imported from: obi.owl

Illumina HiSeq 1500
type: Class
subclass of: DNA sequencer
term editor: Michelle Giglio
term editor: Suvarna Nadendla
textual definition: A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option.
definition source: https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf
editor preferred label: Illumina HiSeq 1500
term editor: Jain Aluvathingal
has curation status: IAO_0000120
imported from: obi.owl

NextSeq 550
type: Class
subclass of: DNA sequencer
definition source: https://www.illumina.com/systems/sequencing-platforms/nextseq.html
term editor: Jain Aluvathingal
term editor: Suvarna Nadendla
textual definition: A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing.
editor preferred label: NextSeq 550
term editor: Michelle Giglio
has curation status: IAO_0000120
imported from: obi.owl

organism
type: Class
subclass of: material entity
term editor: GROUP: OBI Biomaterial Branch
textual definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
definition source: WEB: http://en.wikipedia.org/wiki/Organism
editor preferred label: organism
has curation status: IAO_0000122
imported from: obi.owl

specimen
type: Class
subclass of: material entity
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
textual definition: A material entity that has the specimen role.
editor preferred label: specimen
has curation status: IAO_0000122
imported from: obi.owl

data transformation
type: Class
subclass of: planned process
textual definition: A planned process that produces output data from input data.
definition source: Branch editors
term editor: Philippe Rocca-Serra
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
editor preferred label: data transformation
has curation status: IAO_0000122
imported from: obi.owl

extraction
type: Class
subclass of: material component separation
term editor: Philippe Rocca-Serra
term editor: Person:Bjoern Peters
editor preferred label: extraction
textual definition: A material separation in which a desired component of an input material is separated from the remainder
has curation status: IAO_0000123
imported from: obi.owl

filtration
type: Class
subclass of: material component separation
definition source: OBI-Branch: adapted from wikipedia and wordnet
editor preferred label: filtration
term editor: Philippe Rocca-Serra
textual definition: filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
has curation status: IAO_0000120
imported from: obi.owl

DNA sequencer
type: Class
subclass of: measurement device
textual definition: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
term editor: Trish Whetzel
definition source: MO
editor preferred label: DNA sequencer
has curation status: IAO_0000122
imported from: obi.owl

study design
type: Class
subclass of: plan specification
term editor: PERSON: Chris Stoeckert
textual definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor preferred label: study design
has curation status: IAO_0000122
imported from: obi.owl

collecting specimen from organism
type: Class
subclass of: specimen collection process
definition source: IEDB
term editor: PERSON:Bjoern Peters
textual definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
editor preferred label: collecting specimen from organism
has curation status: IAO_0000122
imported from: obi.owl

environmental material collection process
type: Class
subclass of: specimen collection process
term editor: Bjoern Peters, Alan Ruttenberg
definition source: IEDB
editor preferred label: environmental material collection
textual definition: environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
has curation status: IAO_0000123
imported from: obi.owl

material component separation
type: Class
subclass of: material processing
term editor: Bjoern Peters
definition source: IEDB
textual definition: a material processing in which components of an input material become segregated in space
editor preferred label: material component separation
has curation status: IAO_0000122
imported from: obi.owl

pooling specimens
type: Class
subclass of: material combination
editor preferred label: pooling specimens
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
textual definition: physical combination of several instances of like material
has curation status: IAO_0000125
imported from: obi.owl

lavage
type: Class
subclass of: collecting specimen from organism
subclass of: material component separation
textual definition: A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred label: lavage
has curation status: IAO_0000120
imported from: obi.owl

sequencing assay
type: Class
subclass of: assay
editor preferred label: sequencing assay
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
textual definition: An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
has curation status: IAO_0000125
imported from: obi.owl

nucleic acid extraction
type: Class
subclass of: extraction
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
textual definition: a material separation to recover the nucleic acid fraction of an input material
editor preferred label: nucleic acid extraction
has curation status: IAO_0000125
imported from: obi.owl

antigen
type: Class
subclass of: material entity
definition source: IEDB
term editor: IEDB
editor preferred label: antigen
textual definition: is a material entity that has the antigen role
has curation status: IAO_0000123
imported from: obi.owl

infectious disease
type: Class
subclass of: disease
definition source: IEDB
editor preferred label: infectious disease
term editor: IEDB
textual definition: is a disease caused by an infectious agent
has curation status: IAO_0000123
imported from: obi.owl

allergy
type: Class
subclass of: disease
editor preferred label: allergy
term editor: IEDB
definition source: IEDB
textual definition: is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect
has curation status: IAO_0000123
imported from: obi.owl

disease
type: Class
subclass of: disposition
textual definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
editor preferred label: disease
imported from: obi.owl

treatment
type: Class
subclass of: planned process
editor preferred label: treatment
textual definition: A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
imported from: obi.owl

protein
type: Class
subclass of: peptide
editor preferred label: protein
textual definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
imported from: obi.owl