term editor
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
PERSON:Daniel Schober
term editor
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
definition source
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
imported from
textual definition
definition
definition
PERSON:Daniel Schober
definition
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
definition
label
label
editor preferred label
editor preferred term~editor preferred label
editor preferred term
editor preferred label
editor preferred term
editor preferred term~editor preferred label
editor preferred term
editor preferred label
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred label
editor preferred term
has part
a core relation that holds between a whole and its part
has part
occurs in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs in
contains process
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
site of
has measurement unit label
is about
A (currently) primitive relation that relates an information artifact to an entity.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
person:Alan Ruttenberg
denotes
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
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
person:Alan Ruttenberg
has measurement datum
Alan Ruttenberg
relates a time stamped measurement datum to the measurement datum that was measured
has_specified_input
PERSON: Melanie Coutot
PERSON: Bjoern Peters
has_specified_input
PERSON: Alan Ruttenberg
PERSON: Larry Hunter
The inverse property of is_specified_input_of
has_specified_input
is_specified_input_of
is_specified_input_of
PERSON:Bjoern Peters
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
has_specified_output
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
PERSON: Larry Hunter
PERSON: Bjoern Peters
has_specified_output
The inverse property of is_specified_output_of
has_specified_output
is_manufactured_by
Alan Ruttenberg
Liju Fan
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
is_manufactured_by
is_specified_output_of
Alan Ruttenberg
is_specified_output_of
PERSON:Bjoern Peters
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
has category label
has category label
A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
specifies value of
specifies value of
A relation between a value specification and an entity which the specification is about.
has value specification
PERSON: James A. Overton
A relation between an information content entity and a value specification that specifies its value.
OBI
has value specification
inheres in
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
inheres in
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
has participant
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
has member
SIO
has member is a mereological relation between a collection and an item.
has specified value
OBI
A relation between a value specification and a literal.
has specified value
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
temporal region
process
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
disposition
quality
quality
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
site
material entity
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
material entity
immaterial entity
peptide
peptide
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
deoxyribonucleic acid
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
macromolecule
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
macromolecule
double-stranded DNA
double-stranded DNA
measurement unit label
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
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.
OBI Plan and Planned Process/Roles Branch
OBI_0000217
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
objective specification
action specification
A directive information entity that describes an action the bearer will take.
Alan Ruttenberg
OBI Plan and Planned Process branch
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
datum label
data item
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.
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data item
symbol
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
PERSON: James A. Overton
PERSON: Jonathan Rees
based on Oxford English Dictionary
symbol
numeral
A symbol that denotes a number.
PERSON: Jonathan Rees
numeral
information content entity
A generically dependent continuant that is about some thing.
OBI_0000142
PERSON: Chris Stoeckert
information content entity
integer numeral
A numeral that denotes an integer
PERSON: Jonathan Rees
integer numeral
scalar measurement datum
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
data set
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.
OBI_0000042
data set
group:OBI
person:Allyson Lister
person:Chris Stoeckert
plan specification
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
plan specification
measurement datum
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
OBI_0000305
group:OBI
measurement datum
person:Chris Stoeckert
setting datum
A settings datum is a datum that denotes some configuration of an instrument.
textual entity
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
PERSON: Lawrence Hunter
textual entity
document part
An information content entity that is part of a document.
PERSON: Lawrence Hunter
document part
length measurement datum
A scalar measurement datum that is the result of measurement of length quality
Alan Ruttenberg
mass measurement datum
A scalar measurement datum that is the result of measurement of mass quality
Person:Alan Ruttenberg
time measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
Person:Alan Ruttenberg
email address
Person:Alan Ruttenberg
Person:Chris Stoeckart
email address
centrally registered identifier symbol
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
time stamped measurement datum
notes section
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.
PERSON: Bill Baumgartner
notes section
planned process
A process that realizes a plan which is the concretization of a plan specification.
planned process
branch derived
Bjoern Peters
planned process
material supplier role
material supplier role
PERSON:Jennifer Fostel
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
processed material
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
investigation
Bjoern Peters
OBI branch derived
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
assay
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
OBI branch derived
PlanAndPlannedProcess Branch
assay
culture medium
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
OBI
Person: Jennifer Fostel, Jie Zheng
culture medium
patient role
patient role
GROUP:Role Branch
OBI, CDISC
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
material processing
A planned process which results in physical changes in a specified input material
PERSON: Frank Gibson
OBI branch derived
PERSON: Philippe Rocca Serra
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
material processing
PERSON: Bjoern Peters
specimen role
GROUP: Role Branch
OBI
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
specimen role
incubator
A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
http://www.medterms.com/script/main/art.asp?articlekey=18426
incubator
Frank Gibson
population
PERSON: Philippe Rocca-Serra
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
adapted from Oxford English Dictionnary
population
organization
PERSON: Alan Ruttenberg
PERSON: Philippe Rocca-Serra
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.
PERSON: Susanna Sansone
GROUP: OBI
PERSON: Bjoern Peters
organization
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
DNA extraction
OBI branch derived
PlanAndPlannedProcess Branch
extract
GROUP: OBI Biomatrial Branch
PERSON: Philippe Rocca-Serra
an extract is a material entity which results from an extraction process
extract
enzyme
GROUP:OBI
enzyme
person: Melanie Courtot
(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)
plasmid
group:OBI
person:Melanie Courtot
plasmid
plasmid = DNA and has_quality circular and has_function
(is_realized_as some gene expression) GO:0010467
needle
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.
OBI Instrument
Philippe Rocca-Serra
needle
manufacturer role
OBI
manufacturer role
GROUP: Role Branch
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
DNA sequencing assay
A sequencing assay which determines information on the sequence of a DNA molecule.
url:https://en.wikipedia.org/wiki/DNA_sequencing
DNA sequencing assay
Philippe Rocca-Serra
material combination
material combination
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
bp
bp
data representational model
data representational model
Melanie Courtot
Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
GROUP: OBI
specimen collection process
A planned process with the objective of collecting a specimen.
specimen collection process
Bjoern Peters
average value
PERSON: James Malone
average value
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
PERSON: Monnie McGee
454 Genome Sequence 20
454 Genome Sequence 20
Philippe Rocca-Serra
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.
ABI 377 automated sequencer
Applied Biosystems
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.
ABI 377 automated sequencer
Philippe Rocca-Serra
AB SOLiD System
Philippe Rocca-Serra
Applied Biosystems
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
AB SOLiD System
454 Genome Sequencer FLX
454 Genome Sequencer FLX
is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.
adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
Philippe Rocca-Serra
Illumina Genome Analyzer II
Philippe Rocca-Serra
Illumina Corporation
Illumina Genome Analyzer II
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
Li-Cor 4300 DNA Analysis System
Philippe Rocca-Serra
OBI and Li-Cor
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
Li-Cor 4300 DNA Analysis System
HeliScope Single Molecule Sequencer
HeliScope Single Molecule Sequencer
Philippe Rocca-Serra
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
pathogen role
OBI
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
pathogen role
GROUP: Role Branch
restriction enzyme
an enzyme that has a specific target cleavage sites within nucleic acids
restriction enzyme
Kevin Clancy, Bjoern Peters
material sample role
material sample role
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
measurement device
measurement device
A device in which a measure function inheres.
OBI
GROUP:OBI Philly workshop
polyA RNA extract
PERSON: Chris Stoeckert
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.
polyA RNA extract
PERSON: Jie Zheng
UPenn Group
RNA extract
PERSON: Chris Stoeckert
Group: UPenn Group
PERSON: Jie Zheng
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
RNA extract
real time polymerase chain reaction assay
real time polymerase chain reaction assay
An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
Melanie Courtot
Bjoern Peters
url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
total RNA extract
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
total RNA extract
UPenn Group
infectious agent
infectious agent
IEDB
IEDB
is a material entity bearing the disposition to infect an organism
categorical measurement datum
Bjoern Peters
categorical measurement datum
Bjoern Peters
A measurement datum that is reported on a categorical scale
service provider role
PERSON:Helen Parkinson
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
service provider role
processed specimen
A specimen that has been intentionally physically modified.
Bjoern Peters
processed specimen
A tissue sample that has been sliced and stained for a histology study.
Bjoern Peters
categorical label
Bjoern Peters
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
categorical label
Bjoern Peters
container
A device that can be used to restrict the location of material entities over time
container
PERSON: Bjoern Peters
device
OBI development call 2012-12-17.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
device
PERSON: Helen Parkinson
sequence data
sequence data
Person:Chris Stoeckert
GROUP: OBI
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
DNA sequencing service
A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
DNA sequencing service
nucleic acid extract
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
nucleic acid extract
PERSON: Jie Zheng
UPenn Group
environmental control device
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
Helen Parkinson
OBI
environmental control device
micropipette
http://www.answers.com/topic/micropipette
PERSON: Erik Segerdell
A microinjection device that is used to measure very small volumes of liquids.
micropipette
individual organism identifier
MO_169 Individual
PERSON: Chris Stoeckert, Jie Zheng
a CRID symbol used to distinguish one individual organism from another.
individual organism identifier
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
MO_178 Age
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
age measurement datum
age since birth measurement datum
MO_710 birth
PERSON:Chris Stoeckert, Jie Zheng
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.
age since birth measurement datum
service
service
OBI workshop San Diego 2011
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
Carlo; Matt
RNA sequencing assay
RNA sequencing assay
Bjoern Peters
Bjoern Peters
An assay that determines the sequence of an RNA molecule.
specimen from organism
MO_954 organism_part
PERSON: Chris Stoeckert, Jie Zheng
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).
specimen from organism
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
MO_738 timepoint
Person: Chris Stoeckert
sampling time measurement datum
material maintenance service
material maintenance service
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
PERSON: Matthew Brush
PERSON: Matthew Brush
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.
PERSON: Carlo Torniai
material service
A service which has a material entity as specified input and/or specified output.
material service
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Carlo Torniai
material analysis service
PERSON: Matthew Brush
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
PERSON: Carlo Torniai
PERSON: Matthew Brush
material analysis service
material storage service
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
PERSON: Matthew Brush
PERSON: Carlo Torniai
PERSON: Matthew Brush
material storage service
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
GenBank ID
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
investigation description
A textual entity that describes an investigation.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
investigation description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
specimen identifier
PubMed ID
A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
Person: Chris Stoeckert, Jie Zheng
PubMed ID
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
specimen collection time measurement datum
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
latitude coordinate measurement datum
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
longitude coordinate measurement datum
investigation title
A textual entity that denotes an investigation.
NIAID GSCID-BRC metadata working group
Person:Chris Stoeckert, Jie Zheng
investigation title
country name
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
Website: http://en.wikipedia.org/wiki/Country
country name
investigation identifier
A CRID symbol used to identify an investigation.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zhneg
investigation identifier
grant identifier
A CRID symbol used to identify a grant.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
grant identifier
contact representative role
Person: Chris Stoeckert
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.
contact representative role
reagent
PERSON:Matthew Brush
PERSON:Matthew Brush
(copied from ReO)
Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique.
Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.
In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
reagent
organization of specimen provider principal investigator
NIAID GSCID-BRC metadata working group
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
PERSON: Chris Stoeckert, Jie Zheng
organization of specimen provider principal investigator
target material in specimen specification
NIAID GSCID-BRC metadata working group
PERSON: Chris Stoeckert, Jie Zheng
A plan specification which specifies the type of material that will be assayed in an investigation.
target material in specimen specification
specimen-based scope of investigation specification
PERSON: Chris Stoeckert, Jie Zheng
A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
NIAID GSCID-BRC metadata working group
specimen-based scope of investigation specification
specimen repository organization
NIAID GSCID-BRC metadata working group
An organization that provides a service to store and distribute specimens
PERSON: Chris Stoeckert, Jie Zheng
specimen repository organization
sequencing facility organization
An organization that provides sequence determination service
NIAID GSCID-BRC metadata working group
PERSON: Chris Stoeckert, Jie Zheng
sequencing facility organization
specification of data to be generated in an investigation
An objective specification which indicates the type of data that will be generated and submitted to a database.
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
specification of data to be generated in an investigation
organization of specimen collector
An organization that is the affiliation of the person collecting the specimen
NIAID GSCID-BRC metadata working group
PERSON: Chris Stoeckert, Jie Zheng
organization of specimen collector
email address of sequencing facility contact person
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
An email address of the contact representative at the sequencing facility
email address of sequencing facility contact person
investigation assay specification
A plan specification which indicates the assay type used to obtain data.
NIAID GSCID-BRC metadata working group
PERSON: Chris Stoeckert, Jie Zheng
investigation assay specification
organization of sequencing facility contact person
An organization that is the affiliation of the contact representative at the sequencing facility
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
organization of sequencing facility contact person
comment on investigation
NIAID GSCID-BRC metadata working group
A textual entity that is about any of the aspects of an investigation worth noting
PERSON: Chris Stoeckert, Jie Zheng
comment on investigation
target capture specification
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.
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
target capture specification
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
specimen identifier assigned by specimen repository
specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
NIAID GSCID-BRC metadata working group
PERSON: Chris Stoeckert, Jie Zheng
specimen identifier assigned by sequencing facility
email address of specimen provider principal investigator
NIAID GSCID-BRC metadata working group
An email address of the principal investigator providing the specimens for the investigation
PERSON: Chris Stoeckert, Jie Zheng
email address of specimen provider principal investigator
sequencing service
Person: Jie Zheng
Adpated from 'DNA sequencing service'
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
sequencing service
categorical value specification
A value specification that is specifies one category out of a fixed number of nominal categories
categorical value specification
PERSON:Bjoern Peters
scalar value specification
A value specification that consists of two parts: a numeral and a unit label
PERSON:Bjoern Peters
scalar value specification
value specification
value specification
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
PERSON:Bjoern Peters
N50
Alejandra Gonzalez-Beltran
N50
Philippe Rocca-Serra
adapted from:
"http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c"
(from table 7)
and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html"
the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
contig N50
N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
contig N50
grant agency
NIAID GSCID-BRC metadata working group
PERSON: Jie Zheng, Chris Stoeckert
An organization that provides funding support for projects such as investigations.
grant agency
Genome Analyzer IIx
ENCODE group
Genome Analyzer IIx
An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
Illumina HiSeq 2000
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.
Illumina HiSeq 2000
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
Illumina HiSeq 2500
http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf
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.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
Illumina HiSeq 2500
MiSeq
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.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf
MiSeq
SOLiD 3 Plus System
http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf
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.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
SOLiD 3 Plus System
PacBio RS II
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.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg
http://www.pacificbiosciences.com/products/
PacBio RS II
NextSeq 500
A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
NextSeq 500
http://systems.illumina.com/systems/nextseq-sequencer.html
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
Illumina HiSeq 1000
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
Illumina HiSeq 1000
SOLiD 4 System
http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4
SOLiD 4 System
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.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
Genome Analyzer IIe
Genome Analyzer IIe
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf
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.
Illumina HiSeq 3000
PERSON: Sagar Jain, Richard Scheuermann
Illumina HiSeq 3000
http://www.illumina.com/systems/hiseq-3000-4000.html
A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
Illumina HiSeq 4000
PERSON: Sagar Jain, Richard Scheuermann
http://www.illumina.com/systems/hiseq-3000-4000.html
A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
Illumina HiSeq 4000
specimen container
A container with the function of containing a specimen.
Chris Stoeckert
Duke Biobank, OBIB
specimen container
Illumina Genome Analyzer
Illumina Genome Analyzer
http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html
Person: Chris Stoeckert, Jason Hilton
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.
Illumina HiSeq X Ten
A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html
Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann
Illumina HiSeq X Ten
molecular analysis facility organization
An organization that provides molecular analysis service.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBIB
molecular analysis facility organization
adapter-sequence trimming
Dan Berrios
adapter-sequence trimming
Dan Berrios
A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed).
sequence trimming
sequence trimming
A data transformation in which subsequences of a molecular sequence are cut (removed).
swab specimen
OBIB/OBI
Chris Stoeckert
swab specimen
A specimen that is stored on a swab as the output of a collecting specimen with swab process.
collecting specimen with swab
Chris Stoeckert
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).
collecting specimen with swab
OBIB
ribosomal RNA-depleted RNA extract
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1
An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
Dan Berrios
ribosomal RNA-depleted RNA extract
Illumina NovaSeq 6000
Dan Berrios
Illumina NovaSeq 6000
http://www.illumina.com/systems/sequencing-platforms/novaseq.html
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.
PacBio Sequel
PacBio Sequel
Bonita Lam
Dan Berrios
http://www.pacb.com/products-and-services/pacbio-systems/sequel/
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
PacBio Sequel II
http://www.pacb.com/products-and-services/pacbio-systems/sequel/
PacBio Sequel II
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.
Dan Berrios
Bonita Lam
biopsy
biopsy
Nicole Vasilevsky
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.
Damion Dooley
https://en.wikipedia.org/wiki/Biopsy
image guided biopsy
image guided biopsy
https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922
Damion Dooley
A biopsy which uses an imaging procedure to guide a needle biopsy.
needle biopsy
https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749
A biopsy that uses a hollow needle to extract cells.
Damion Dooley
needle biopsy
polymerase chain reaction assay
polymerase chain reaction assay
VEuPathDB
An assay that uses polymerase chain reaction technique to amplify DNA.
VEuPathDB
Oxford Nanopore MinION
https://nanoporetech.com/products/minion
PERSON: Bonita Lam
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.
Oxford Nanopore MinION
Oxford Nanopore GridION Mk1
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.
Oxford Nanopore GridION Mk1
PERSON: Bonita Lam
https://nanoporetech.com/products/gridion
Oxford Nanopore PromethION
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.
PERSON: Bonita Lam
https://nanoporetech.com/products/promethion
Oxford Nanopore PromethION
cDNA library
A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription.
Dan Berrios
cDNA library
modified from Wikipedia
tracheal aspirate specimen
Asiyah Yu Lin ORCID:0000-0003-2620-0345
PMID:25338241
tracheal aspirate specimen
A specimen that is collected with a suctioning tube from the trachea.
personal protective device
personal protective device
https://en.wikipedia.org/wiki/Personal_protective_equipment
A device which is a wearable garment designed to protect the wearer's body from injury or infection.
https://orcid.org/0000-0002-8844-9165
face mask
https://orcid.org/0000-0002-8844-9165
A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles.
Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask
face mask
non-medical mask
https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html
https://orcid.org/0000-0002-8844-9165
non-medical mask
A face mask not manufactured according to medical equipment standards.
medical mask
A face mask manufactured according to a recognized medical equipment standard.
https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html
medical mask
https://orcid.org/0000-0002-9578-0788
N95 respirator
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.
N95 respirator
https://en.wikipedia.org/wiki/N95_mask
https://orcid.org/0000-0002-8844-9165
face shield
https://orcid.org/0000-0002-8844-9165
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.
https://en.wikipedia.org/wiki/Face_shield
face shield
patient gown
patient gown
https://orcid.org/0000-0002-8844-9165
https://en.wikipedia.org/wiki/Patient_gown
A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff.
scrubs
https://orcid.org/0000-0002-8844-9165
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.
https://en.wikipedia.org/wiki/Scrubs_(clothing)
scrubs
reusable patient gown
https://en.wikipedia.org/wiki/Patient_gown
A patient gown intended to be reused after being laundered.
https://orcid.org/0000-0002-8844-9165
reusable patient gown
disposable patient gown
https://en.wikipedia.org/wiki/Patient_gown
A patient gown intended for a single period of continuous use and then disposed of.
disposable patient gown
https://orcid.org/0000-0002-8844-9165
medical gown
A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional.
https://en.wikipedia.org/wiki/Medical_gown
https://orcid.org/0000-0002-8844-9165
medical gown
surgical gown
https://orcid.org/0000-0002-8844-9165
OBI
surgical gown
A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures.
personal protective glove
OBI
personal protective glove
https://orcid.org/0000-0002-8844-9165
A personal protective device which is a glove.
personal protective clothing item
personal protective clothing item
A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing.
OBI
https://orcid.org/0000-0002-8844-9165
laboratory coat
https://en.wikipedia.org/wiki/White_coat
A personal protective clothing item which is an overcoat worn by medical or laboratory professionals.
laboratory coat
https://orcid.org/0000-0002-8844-9165
medical glove
A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients.
https://orcid.org/0000-0002-8844-9165
medical glove
https://en.wikipedia.org/wiki/Medical_glove
nitrile glove
https://orcid.org/0000-0002-8844-9165
https://en.wikipedia.org/wiki/Medical_glove
nitrile glove
A personal protective glove which is made out of nitrile rubber.
footwear cover
https://en.wiktionary.org/wiki/shoecover
https://orcid.org/0000-0002-8844-9165
A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants.
footwear cover
disposable footwear cover
A footwear cover which is designed for a single period of continuous use and then disposed of.
disposable footwear cover
https://orcid.org/0000-0002-8844-9165
OBI
reusable footwear cover
OBI
https://orcid.org/0000-0002-8844-9165
reusable footwear cover
A footwear cover which is designed for repeated use.
surgical N95 respirator
https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf
surgical N95 respirator
A N95 respirator which has been approved by the FDA as a surgical mask.
https://orcid.org/0000-0002-8844-9165
protective coverall
https://www.safeopedia.com/definition/863/disposable-coveralls
https://orcid.org/0000-0002-8844-9165
protective coverall
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.
protective sleeve
https://orcid.org/0000-0002-8844-9165
https://www.safeopedia.com/definition/974/protective-sleeves
A personal protective clothing item which is a protective cover worn over the arm.
protective sleeve
protective apron
https://en.wikipedia.org/wiki/Apron
https://orcid.org/0000-0002-8844-9165
A personal protective clothing item which is an apron.
protective apron
medical cap
https://orcid.org/0000-0002-8844-9165
https://en.wikipedia.org/wiki/Scrubs_(clothing)
medical cap
A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp.
specimen collection device
specimen collection device
https://orcid.org/0000-0002-8844-9165
A container used to collect a specimen.
specimen pad
Derived from NCIT sponge definition.
https://orcid.org/0000-0002-8844-9165
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.
specimen pad
specimen collection swab stick
https://orcid.org/0000-0002-8844-9165
A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material.
specimen collection swab stick
https://medical-dictionary.thefreedictionary.com/swab
drag swab
https://orcid.org/0000-0002-8844-9165
drag swab
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
https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses
pre-moistened swab stick
pre-moistened swab stick
https://orcid.org/0000-0002-8844-9165
A specimen collection swab stick that is pre-moistened with liquid prior to sampling.
surface wipe
https://orcid.org/0000-0002-8844-9165
surface wipe
A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces.
https://www.science.gov/topicpages/s/surface+wipe+sampling.html
Illumina MiniSeq
url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html
PERSON: Bonita Lam
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.
Illumina MiniSeq
Illumina HiSeq 1500
Michelle Giglio
Suvarna Nadendla
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.
https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf
Illumina HiSeq 1500
Jain Aluvathingal
NextSeq 550
https://www.illumina.com/systems/sequencing-platforms/nextseq.html
Jain Aluvathingal
Suvarna Nadendla
A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing.
NextSeq 550
Michelle Giglio
organism
GROUP: OBI Biomaterial Branch
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
WEB: http://en.wikipedia.org/wiki/Organism
organism
specimen
GROUP: OBI Biomaterial Branch
PERSON: James Malone
PERSON: Philippe Rocca-Serra
A material entity that has the specimen role.
specimen
data transformation
A planned process that produces output data from input data.
Branch editors
Philippe Rocca-Serra
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data transformation
extraction
Philippe Rocca-Serra
Person:Bjoern Peters
extraction
A material separation in which a desired component of an input material is separated from the remainder
filtration
OBI-Branch: adapted from wikipedia and wordnet
filtration
Philippe Rocca-Serra
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
DNA sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Trish Whetzel
MO
DNA sequencer
study design
PERSON: Chris Stoeckert
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.
study design
collecting specimen from organism
IEDB
PERSON:Bjoern Peters
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
collecting specimen from organism
environmental material collection process
Bjoern Peters, Alan Ruttenberg
IEDB
environmental material collection
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.
material component separation
Bjoern Peters
IEDB
a material processing in which components of an input material become segregated in space
material component separation
pooling specimens
pooling specimens
OBI branch derived
PlanAndPlannedProcess Branch
physical combination of several instances of like material
lavage
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
OBI branch derived
PlanAndPlannedProcess Branch
lavage
sequencing assay
sequencing assay
OBI branch derived
PlanAndPlannedProcess Branch
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
nucleic acid extraction
OBI branch derived
PlanAndPlannedProcess Branch
a material separation to recover the nucleic acid fraction of an input material
nucleic acid extraction
antigen
IEDB
IEDB
antigen
is a material entity that has the antigen role
infectious disease
IEDB
infectious disease
IEDB
is a disease caused by an infectious agent
allergy
allergy
IEDB
IEDB
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
disease
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
disease
treatment
treatment
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
protein
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.