term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
PERSON:Daniel Schober
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
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
imported from
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor preferred term~editor preferred label
editor preferred label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
has part
a core relation that holds between a whole and its 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
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
has measurement datum
Alan Ruttenberg
relates a time stamped measurement datum to the measurement datum that was measured
has_specified_input
PERSON: Alan Ruttenberg
The inverse property of is_specified_input_of
is_specified_input_of
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.
has_specified_output
The inverse property of is_specified_output_of
is_manufactured_by
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_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
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
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
has participant
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has member
has member is a mereological relation between a collection and an item.
has specified value
A relation between a value specification and a literal.
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
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
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
immaterial entity
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.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
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.
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.
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: Melanie Courtot
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
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
action specification
A directive information entity that describes an action the bearer will take.
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
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: Chris Stoeckert
PERSON: Jonathan Rees
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
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
A generically dependent continuant that is about some thing.
integer numeral
A numeral that denotes an integer
scalar measurement datum
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
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.
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.
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
document part
An information content entity that is part of a document.
length measurement datum
A scalar measurement datum that is the result of measurement of length quality
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
email address
Person:Chris Stoeckart
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: Bill Hogan
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
planned process
A process that realizes a plan which is the concretization of a plan specification.
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.
investigation
Bjoern Peters
OBI branch derived
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
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.
PlanAndPlannedProcess Branch
culture medium
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
OBI
Person: Jennifer Fostel, Jie Zheng
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
specimen role
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
A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
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
organization
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.
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
extract
an extract is a material entity which results from an extraction process
enzyme
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
plasmid
plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
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.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
A sequencing assay which determines information on the sequence of a DNA molecule.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
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.
A planned process with the objective of collecting a specimen.
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.
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.
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.
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
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
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
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
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
an enzyme that has a specific target cleavage sites within nucleic acids
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
A device in which a measure function inheres.
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.
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
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.
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
infectious agent
IEDB
is a material entity bearing the disposition to infect an organism
A measurement datum that is reported on a categorical scale
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
A device that can be used to restrict the location of material entities over time
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
A microinjection device that is used to measure very small volumes of liquids.
individual organism identifier
MO_169 Individual
a CRID symbol used to distinguish one individual organism from another.
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
An assay that determines the sequence of an RNA molecule.
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
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
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.
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.
A service which has a material entity as specified input and/or specified output.
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.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
investigation description
A textual entity that describes an investigation.
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
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.
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.
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
investigation title
A textual entity that denotes an investigation.
Person:Chris Stoeckert, Jie Zheng
country name
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
Website: http://en.wikipedia.org/wiki/Country
investigation identifier
A CRID symbol used to identify an investigation.
Person: Chris Stoeckert, Jie Zhneg
grant identifier
A CRID symbol used to identify a grant.
contact representative role
A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
reagent
(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.
organization of specimen provider principal investigator
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
target material in specimen specification
A plan specification which specifies the type of material that will be assayed in an investigation.
specimen-based scope of investigation specification
A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
specimen repository organization
An organization that provides a service to store and distribute specimens
sequencing facility organization
An organization that provides sequence determination service
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.
organization of specimen collector
An organization that is the affiliation of the person collecting the specimen
email address of sequencing facility contact person
An email address of the contact representative at the sequencing facility
investigation assay specification
A plan specification which indicates the assay type used to obtain data.
organization of sequencing facility contact person
An organization that is the affiliation of the contact representative at the sequencing facility
comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting
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.
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
email address of specimen provider principal investigator
An email address of the principal investigator providing the specimens for the investigation
sequencing service
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
N50
Alejandra Gonzalez-Beltran
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.
adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
grant agency
An organization that provides funding support for projects such as investigations.
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
A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
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.
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.
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.
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.
A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
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.
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.
A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
A container with the function of containing a specimen.
A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.
A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann
molecular analysis facility organization
An organization that provides molecular analysis service.
A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed).
A data transformation in which subsequences of a molecular sequence are cut (removed).
A specimen that is stored on a swab as the output of a collecting specimen with swab process.
A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
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.
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
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.
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.
A biopsy which uses an imaging procedure to guide a needle biopsy.
A biopsy that uses a hollow needle to extract cells.
An assay that uses polymerase chain reaction technique to amplify DNA.
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.
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.
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.
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
modified from Wikipedia
A specimen that is collected with a suctioning tube from the trachea.
A device which is a wearable garment designed to protect the wearer's body from injury or infection.
A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles.
Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask
A face mask not manufactured according to medical equipment standards.
A face mask manufactured according to a recognized medical equipment standard.
A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles.
A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials.
A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff.
A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap.
A patient gown intended to be reused after being laundered.
A patient gown intended for a single period of continuous use and then disposed of.
A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional.
A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures.
A personal protective device which is a glove.
A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing.
A personal protective clothing item which is an overcoat worn by medical or laboratory professionals.
A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients.
A personal protective glove which is made out of nitrile rubber.
A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants.
A footwear cover which is designed for a single period of continuous use and then disposed of.
A footwear cover which is designed for repeated use.
A N95 respirator which has been approved by the FDA as a surgical mask.
A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination.
A personal protective clothing item which is a protective cover worn over the arm.
A personal protective clothing item which is an apron.
A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp.
A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter.
A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material.
A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string
A specimen collection swab stick that is pre-moistened with liquid prior to sampling.
A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces.
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.
A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option.
A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing.
organism
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
specimen
GROUP: OBI Biomaterial Branch
A material entity that has the specimen role.
data transformation
A planned process that produces output data from input data.
Branch editors
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
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 is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
study design
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
collecting specimen from organism
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
environmental material collection process
Bjoern Peters, Alan Ruttenberg
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
a material processing in which components of an input material become segregated in space
pooling specimens
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
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
nucleic acid extraction
a material separation to recover the nucleic acid fraction of an input material
antigen
is a material entity that has the antigen role
infectious disease
is a disease caused by an infectious agent
allergy
is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
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
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.