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.